Starting phenix.real_space_refine
on Tue Mar  3 13:43:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.176
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ymd_33927/03_2026/7ymd_33927.map"
  }
  resolution = 4.176
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.007
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: 4
    Type Number    sf(0)   Gaussians
     S      25      5.16       5
     C    3575      2.51       5
     N     969      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5653
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 816
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "B"
      Number of atoms: 2573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 322, 2573
          Classifications: {'peptide': 322}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 319}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "C"
      Number of atoms: 2264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2264
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 277}
          Chain breaks: 1
  Time building chain proxies: 1.33, per 1000 atoms: 0.24
  Number of scatterers: 5653
  At special positions: 0
  Unit cell: (77.256, 83.52, 99.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      25     16.00
     O    1084      8.00
     N     969      7.00
     C    3575      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 383.8 milliseconds
  

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1344

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 5 sheets defined
      50.9% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 114 through 121
    Processing helix  chain 'A' and resid 131 through 140
    Processing helix  chain 'A' and resid 199 through 211
      removed outlier: 3.523A  pdb=" N   ARG A 202 " --> pdb=" O   THR A 199 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   HIS A 203 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   TYR A 205 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLN A 207 " --> pdb=" O   SER A 204 " (cutoff:3.500A)
      removed outlier: 4.833A  pdb=" N   GLN A 208 " --> pdb=" O   TYR A 205 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   SER A 210 " --> pdb=" O   GLN A 207 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   HIS A 211 " --> pdb=" O   GLN A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 219 through 227
      removed outlier: 4.243A  pdb=" N   ILE A 223 " --> pdb=" O   ASN A 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 27
      removed outlier: 3.529A  pdb=" N   ALA B  18 " --> pdb=" O   GLY B  14 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 49
      removed outlier: 5.015A  pdb=" N   ASP B  47 " --> pdb=" O   ARG B  43 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ALA B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER B  49 " --> pdb=" O   GLU B  45 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 77
      removed outlier: 4.064A  pdb=" N   LEU B  77 " --> pdb=" O   VAL B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 97
      removed outlier: 4.346A  pdb=" N   LYS B  97 " --> pdb=" O   ALA B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 151 through 168
    Processing helix  chain 'B' and resid 181 through 195
      removed outlier: 3.881A  pdb=" N   GLU B 186 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 219
    Processing helix  chain 'B' and resid 223 through 237
    Processing helix  chain 'B' and resid 251 through 258
      removed outlier: 3.575A  pdb=" N   ILE B 255 " --> pdb=" O   ASP B 251 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 258 through 266
    Processing helix  chain 'B' and resid 306 through 316
    Processing helix  chain 'C' and resid 8 through 25
      removed outlier: 4.549A  pdb=" N   LEU C  12 " --> pdb=" O   SER C   8 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 42
      removed outlier: 4.054A  pdb=" N   ARG C  29 " --> pdb=" O   ASN C  25 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   LYS C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLU C  40 " --> pdb=" O   LEU C  36 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLN C  42 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 63
    Processing helix  chain 'C' and resid 68 through 83
    Processing helix  chain 'C' and resid 94 through 99
      removed outlier: 4.030A  pdb=" N   ASN C  98 " --> pdb=" O   LYS C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 134 through 146
      removed outlier: 3.522A  pdb=" N   PHE C 138 " --> pdb=" O   ASN C 134 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   THR C 146 " --> pdb=" O   GLN C 142 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 146 through 151
      removed outlier: 3.744A  pdb=" N   ILE C 151 " --> pdb=" O   TYR C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 155
    Processing helix  chain 'C' and resid 177 through 195
    Processing helix  chain 'C' and resid 201 through 209
    Processing helix  chain 'C' and resid 210 through 212
      No H-bonds generated for 'chain 'C' and resid 210 through 212'
    Processing helix  chain 'C' and resid 226 through 237
    Processing helix  chain 'C' and resid 259 through 266
    Processing helix  chain 'C' and resid 267 through 280
    Processing helix  chain 'C' and resid 282 through 287
      removed outlier: 4.455A  pdb=" N   LYS C 287 " --> pdb=" O   GLU C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 289 through 298
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 33
      removed outlier: 3.573A  pdb=" N   CYS B  32 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE B 133 " --> pdb=" O   CYS B  32 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 206 through 208
      removed outlier: 6.194A  pdb=" N   SER B 207 " --> pdb=" O   ILE B 336 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   GLY B 281 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 240 through 242
    Processing sheet with id=AA4, first strand: chain 'C' and resid 46 through 47
      removed outlier: 4.690A  pdb=" N   LYS C 122 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE C 124 " --> pdb=" O   GLN C  89 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN C  89 " --> pdb=" O   ILE C 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 199 through 200
      removed outlier: 3.954A  pdb=" N   ILE C 199 " --> pdb=" O   TYR C 256 " (cutoff:3.500A)

    233 hydrogen bonds defined for protein.
