Starting phenix.real_space_refine
on Sun Apr  5 10:54:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.94
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9rma_54053/04_2026/9rma_54053_trim.cif"
  }
  resolution = 3.94
  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=   0.020
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: 6
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     S      18      5.16       5
     C    3056      2.51       5
     N     823      2.21       5
     O     918      1.98       5
     H    4716      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9532
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 3001
          Classifications: {'peptide': 185}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 176}
    Chain: "C"
      Number of atoms: 6500
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 422, 6500
          Classifications: {'peptide': 422}
          Link IDs: {'PTRANS': 15, 'TRANS': 406}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.76, per 1000 atoms: 0.18
  Number of scatterers: 9532
  At special positions: 0
  Unit cell: (82.56, 68.37, 108.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      1     24.99
     S      18     16.00
     O     918      8.00
     N     823      7.00
     C    3056      6.00
     H    4716      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C 409 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  51 " - pdb=" SG  CYS C 420 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 184 " - pdb=" SG  CYS C 241 " 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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 224 "
  Time building additional restraints: 0.86
  Conformation dependent library (CDL) restraints added in 261.5 milliseconds
  

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1114

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 4 sheets defined
      49.3% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 146 through 165
    Processing helix  chain 'A' and resid 185 through 192
    Processing helix  chain 'A' and resid 194 through 200
      removed outlier: 4.170A  pdb=" N   LEU A 198 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 222
    Processing helix  chain 'A' and resid 224 through 228
      removed outlier: 3.563A  pdb=" N   GLY A 228 " --> pdb=" O   ILE A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 262
      removed outlier: 3.606A  pdb=" N   GLU A 262 " --> pdb=" O   GLU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 303 through 311
    Processing helix  chain 'C' and resid 80 through 87
      removed outlier: 3.741A  pdb=" N   HIS C  85 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 93 through 115
      Proline residue:  C 103  - end of helix
    Processing helix  chain 'C' and resid 116 through 121
      removed outlier: 4.274A  pdb=" N   PHE C 120 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 143
    Processing helix  chain 'C' and resid 158 through 172
    Processing helix  chain 'C' and resid 179 through 194
      removed outlier: 3.729A  pdb=" N   LEU C 183 " --> pdb=" O   ASP C 179 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 213 through 217
      removed outlier: 3.633A  pdb=" N   LEU C 216 " --> pdb=" O   ILE C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 238
      removed outlier: 3.846A  pdb=" N   ALA C 225 " --> pdb=" O   GLU C 221 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 247 through 262
    Processing helix  chain 'C' and resid 268 through 281
    Processing helix  chain 'C' and resid 287 through 296
    Processing helix  chain 'C' and resid 297 through 301
    Processing helix  chain 'C' and resid 308 through 326
    Processing helix  chain 'C' and resid 331 through 343
      removed outlier: 3.676A  pdb=" N   VAL C 335 " --> pdb=" O   PHE C 331 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 351 through 368
      removed outlier: 3.811A  pdb=" N   THR C 355 " --> pdb=" O   SER C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 400 through 404
    Processing helix  chain 'C' and resid 415 through 417
      No H-bonds generated for 'chain 'C' and resid 415 through 417'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 184
      removed outlier: 6.713A  pdb=" N   LEU A 173 " --> pdb=" O   HIS A 183 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP A 140 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   LYS A 235 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.772A  pdb=" N   TYR A 267 " --> pdb=" O   LYS A 235 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   LEU A 237 " --> pdb=" O   TYR A 267 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   ILE A 269 " --> pdb=" O   LEU A 237 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8
    Processing sheet with id=AA3, first strand: chain 'C' and resid 11 through 14
      removed outlier: 6.951A  pdb=" N   ARG C  39 " --> pdb=" O   GLY C  48 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   GLY C  48 " --> pdb=" O   ARG C  39 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 11 through 14

    262 hydrogen bonds defined for protein.
    720 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: 1.98

  Time building geometry restraints manager: 1.23 seconds

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

  Histogram of bond lengths:
        0.79 -     1.00: 4714
        1.00 -     1.21: 2
        1.21 -     1.42: 2061
        1.42 -     1.63: 2821
        1.63 -     1.84: 30
  Bond restraints: 9628
  Sorted by residual:
  bond pdb=" CE1 TYR C 407 "
       pdb=" HE1 TYR C 407 "
    ideal  model  delta    sigma   weight residual
    0.930  0.785  0.145 2.00e-02 2.50e+03 5.24e+01
  bond pdb=" OH  TYR C 407 "
       pdb=" HH  TYR C 407 "
    ideal  model  delta    sigma   weight residual
    0.840  0.975 -0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" CE1 TYR C 407 "
       pdb=" CZ  TYR C 407 "
    ideal  model  delta    sigma   weight residual
    1.378  1.218  0.160 2.40e-02 1.74e+03 4.44e+01
  bond pdb=" CZ  TYR C 407 "
       pdb=" OH  TYR C 407 "
    ideal  model  delta    sigma   weight residual
    1.376  1.452 -0.076 2.10e-02 2.27e+03 1.30e+01
  bond pdb=" CD1 TYR C 407 "
       pdb=" CE1 TYR C 407 "
    ideal  model  delta    sigma   weight residual
    1.382  1.287  0.095 3.00e-02 1.11e+03 9.93e+00
  ... (remaining 9623 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.77: 17132
        4.77 -     9.53: 188
        9.53 -    14.30: 37
       14.30 -    19.06: 4
       19.06 -    23.83: 2
  Bond angle restraints: 17363
  Sorted by residual:
  angle pdb=" CE2 TYR C 407 "
        pdb=" CZ  TYR C 407 "
        pdb=" OH  TYR C 407 "
      ideal   model   delta    sigma   weight residual
     119.90  143.73  -23.83 3.00e+00 1.11e-01 6.31e+01
  angle pdb=" CE1 TYR C 407 "
        pdb=" CZ  TYR C 407 "
        pdb=" OH  TYR C 407 "
      ideal   model   delta    sigma   weight residual
     119.90   99.33   20.57 3.00e+00 1.11e-01 4.70e+01
  angle pdb=" CB  GLN C 267 "
        pdb=" CG  GLN C 267 "
        pdb=" CD  GLN C 267 "
      ideal   model   delta    sigma   weight residual
     112.60  122.27   -9.67 1.70e+00 3.46e-01 3.23e+01
  angle pdb=" CD  GLU C  56 "
        pdb=" CG  GLU C  56 "
        pdb=" HG2 GLU C  56 "
      ideal   model   delta    sigma   weight residual
     108.00   91.49   16.51 3.00e+00 1.11e-01 3.03e+01
  angle pdb=" CA  GLN C 267 "
        pdb=" CB  GLN C 267 "
        pdb=" CG  GLN C 267 "
      ideal   model   delta    sigma   weight residual
     114.10  124.53  -10.43 2.00e+00 2.50e-01 2.72e+01
  ... (remaining 17358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.62: 3869
       16.62 -    33.25: 450
       33.25 -    49.87: 164
       49.87 -    66.50: 62
       66.50 -    83.12: 15
  Dihedral angle restraints: 4560
    sinusoidal: 2495
      harmonic: 2065
  Sorted by residual:
  dihedral pdb=" CA  SER C  22 "
           pdb=" C   SER C  22 "
           pdb=" N   CYS C  23 "
           pdb=" CA  CYS C  23 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.97   29.03     0      5.00e+00 4.00e-02 3.37e+01
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C 409 "
           pdb=" CB  CYS C 409 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.98   48.02     1      1.00e+01 1.00e-02 3.18e+01
  dihedral pdb=" CA  TYR A 176 "
           pdb=" C   TYR A 176 "
           pdb=" N   SER A 177 "
           pdb=" CA  SER A 177 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.31   25.69     0      5.00e+00 4.00e-02 2.64e+01
  ... (remaining 4557 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 631
       0.085 -    0.169: 88
       0.169 -    0.254: 6
       0.254 -    0.338: 1
       0.338 -    0.423: 1
  Chirality restraints: 727
  Sorted by residual:
  chirality pdb=" CB  VAL C 336 "
            pdb=" CA  VAL C 336 "
            pdb=" CG1 VAL C 336 "
            pdb=" CG2 VAL C 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.21   -0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CB  VAL C 182 "
            pdb=" CA  VAL C 182 "
            pdb=" CG1 VAL C 182 "
            pdb=" CG2 VAL C 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.86e+00
  chirality pdb=" CB  ILE C  52 "
            pdb=" CA  ILE C  52 "
            pdb=" CG1 ILE C  52 "
            pdb=" CG2 ILE C  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 724 not shown)