    669 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.73

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1877
        1.34 -     1.46: 874
        1.46 -     1.58: 2954
        1.58 -     1.69: 0
        1.69 -     1.81: 39
  Bond restraints: 5744
  Sorted by residual:
  bond pdb=" N   ALA A 114 "
       pdb=" CA  ALA A 114 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  bond pdb=" N   ASP C   7 "
       pdb=" CA  ASP C   7 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 2.95e+00
  bond pdb=" N   ASN B 286 "
       pdb=" CA  ASN B 286 "
    ideal  model  delta    sigma   weight residual
    1.457  1.468 -0.011 1.29e-02 6.01e+03 6.99e-01
  bond pdb=" CB  GLU B  45 "
       pdb=" CG  GLU B  45 "
    ideal  model  delta    sigma   weight residual
    1.520  1.543 -0.023 3.00e-02 1.11e+03 5.84e-01
  bond pdb=" N   THR C 168 "
       pdb=" CA  THR C 168 "
    ideal  model  delta    sigma   weight residual
    1.457  1.466 -0.009 1.29e-02 6.01e+03 4.69e-01
  ... (remaining 5739 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 7412
        1.04 -     2.08: 278
        2.08 -     3.12: 41
        3.12 -     4.15: 16
        4.15 -     5.19: 3
  Bond angle restraints: 7750
  Sorted by residual:
  angle pdb=" C   ASN B 286 "
        pdb=" CA  ASN B 286 "
        pdb=" CB  ASN B 286 "
      ideal   model   delta    sigma   weight residual
     110.42  115.61   -5.19 1.99e+00 2.53e-01 6.81e+00
  angle pdb=" C   TYR A 212 "
        pdb=" N   ASN A 213 "
        pdb=" CA  ASN A 213 "
      ideal   model   delta    sigma   weight residual
     121.54  125.73   -4.19 1.91e+00 2.74e-01 4.81e+00
  angle pdb=" C   LYS C 196 "
        pdb=" N   ASN C 197 "
        pdb=" CA  ASN C 197 "
      ideal   model   delta    sigma   weight residual
     121.54  125.46   -3.92 1.91e+00 2.74e-01 4.20e+00
  angle pdb=" C   THR C 168 "
        pdb=" CA  THR C 168 "
        pdb=" CB  THR C 168 "
      ideal   model   delta    sigma   weight residual
     110.42  114.48   -4.06 1.99e+00 2.53e-01 4.15e+00
  angle pdb=" C   ARG A 127 "
        pdb=" CA  ARG A 127 "
        pdb=" CB  ARG A 127 "
      ideal   model   delta    sigma   weight residual
     109.54  112.83   -3.29 1.84e+00 2.95e-01 3.19e+00
  ... (remaining 7745 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3220
       17.94 -    35.88: 219
       35.88 -    53.82: 40
       53.82 -    71.76: 7
       71.76 -    89.69: 3
  Dihedral angle restraints: 3489
    sinusoidal: 1422
      harmonic: 2067
  Sorted by residual:
  dihedral pdb=" CA  ARG A 127 "
           pdb=" C   ARG A 127 "
           pdb=" N   SER A 128 "
           pdb=" CA  SER A 128 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.48  -24.52     0      5.00e+00 4.00e-02 2.40e+01
  dihedral pdb=" CA  CYS B  32 "
           pdb=" C   CYS B  32 "
           pdb=" N   HIS B  33 "
           pdb=" CA  HIS B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.01  -16.99     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  MET B 265 "
           pdb=" C   MET B 265 "
           pdb=" N   TYR B 266 "
           pdb=" CA  TYR B 266 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.73   16.27     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 3486 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 562
       0.025 -    0.050: 190
       0.050 -    0.075: 73
       0.075 -    0.100: 34
       0.100 -    0.125: 25
  Chirality restraints: 884
  Sorted by residual:
  chirality pdb=" CA  VAL C 129 "
            pdb=" N   VAL C 129 "
            pdb=" C   VAL C 129 "
            pdb=" CB  VAL C 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.90e-01
  chirality pdb=" CA  ILE C 124 "
            pdb=" N   ILE C 124 "
            pdb=" C   ILE C 124 "
            pdb=" CB  ILE C 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.52e-01
  chirality pdb=" CA  ILE C 254 "
            pdb=" N   ILE C 254 "
            pdb=" C   ILE C 254 "
            pdb=" CB  ILE C 254 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.49e-01
  ... (remaining 881 not shown)

  Planarity restraints: 993
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 160 "    0.009 2.00e-02 2.50e+03   7.84e-03 1.54e+00