  Planarity restraints: 1445
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 407 "    0.026 2.00e-02 2.50e+03   3.46e-02 3.60e+01
        pdb=" CG  TYR C 407 "    0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 407 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 407 "   -0.052 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 407 "   -0.023 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 407 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 407 "    0.023 2.00e-02 2.50e+03
        pdb=" OH  TYR C 407 "    0.064 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 407 "   -0.001 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 407 "    0.002 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 407 "   -0.063 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 407 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS C 209 "   -0.005 2.00e-02 2.50e+03   2.60e-02 1.52e+01
        pdb=" CG  HIS C 209 "    0.059 2.00e-02 2.50e+03
        pdb=" ND1 HIS C 209 "   -0.047 2.00e-02 2.50e+03
        pdb=" CD2 HIS C 209 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE1 HIS C 209 "    0.008 2.00e-02 2.50e+03
        pdb=" NE2 HIS C 209 "    0.001 2.00e-02 2.50e+03
        pdb=" HD1 HIS C 209 "   -0.002 2.00e-02 2.50e+03
        pdb=" HD2 HIS C 209 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE1 HIS C 209 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 408 "    0.007 2.00e-02 2.50e+03   2.16e-02 1.40e+01
        pdb=" CG  TYR C 408 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 408 "    0.038 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 408 "    0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 408 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 408 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 408 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C 408 "   -0.025 2.00e-02 2.50e+03
        pdb=" HD1 TYR C 408 "   -0.000 2.00e-02 2.50e+03
        pdb=" HD2 TYR C 408 "   -0.003 2.00e-02 2.50e+03
        pdb=" HE1 TYR C 408 "    0.005 2.00e-02 2.50e+03
        pdb=" HE2 TYR C 408 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1442 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.35: 3003
        2.35 -     2.91: 21088
        2.91 -     3.47: 25135
        3.47 -     4.04: 33025
        4.04 -     4.60: 49644
  Nonbonded interactions: 131895
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 407 "
            pdb=" HE1 TYR C 407 "
     model   vdw
     1.787 1.960
  nonbonded pdb=" HE1 TYR C 407 "
            pdb=" HH  TYR C 407 "
     model   vdw
     1.793 2.100
  nonbonded pdb=" HB2 SER C 385 "
            pdb=" HG  SER C 385 "
     model   vdw
     1.945 1.816
  nonbonded pdb=" HB  VAL C 182 "
            pdb="HG23 VAL C 182 "
     model   vdw
     1.999 1.952
  nonbonded pdb=" H   ASN C 301 "
            pdb=" H   ARG C 302 "
     model   vdw
     2.004 2.100
  ... (remaining 131890 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:             1.110
  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:             0.030
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.610
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.250
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7537
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      :  0.008   0.160   4917  Z= 0.344
  Angle     :  1.302  23.826   6650  Z= 0.649
  Chirality :  0.059   0.423    727
  Planarity :  0.007   0.075    863
  Dihedral  : 17.324  83.122   1846
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 0.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.99 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 20.12 %
    Favored  : 78.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.81 (0.30), residues: 601
  helix: -0.60 (0.28), residues: 258
  sheet: -1.18 (0.51), residues: 92
  loop : -1.74 (0.35), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.003   ARG C 302 
 TYR   0.050   0.004   TYR C 408 
 PHE   0.027   0.003   PHE C 258 
 TRP   0.016   0.003   TRP C 426 
 HIS   0.042   0.008   HIS C 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00781 ( 4912)
  covalent geometry    : angle       1.29691 ( 6638)
  SS BOND              : bond        0.00949 (    3)
  SS BOND              : angle       1.41133 (    6)
  hydrogen bonds       : bond        0.15822 (  254)
  hydrogen bonds       : angle       6.18539 (  720)
  link_BETA1-4         : bond        0.00287 (    1)
  link_BETA1-4         : angle       4.97239 (    3)
  link_NAG-ASN         : bond        0.00100 (    1)
  link_NAG-ASN         : angle       3.07961 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  82 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  269 ILE cc_start: 0.8629 (mm) cc_final: 0.8353 (tp)
REVERT: C  212 MET cc_start: 0.8421 (mmt) cc_final: 0.8193 (mmt)
REVERT: C  231 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8826 (pp)
REVERT: C  396 MET cc_start: 0.8104 (mmp) cc_final: 0.7676 (mmp)
REVERT: C  425 TYR cc_start: 0.8710 (m-80) cc_final: 0.8358 (m-10)
  outliers start: 7
  outliers final: 1
  residues processed: 77
  average time/residue: 0.1822
  time to fit residues: 17.6213
Evaluate side-chains
  55 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  282 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 227 ASN
C 219 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.060653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.048995 restraints weight = 77251.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.051733 restraints weight = 38918.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.053590 restraints weight = 24069.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.054889 restraints weight = 16733.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.055869 restraints weight = 12608.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4917  Z= 0.138
  Angle     :  0.600   6.771   6650  Z= 0.307
  Chirality :  0.039   0.138    727
  Planarity :  0.004   0.046    863
  Dihedral  :  5.345  34.586    703
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.95 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.34 (0.33), residues: 601
  helix:  1.00 (0.31), residues: 258
  sheet: -1.15 (0.49), residues: 97
  loop : -1.09 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 284 
 TYR   0.012   0.001   TYR C 422 
 PHE   0.008   0.001   PHE C 329 
 TRP   0.007   0.001   TRP C 338 
 HIS   0.003   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 4912)
  covalent geometry    : angle       0.59049 ( 6638)
  SS BOND              : bond        0.00280 (    3)
  SS BOND              : angle       0.81216 (    6)
  hydrogen bonds       : bond        0.04045 (  254)
  hydrogen bonds       : angle       4.97022 (  720)
  link_BETA1-4         : bond        0.00288 (    1)
  link_BETA1-4         : angle       3.34174 (    3)
  link_NAG-ASN         : bond        0.00020 (    1)
  link_NAG-ASN         : angle       3.67983 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  61 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 53
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  269 ILE cc_start: 0.8817 (mm) cc_final: 0.8395 (tp)
REVERT: C  212 MET cc_start: 0.8187 (mmt) cc_final: 0.7911 (mmt)
REVERT: C  231 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8471 (pp)
REVERT: C  396 MET cc_start: 0.7883 (mmp) cc_final: 0.7431 (mmp)
REVERT: C  425 TYR cc_start: 0.8478 (m-80) cc_final: 0.8084 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 60
  average time/residue: 0.2213
  time to fit residues: 16.3017
Evaluate side-chains
  53 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain C residue   85 HIS
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  341 GLU
Chi-restraints excluded: chain C residue  413 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 387 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.056309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.044690 restraints weight = 80854.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.047323 restraints weight = 40169.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.049122 restraints weight = 25014.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.050406 restraints weight = 17646.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.051275 restraints weight = 13484.905|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.3800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.067   4917  Z= 0.294
  Angle     :  0.753   8.901   6650  Z= 0.403
  Chirality :  0.043   0.190    727
  Planarity :  0.005   0.068    863
  Dihedral  :  6.122  45.038    700
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 18.36 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.83 (0.32), residues: 601
  helix:  0.59 (0.30), residues: 262
  sheet: -1.55 (0.47), residues: 88
  loop : -1.32 (0.37), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 181 
 TYR   0.014   0.002   TYR C 422 
 PHE   0.013   0.002   PHE C 258 
 TRP   0.018   0.002   TRP C 338 
 HIS   0.012   0.002   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00609 ( 4912)
  covalent geometry    : angle       0.73999 ( 6638)
  SS BOND              : bond        0.00191 (    3)
  SS BOND              : angle       0.57397 (    6)
  hydrogen bonds       : bond        0.04108 (  254)
  hydrogen bonds       : angle       5.48785 (  720)
  link_BETA1-4         : bond        0.01089 (    1)
  link_BETA1-4         : angle       4.14348 (    3)
  link_NAG-ASN         : bond        0.01029 (    1)
  link_NAG-ASN         : angle       5.16263 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  54 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  147 SER cc_start: 0.8640 (OUTLIER) cc_final: 0.7816 (p)
REVERT: C  396 MET cc_start: 0.7939 (mmp) cc_final: 0.7581 (mmp)
REVERT: C  425 TYR cc_start: 0.8627 (m-80) cc_final: 0.8162 (m-10)
  outliers start: 14
  outliers final: 10
  residues processed: 52
  average time/residue: 0.1687
  time to fit residues: 11.4863
Evaluate side-chains
  48 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  222 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  147 SER
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  279 LEU
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 42 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
C 281 GLN
C 387 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.056816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.045604 restraints weight = 78110.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.048194 restraints weight = 38240.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.049914 restraints weight = 23559.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.051154 restraints weight = 16562.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.052073 restraints weight = 12557.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.3982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4917  Z= 0.130
  Angle     :  0.579   6.662   6650  Z= 0.296
  Chirality :  0.040   0.178    727
  Planarity :  0.004   0.041    863
  Dihedral  :  5.383  43.628    700
  Min Nonbonded Distance : 1.939