        pdb=" CG  TRP B 160 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 160 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 160 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 160 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 160 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 160 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 160 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 160 "   -0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 160 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 242 "    0.019 5.00e-02 4.00e+02   2.83e-02 1.28e+00
        pdb=" N   PRO A 243 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 243 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 243 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 196 "    0.005 2.00e-02 2.50e+03   1.11e-02 1.22e+00
        pdb=" C   LYS C 196 "   -0.019 2.00e-02 2.50e+03
        pdb=" O   LYS C 196 "    0.007 2.00e-02 2.50e+03
        pdb=" N   ASN C 197 "    0.006 2.00e-02 2.50e+03
  ... (remaining 990 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 79
        2.60 -     3.18: 5545
        3.18 -     3.75: 8420
        3.75 -     4.33: 11466
        4.33 -     4.90: 18681
  Nonbonded interactions: 44191
  Sorted by model distance:
  nonbonded pdb=" O   SER B 213 "
            pdb=" OG1 THR B 214 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OE2 GLU A 214 "
            pdb=" CG  GLN A 217 "
     model   vdw
     2.216 3.440
  nonbonded pdb=" O   LEU C  80 "
            pdb=" N   GLY C  85 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" OH  TYR B  20 "
            pdb=" O   PRO C 130 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" O   LYS C 287 "
            pdb=" OG  SER C 288 "
     model   vdw
     2.263 3.040
  ... (remaining 44186 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.170
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.010
  Process input model:                     7.060
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6938
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      :  0.002   0.033   5744  Z= 0.105
  Angle     :  0.481   5.193   7750  Z= 0.278
  Chirality :  0.037   0.125    884
  Planarity :  0.002   0.028    993
  Dihedral  : 12.735  89.694   2145
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.35), residues: 693
  helix:  1.35 (0.31), residues: 330
  sheet: -0.54 (1.16), residues: 22
  loop : -1.13 (0.36), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 127 
 TYR   0.008   0.001   TYR B 261 
 PHE   0.015   0.001   PHE B 165 
 TRP   0.022   0.001   TRP B 160 
 HIS   0.007   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00202 ( 5744)
  covalent geometry    : angle       0.48080 ( 7750)
  hydrogen bonds       : bond        0.15571 (  233)
  hydrogen bonds       : angle       5.41177 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 MET cc_start: 0.8043 (tpp) cc_final: 0.7779 (tpp)
REVERT: B  222 LEU cc_start: 0.8632 (mm) cc_final: 0.7901 (tp)
REVERT: C  197 ASN cc_start: 0.7333 (p0) cc_final: 0.7109 (p0)
REVERT: C  224 ASN cc_start: 0.8580 (m-40) cc_final: 0.8119 (t0)
REVERT: C  257 ARG cc_start: 0.7979 (mmm-85) cc_final: 0.7443 (tpt-90)
REVERT: C  299 ASP cc_start: 0.7148 (p0) cc_final: 0.6435 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.0588
  time to fit residues: 14.2277
Evaluate side-chains
  146 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 303 GLN
C  89 GLN
C 145 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.193693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.148740 restraints weight = 9486.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.153904 restraints weight = 6193.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.157481 restraints weight = 4717.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.159472 restraints weight = 3923.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.161428 restraints weight = 3494.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7243
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5744  Z= 0.159
  Angle     :  0.594   9.566   7750  Z= 0.313
  Chirality :  0.043   0.148    884
  Planarity :  0.004   0.047    993
  Dihedral  :  4.089  18.051    757
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.34), residues: 693
  helix:  0.92 (0.30), residues: 334
  sheet: -1.63 (0.96), residues: 26
  loop : -1.04 (0.37), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 242 
 TYR   0.015   0.002   TYR C  84 
 PHE   0.014   0.002   PHE B 248 
 TRP   0.021   0.002   TRP B 160 