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.75 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -0.33 (0.33), residues: 601
  helix:  1.12 (0.31), residues: 261
  sheet: -1.29 (0.47), residues: 88
  loop : -1.21 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.009   0.001   TYR C 393 
 PHE   0.012   0.001   PHE A 180 
 TRP   0.008   0.001   TRP C 338 
 HIS   0.004   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 4912)
  covalent geometry    : angle       0.56699 ( 6638)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.62743 (    6)
  hydrogen bonds       : bond        0.03454 (  254)
  hydrogen bonds       : angle       4.94266 (  720)
  link_BETA1-4         : bond        0.00170 (    1)
  link_BETA1-4         : angle       3.96781 (    3)
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       3.86169 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  49 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 37
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9437 (ppp) cc_final: 0.9117 (tmm)
  outliers start: 12
  outliers final: 9
  residues processed: 47
  average time/residue: 0.1902
  time to fit residues: 11.3510
Evaluate side-chains
  44 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  155 ARG
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 20 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 387 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.056169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.045110 restraints weight = 78221.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.047635 restraints weight = 38309.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.049328 restraints weight = 23871.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.050552 restraints weight = 16777.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.051454 restraints weight = 12757.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.4436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4917  Z= 0.153
  Angle     :  0.570   7.068   6650  Z= 0.295
  Chirality :  0.039   0.174    727
  Planarity :  0.004   0.040    863
  Dihedral  :  5.222  41.669    700
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 19.73 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.02 (0.34), residues: 601
  helix:  1.45 (0.32), residues: 261
  sheet: -1.07 (0.48), residues: 86
  loop : -1.09 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.009   0.001   TYR C 277 
 PHE   0.010   0.001   PHE C 258 
 TRP   0.008   0.001   TRP C 338 
 HIS   0.003   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 4912)
  covalent geometry    : angle       0.55806 ( 6638)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       0.72454 (    6)
  hydrogen bonds       : bond        0.03263 (  254)
  hydrogen bonds       : angle       4.81448 (  720)
  link_BETA1-4         : bond        0.00389 (    1)
  link_BETA1-4         : angle       3.80051 (    3)
  link_NAG-ASN         : bond        0.00229 (    1)
  link_NAG-ASN         : angle       3.83563 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  47 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9379 (ppp) cc_final: 0.9081 (tmm)
REVERT: C  425 TYR cc_start: 0.8559 (m-80) cc_final: 0.8047 (m-10)
  outliers start: 10
  outliers final: 10
  residues processed: 46
  average time/residue: 0.1830
  time to fit residues: 10.8359
Evaluate side-chains
  45 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  413 TRP
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.1980
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 387 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.056596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.045091 restraints weight = 79118.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.047712 restraints weight = 38618.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.049447 restraints weight = 23915.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.050744 restraints weight = 16898.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.051655 restraints weight = 12867.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4917  Z= 0.111
  Angle     :  0.544   7.222   6650  Z= 0.276
  Chirality :  0.039   0.161    727
  Planarity :  0.003   0.041    863
  Dihedral  :  5.025  39.803    700
  Min Nonbonded Distance : 1.958

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.90 %
    Favored  : 77.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.21 (0.34), residues: 601
  helix:  1.65 (0.32), residues: 261
  sheet: -0.90 (0.50), residues: 86
  loop : -1.07 (0.38), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 208 
 TYR   0.007   0.001   TYR C 393 
 PHE   0.011   0.001   PHE C 258 
 TRP   0.007   0.001   TRP C 338 
 HIS   0.003   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 4912)
  covalent geometry    : angle       0.53287 ( 6638)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.67360 (    6)
  hydrogen bonds       : bond        0.03210 (  254)
  hydrogen bonds       : angle       4.69184 (  720)
  link_BETA1-4         : bond        0.00116 (    1)
  link_BETA1-4         : angle       3.66279 (    3)
  link_NAG-ASN         : bond        0.00014 (    1)
  link_NAG-ASN         : angle       3.51056 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  45 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9379 (ppp) cc_final: 0.9092 (tmm)
REVERT: C  425 TYR cc_start: 0.8603 (m-80) cc_final: 0.8062 (m-10)
  outliers start: 10
  outliers final: 10
  residues processed: 44
  average time/residue: 0.1792
  time to fit residues: 10.2185
Evaluate side-chains
  45 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  149 PHE
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  413 TRP
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 6 optimal weight:    0.3980
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 56 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.6788