 HIS   0.006   0.001   HIS A 147 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 5744)
  covalent geometry    : angle       0.59381 ( 7750)
  hydrogen bonds       : bond        0.03384 (  233)
  hydrogen bonds       : angle       4.49131 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 LEU cc_start: 0.8382 (mp) cc_final: 0.8163 (mp)
REVERT: B  163 GLU cc_start: 0.8565 (tt0) cc_final: 0.8121 (mm-30)
REVERT: B  222 LEU cc_start: 0.8658 (mm) cc_final: 0.8052 (tp)
REVERT: B  303 GLN cc_start: 0.5484 (mp10) cc_final: 0.4828 (mp10)
REVERT: C   31 MET cc_start: 0.8646 (tpp) cc_final: 0.8385 (tpp)
REVERT: C  139 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8553 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.0620
  time to fit residues: 14.7605
Evaluate side-chains
  145 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 57 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 37 optimal weight:    9.9990
   chunk 13 optimal weight:    7.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  56 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.191139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.146315 restraints weight = 9602.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.151211 restraints weight = 6245.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.154468 restraints weight = 4747.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.156636 restraints weight = 3986.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.158202 restraints weight = 3550.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   5744  Z= 0.160
  Angle     :  0.602   8.366   7750  Z= 0.318
  Chirality :  0.043   0.197    884
  Planarity :  0.003   0.040    993
  Dihedral  :  4.334  21.984    757
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.02 %
    Favored  : 96.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.54 (0.33), residues: 693
  helix:  0.54 (0.29), residues: 336
  sheet: -2.06 (0.90), residues: 26
  loop : -1.12 (0.37), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 237 
 TYR   0.020   0.002   TYR B 313 
 PHE   0.019   0.002   PHE C 135 
 TRP   0.022   0.002   TRP B 160 
 HIS   0.006   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 5744)
  covalent geometry    : angle       0.60178 ( 7750)
  hydrogen bonds       : bond        0.03438 (  233)
  hydrogen bonds       : angle       4.44442 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8109 (mmm) cc_final: 0.7305 (tpp)
REVERT: B   33 HIS cc_start: 0.8911 (t70) cc_final: 0.8248 (t-90)
REVERT: B   34 GLU cc_start: 0.7487 (pm20) cc_final: 0.7213 (pm20)
REVERT: B  158 MET cc_start: 0.8317 (tpp) cc_final: 0.8046 (tpp)
REVERT: B  163 GLU cc_start: 0.8592 (tt0) cc_final: 0.8076 (mm-30)
REVERT: C   48 ARG cc_start: 0.8621 (tpt-90) cc_final: 0.8235 (mmm160)
REVERT: C  149 GLU cc_start: 0.8406 (pm20) cc_final: 0.8202 (pm20)
REVERT: C  197 ASN cc_start: 0.7297 (p0) cc_final: 0.5888 (p0)
REVERT: C  237 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8607 (ttm170)
REVERT: C  257 ARG cc_start: 0.7233 (tpt170) cc_final: 0.6387 (tpt170)
  outliers start: 1
  outliers final: 1
  residues processed: 181
  average time/residue: 0.0717
  time to fit residues: 17.1000
Evaluate side-chains
  154 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 153
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 12 optimal weight:   10.0000
   chunk 9 optimal weight:    0.0670
   chunk 17 optimal weight:    8.9990
   chunk 22 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 67 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 35 optimal weight:    9.9990
   chunk 31 optimal weight:    0.7980
   chunk 68 optimal weight:    0.4980
   overall best weight:    1.8722

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 164 GLN
B 280 GLN
C  56 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4311 r_free = 0.4311 target = 0.193606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.145387 restraints weight = 9797.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.150909 restraints weight = 6264.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.154633 restraints weight = 4730.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.157108 restraints weight = 3951.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.158714 restraints weight = 3508.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5744  Z= 0.142
  Angle     :  0.591   7.949   7750  Z= 0.311