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

Flipped N/Q/H residues before XYZ refinement:
C 387 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.055110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.043675 restraints weight = 79956.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.046219 restraints weight = 39416.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.047945 restraints weight = 24580.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.049155 restraints weight = 17390.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.050055 restraints weight = 13418.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
moved from start:          0.5288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4917  Z= 0.185
  Angle     :  0.581   7.879   6650  Z= 0.303
  Chirality :  0.039   0.166    727
  Planarity :  0.004   0.040    863
  Dihedral  :  5.222  41.626    700
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.90 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.02 (0.34), residues: 601
  helix:  1.39 (0.31), residues: 262
  sheet: -1.00 (0.50), residues: 86
  loop : -1.07 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 208 
 TYR   0.008   0.001   TYR C 277 
 PHE   0.013   0.001   PHE C 258 
 TRP   0.007   0.001   TRP C 338 
 HIS   0.003   0.001   HIS A 183 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 4912)
  covalent geometry    : angle       0.56941 ( 6638)
  SS BOND              : bond        0.00126 (    3)
  SS BOND              : angle       0.73723 (    6)
  hydrogen bonds       : bond        0.03235 (  254)
  hydrogen bonds       : angle       4.86717 (  720)
  link_BETA1-4         : bond        0.00595 (    1)
  link_BETA1-4         : angle       3.70850 (    3)
  link_NAG-ASN         : bond        0.00469 (    1)
  link_NAG-ASN         : angle       3.94048 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  43 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 29
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9366 (ppp) cc_final: 0.9069 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 42
  average time/residue: 0.1610
  time to fit residues: 8.9510
Evaluate side-chains
  40 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 29
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  240 ILE
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  149 PHE
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   chunk 29 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.055658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.044244 restraints weight = 78562.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.046755 restraints weight = 38748.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.048508 restraints weight = 24275.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.049744 restraints weight = 17169.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.050602 restraints weight = 13157.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.5371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4917  Z= 0.117
  Angle     :  0.559   6.763   6650  Z= 0.284
  Chirality :  0.039   0.157    727
  Planarity :  0.004   0.041    863
  Dihedral  :  4.988  40.065    700
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.90 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: 601
  helix:  1.68 (0.32), residues: 262
  sheet: -0.78 (0.51), residues: 86
  loop : -1.00 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 152 
 TYR   0.008   0.001   TYR C 393 
 PHE   0.012   0.001   PHE C 258 
 TRP   0.007   0.001   TRP C 338 
 HIS   0.002   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 4912)
  covalent geometry    : angle       0.54925 ( 6638)
  SS BOND              : bond        0.00165 (    3)
  SS BOND              : angle       0.68721 (    6)
  hydrogen bonds       : bond        0.03151 (  254)
  hydrogen bonds       : angle       4.64739 (  720)
  link_BETA1-4         : bond        0.00025 (    1)
  link_BETA1-4         : angle       3.58992 (    3)
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       3.42191 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  40 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9327 (ppp) cc_final: 0.9017 (tmm)
REVERT: C  407 TYR cc_start: 0.7502 (m-10) cc_final: 0.7172 (m-10)
  outliers start: 12
  outliers final: 11
  residues processed: 38
  average time/residue: 0.1505
  time to fit residues: 7.8134
Evaluate side-chains
  39 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  149 PHE
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  413 TRP
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 55 optimal weight:    0.5980
   chunk 53 optimal weight:    0.6980
   chunk 54 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.9984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.055473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.044045 restraints weight = 78513.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.046573 restraints weight = 38584.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.048312 restraints weight = 24038.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.049489 restraints weight = 17005.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.050443 restraints weight = 13169.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.5578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4917  Z= 0.125
  Angle     :  0.548   6.340   6650  Z= 0.279
  Chirality :  0.038   0.156    727
  Planarity :  0.003   0.040    863
  Dihedral  :  4.942  37.853    700
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.09 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.40 (0.34), residues: 601
  helix:  1.80 (0.32), residues: 262
  sheet: -0.74 (0.51), residues: 86
  loop : -1.02 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 268 
 TYR   0.005   0.001   TYR C 277 
 PHE   0.008   0.001   PHE A 180 
 TRP   0.006   0.001   TRP C 338 
 HIS   0.002   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4912)
  covalent geometry    : angle       0.53834 ( 6638)
  SS BOND              : bond        0.00169 (    3)
  SS BOND              : angle       0.76750 (    6)
  hydrogen bonds       : bond        0.03070 (  254)
  hydrogen bonds       : angle       4.59958 (  720)
  link_BETA1-4         : bond        0.00253 (    1)
  link_BETA1-4         : angle       3.44320 (    3)
  link_NAG-ASN         : bond        0.00033 (    1)
  link_NAG-ASN         : angle       3.41897 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  38 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 27
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9284 (ppp) cc_final: 0.8943 (tmm)
REVERT: C  407 TYR cc_start: 0.7596 (m-10) cc_final: 0.7249 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 37
  average time/residue: 0.1553
  time to fit residues: 7.7664
Evaluate side-chains
  37 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   chunk 5 optimal weight:    4.9990
   chunk 59 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    1.0582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.055164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.043781 restraints weight = 78085.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.046312 restraints weight = 38497.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.048044 restraints weight = 24082.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.049304 restraints weight = 17005.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.050166 restraints weight = 12947.866|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.5840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4917  Z= 0.125
  Angle     :  0.548   7.155   6650  Z= 0.278
  Chirality :  0.039   0.154    727
  Planarity :  0.003   0.040    863
  Dihedral  :  4.817  36.582    700
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 21.29 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.45 (0.34), residues: 601
  helix:  1.87 (0.32), residues: 262
  sheet: -0.67 (0.52), residues: 86
  loop : -1.03 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 337 
 TYR   0.009   0.001   TYR C 263 
 PHE   0.011   0.001   PHE C 258 
 TRP   0.006   0.001   TRP C 338 
 HIS   0.002   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00262 ( 4912)
  covalent geometry    : angle       0.53874 ( 6638)
  SS BOND              : bond        0.00171 (    3)
  SS BOND              : angle       0.69534 (    6)
  hydrogen bonds       : bond        0.03004 (  254)
  hydrogen bonds       : angle       4.53750 (  720)
  link_BETA1-4         : bond        0.00253 (    1)
  link_BETA1-4         : angle       3.34651 (    3)
  link_NAG-ASN         : bond        0.00056 (    1)
  link_NAG-ASN         : angle       3.31205 (    3)

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

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

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1202 Ramachandran restraints generated.
    601 Oldfield, 0 Emsley, 601 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue SER  142 is missing expected H atoms. Skipping.
Residue SER  144 is missing expected H atoms. Skipping.
Residue THR  209 is missing expected H atoms. Skipping.
Evaluate side-chains
  37 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  224 MET cc_start: 0.9253 (ppp) cc_final: 0.8922 (tmm)
REVERT: C  407 TYR cc_start: 0.7554 (m-10) cc_final: 0.7288 (m-10)
  outliers start: 10
  outliers final: 10
  residues processed: 36
  average time/residue: 0.1568
  time to fit residues: 7.6225
Evaluate side-chains
  37 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 27
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  310 ASN
Chi-restraints excluded: chain C residue   12 LEU
Chi-restraints excluded: chain C residue  102 THR
Chi-restraints excluded: chain C residue  152 PHE
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  257 ASP
Chi-restraints excluded: chain C residue  372 HIS
Chi-restraints excluded: chain C residue  432 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    0.0470
   chunk 29 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   chunk 34 optimal weight:    7.9990
   chunk 1 optimal weight:    0.9990
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    4.9990
   overall best weight:    1.1284

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.055074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.043685 restraints weight = 78751.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.046213 restraints weight = 38695.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.047956 restraints weight = 24044.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.049198 restraints weight = 17014.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.050127 restraints weight = 12980.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8051
moved from start:          0.6100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4917  Z= 0.131
  Angle     :  0.555   8.465   6650  Z= 0.282
  Chirality :  0.038   0.153    727
  Planarity :  0.003   0.040    863
  Dihedral  :  4.793  35.384    700
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 21.48 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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:  0.45 (0.34), residues: 601
  helix:  1.86 (0.32), residues: 262
  sheet: -0.66 (0.53), residues: 86
  loop : -1.02 (0.38), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 337 
 TYR   0.008   0.001   TYR C 393 
 PHE   0.010   0.001   PHE C 258 
 TRP   0.007   0.001   TRP C 338 
 HIS   0.002   0.001   HIS C 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4912)
  covalent geometry    : angle       0.54623 ( 6638)
  SS BOND              : bond        0.00168 (    3)
  SS BOND              : angle       0.77785 (    6)
  hydrogen bonds       : bond        0.03006 (  254)
  hydrogen bonds       : angle       4.58965 (  720)
  link_BETA1-4         : bond        0.00201 (    1)
  link_BETA1-4         : angle       3.27151 (    3)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       3.42236 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1803.44 seconds
wall clock time: 31 minutes 24.46 seconds (1884.46 seconds total)