  Chirality :  0.042   0.171    884
  Planarity :  0.003   0.039    993
  Dihedral  :  4.419  23.163    757
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.23 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.66 (0.33), residues: 693
  helix:  0.50 (0.29), residues: 336
  sheet: -2.36 (0.87), residues: 26
  loop : -1.24 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  43 
 TYR   0.022   0.002   TYR A 227 
 PHE   0.024   0.002   PHE C 207 
 TRP   0.019   0.002   TRP B 160 
 HIS   0.008   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5744)
  covalent geometry    : angle       0.59079 ( 7750)
  hydrogen bonds       : bond        0.03244 (  233)
  hydrogen bonds       : angle       4.34105 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 176
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 MET cc_start: 0.8250 (mmm) cc_final: 0.7366 (tpp)
REVERT: B  261 TYR cc_start: 0.8198 (t80) cc_final: 0.7910 (t80)
REVERT: C   31 MET cc_start: 0.8793 (tpp) cc_final: 0.8300 (tpp)
REVERT: C   48 ARG cc_start: 0.8624 (tpt-90) cc_final: 0.8248 (mmm160)
REVERT: C  149 GLU cc_start: 0.8260 (pm20) cc_final: 0.7861 (pm20)
REVERT: C  237 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8778 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0687
  time to fit residues: 16.0809
Evaluate side-chains
  147 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 147
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.2980
   chunk 63 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0980
   chunk 57 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    6.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 164 GLN
B 280 GLN
C  56 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.192808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.146406 restraints weight = 9748.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.151503 restraints weight = 6355.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.154977 restraints weight = 4852.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.156925 restraints weight = 4070.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.158918 restraints weight = 3652.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5744  Z= 0.130
  Angle     :  0.583   8.392   7750  Z= 0.303
  Chirality :  0.042   0.153    884
  Planarity :  0.003   0.041    993
  Dihedral  :  4.483  23.684    757
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.37 %
    Favored  : 91.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.67 (0.33), residues: 693
  helix:  0.49 (0.29), residues: 336
  sheet: -2.36 (0.88), residues: 26
  loop : -1.25 (0.36), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 257 
 TYR   0.021   0.002   TYR B 313 
 PHE   0.019   0.002   PHE C 207 
 TRP   0.021   0.002   TRP B 160 
 HIS   0.008   0.002   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5744)
  covalent geometry    : angle       0.58265 ( 7750)
  hydrogen bonds       : bond        0.03156 (  233)
  hydrogen bonds       : angle       4.34408 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 ILE cc_start: 0.9014 (mp) cc_final: 0.8714 (pt)
REVERT: B  158 MET cc_start: 0.8297 (tpp) cc_final: 0.7768 (mmm)
REVERT: B  261 TYR cc_start: 0.8142 (t80) cc_final: 0.7855 (t80)
REVERT: B  268 LEU cc_start: 0.9162 (tp) cc_final: 0.8933 (tp)
REVERT: C   31 MET cc_start: 0.8759 (tpp) cc_final: 0.8270 (tpp)
REVERT: C  139 LYS cc_start: 0.8805 (tttt) cc_final: 0.8509 (tttm)
REVERT: C  149 GLU cc_start: 0.8447 (pm20) cc_final: 0.8214 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.0603
  time to fit residues: 14.7621
Evaluate side-chains
  152 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:    8.9990
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    0.1980
   chunk 17 optimal weight:   20.0000
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
C  56 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.191876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.145915 restraints weight = 9656.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.151231 restraints weight = 6248.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.154821 restraints weight = 4709.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.157151 restraints weight = 3909.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.158693 restraints weight = 3466.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5744  Z= 0.139
  Angle     :  0.604   8.635   7750  Z= 0.316
  Chirality :  0.042   0.167    884
  Planarity :  0.003   0.041    993
  Dihedral  :  4.586  24.396    757
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.80 %
    Favored  : 91.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.33), residues: 693
  helix:  0.47 (0.29), residues: 335
  sheet: -2.26 (0.90), residues: 26
  loop : -1.37 (0.36), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 131 
 TYR   0.017   0.002   TYR A 227 
 PHE   0.018   0.002   PHE C 207 
 TRP   0.020   0.002   TRP B 160 
 HIS   0.008   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 5744)
  covalent geometry    : angle       0.60424 ( 7750)
  hydrogen bonds       : bond        0.03133 (  233)
  hydrogen bonds       : angle       4.38497 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 MET cc_start: 0.5834 (ttt) cc_final: 0.5518 (ttm)
REVERT: B   89 ILE cc_start: 0.8982 (mp) cc_final: 0.8639 (pt)
REVERT: B  261 TYR cc_start: 0.8124 (t80) cc_final: 0.7894 (t80)
REVERT: C   31 MET cc_start: 0.8823 (tpp) cc_final: 0.8321 (tpp)
REVERT: C  209 GLU cc_start: 0.8496 (tp30) cc_final: 0.7988 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0564
  time to fit residues: 13.4545
Evaluate side-chains
  144 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 18 optimal weight:   40.0000
   chunk 26 optimal weight:   10.0000
   chunk 41 optimal weight:   20.0000
   chunk 65 optimal weight:    5.9990
   chunk 64 optimal weight:    7.9990
   chunk 37 optimal weight:   30.0000
   chunk 54 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.1188

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  52 ASN
B 280 GLN
C  52 GLN
C  56 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.186720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140661 restraints weight = 9565.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.145633 restraints weight = 6243.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.149057 restraints weight = 4708.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.151244 restraints weight = 3927.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.152822 restraints weight = 3490.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5744  Z= 0.197
  Angle     :  0.679   9.087   7750  Z= 0.351
  Chirality :  0.045   0.163    884
  Planarity :  0.004   0.041    993
  Dihedral  :  4.848  23.760    757
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.43 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.95 (0.33), residues: 693
  helix:  0.31 (0.29), residues: 342
  sheet: -2.54 (0.86), residues: 26
  loop : -1.47 (0.36), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 131 
 TYR   0.030   0.003   TYR B 266 
 PHE   0.016   0.002   PHE C 207 
 TRP   0.020   0.002   TRP B 160 
 HIS   0.007   0.002   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 ( 5744)
  covalent geometry    : angle       0.67878 ( 7750)
  hydrogen bonds       : bond        0.03665 (  233)
  hydrogen bonds       : angle       4.54098 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   89 ILE cc_start: 0.9033 (mp) cc_final: 0.8667 (pt)
REVERT: B  265 MET cc_start: 0.8882 (tmm) cc_final: 0.8651 (tmm)
REVERT: C   31 MET cc_start: 0.8880 (tpp) cc_final: 0.8323 (tpp)
REVERT: C   52 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8239 (mm-40)
REVERT: C  146 THR cc_start: 0.8496 (p) cc_final: 0.8107 (p)
REVERT: C  209 GLU cc_start: 0.8441 (tp30) cc_final: 0.8022 (tp30)
REVERT: C  276 GLN cc_start: 0.8771 (pt0) cc_final: 0.8440 (tp-100)
  outliers start: 1
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0622
  time to fit residues: 14.2009
Evaluate side-chains
  137 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:   30.0000
   chunk 39 optimal weight:   20.0000
   chunk 46 optimal weight:    8.9990
   chunk 9 optimal weight:    6.9990
   chunk 64 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 27 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0370
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
C  56 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.190458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.144951 restraints weight = 9445.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.150008 restraints weight = 6116.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.153016 restraints weight = 4624.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.155539 restraints weight = 3901.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.156845 restraints weight = 3451.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5744  Z= 0.126
  Angle     :  0.618   9.247   7750  Z= 0.322
  Chirality :  0.043   0.162    884
  Planarity :  0.003   0.040    993
  Dihedral  :  4.701  24.706    757
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.33), residues: 693
  helix:  0.45 (0.29), residues: 335
  sheet: -2.24 (0.91), residues: 26
  loop : -1.46 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 131 
 TYR   0.032   0.002   TYR B 266 
 PHE   0.020   0.002   PHE A 215 
 TRP   0.020   0.002   TRP B 160 
 HIS   0.009   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 5744)
  covalent geometry    : angle       0.61759 ( 7750)
  hydrogen bonds       : bond        0.03277 (  233)
  hydrogen bonds       : angle       4.52550 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 LEU cc_start: 0.8193 (mp) cc_final: 0.7702 (mp)
REVERT: A  228 ASN cc_start: 0.7875 (t0) cc_final: 0.7634 (t0)
REVERT: B   15 ASP cc_start: 0.8062 (t70) cc_final: 0.7391 (t70)
REVERT: B   19 LYS cc_start: 0.8644 (mttt) cc_final: 0.8232 (mttt)
REVERT: B   42 MET cc_start: 0.9063 (mtt) cc_final: 0.8587 (mtt)
REVERT: B  305 TRP cc_start: 0.5818 (m-90) cc_final: 0.5207 (m-90)
REVERT: C   31 MET cc_start: 0.8835 (tpp) cc_final: 0.8370 (tpp)
REVERT: C  149 GLU cc_start: 0.8031 (mp0) cc_final: 0.7757 (mp0)
REVERT: C  209 GLU cc_start: 0.8422 (tp30) cc_final: 0.8021 (tp30)
REVERT: C  276 GLN cc_start: 0.8661 (pt0) cc_final: 0.8315 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.0673
  time to fit residues: 15.5071
Evaluate side-chains
  146 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 1 optimal weight:    8.9990
   chunk 63 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 61 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 28 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
C  56 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.188971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.140715 restraints weight = 9773.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.145871 restraints weight = 6459.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.149310 restraints weight = 4937.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151198 restraints weight = 4154.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.153083 restraints weight = 3733.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.3547

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5744  Z= 0.172
  Angle     :  0.680   9.170   7750  Z= 0.347
  Chirality :  0.044   0.141    884
  Planarity :  0.003   0.040    993
  Dihedral  :  4.840  24.077    757
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.24 %
    Favored  : 90.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.32), residues: 693
  helix:  0.28 (0.29), residues: 335
  sheet: -2.21 (0.91), residues: 26
  loop : -1.55 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 237 
 TYR   0.041   0.003   TYR B 266 
 PHE   0.016   0.002   PHE C 207 
 TRP   0.023   0.002   TRP B 160 
 HIS   0.008   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 5744)
  covalent geometry    : angle       0.67976 ( 7750)
  hydrogen bonds       : bond        0.03445 (  233)
  hydrogen bonds       : angle       4.66631 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  218 PHE cc_start: 0.6391 (t80) cc_final: 0.5981 (t80)
REVERT: A  226 LEU cc_start: 0.8271 (mp) cc_final: 0.7817 (mp)
REVERT: A  228 ASN cc_start: 0.8040 (t0) cc_final: 0.7803 (t0)
REVERT: B   15 ASP cc_start: 0.8086 (t70) cc_final: 0.7336 (t70)
REVERT: B   19 LYS cc_start: 0.8700 (mttt) cc_final: 0.8289 (mttt)
REVERT: B  305 TRP cc_start: 0.5586 (m-90) cc_final: 0.5034 (m-90)
REVERT: C   31 MET cc_start: 0.8886 (tpp) cc_final: 0.8360 (tpp)
REVERT: C  140 ILE cc_start: 0.8469 (pt) cc_final: 0.8265 (pt)
REVERT: C  181 TYR cc_start: 0.9051 (t80) cc_final: 0.8724 (t80)
REVERT: C  209 GLU cc_start: 0.8367 (tp30) cc_final: 0.8021 (tp30)
REVERT: C  276 GLN cc_start: 0.8713 (pt0) cc_final: 0.8498 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.0551
  time to fit residues: 12.3663
Evaluate side-chains
  140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 68 optimal weight:    0.0870
   chunk 53 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   chunk 24 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.1760

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
C  56 HIS
C 118 HIS
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.189187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144492 restraints weight = 9576.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.149804 restraints weight = 6070.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.153310 restraints weight = 4489.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.155373 restraints weight = 3702.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.157142 restraints weight = 3292.108|
|-----------------------------------------------------------------------------|
r_work (final): 0.3919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   5744  Z= 0.134
  Angle     :  0.658   9.459   7750  Z= 0.340
  Chirality :  0.043   0.145    884
  Planarity :  0.003   0.040    993
  Dihedral  :  4.750  24.327    757
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.51 %
    Favored  : 91.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.04 (0.32), residues: 693
  helix:  0.23 (0.29), residues: 336
  sheet: -2.13 (0.93), residues: 26
  loop : -1.53 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 131 
 TYR   0.029   0.002   TYR B 266 
 PHE   0.014   0.002   PHE C  69 
 TRP   0.023   0.002   TRP B 160 
 HIS   0.007   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5744)
  covalent geometry    : angle       0.65815 ( 7750)
  hydrogen bonds       : bond        0.03375 (  233)
  hydrogen bonds       : angle       4.66286 (  669)

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

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

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1386 Ramachandran restraints generated.
    693 Oldfield, 0 Emsley, 693 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  226 LEU cc_start: 0.8313 (mp) cc_final: 0.7810 (mp)
REVERT: A  228 ASN cc_start: 0.7983 (t0) cc_final: 0.7744 (t0)
REVERT: B   15 ASP cc_start: 0.8056 (t70) cc_final: 0.7349 (t70)
REVERT: B   19 LYS cc_start: 0.8646 (mttt) cc_final: 0.8258 (mttt)
REVERT: B   29 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8178 (tpp-160)
REVERT: B   34 GLU cc_start: 0.7596 (pm20) cc_final: 0.7290 (pm20)
REVERT: B   68 ILE cc_start: 0.9388 (mm) cc_final: 0.9064 (mm)
REVERT: B  305 TRP cc_start: 0.5673 (m-90) cc_final: 0.5136 (m-90)
REVERT: C   31 MET cc_start: 0.8863 (tpp) cc_final: 0.8398 (tpp)
REVERT: C   72 MET cc_start: 0.8317 (tpt) cc_final: 0.7978 (tpp)
REVERT: C  209 GLU cc_start: 0.8309 (tp30) cc_final: 0.7923 (tp30)
REVERT: C  276 GLN cc_start: 0.8670 (pt0) cc_final: 0.8453 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.0632
  time to fit residues: 14.4592
Evaluate side-chains
  140 residues out of total 633 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:   10.0000
   chunk 68 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 40 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 9 optimal weight:   10.0000
   chunk 37 optimal weight:   30.0000
   chunk 60 optimal weight:    0.0060
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 134 ASN
A 228 ASN
** B  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 GLN
** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 276 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.190423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.146830 restraints weight = 9197.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.151855 restraints weight = 5866.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154931 restraints weight = 4378.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.157559 restraints weight = 3655.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.158970 restraints weight = 3201.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.3650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   5744  Z= 0.139
  Angle     :  0.661   9.541   7750  Z= 0.336
  Chirality :  0.043   0.149    884
  Planarity :  0.003   0.041    993
  Dihedral  :  4.691  24.187    757
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.23 %
    Favored  : 91.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.32), residues: 693
  helix:  0.09 (0.28), residues: 341
  sheet: -2.07 (0.92), residues: 26
  loop : -1.55 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 131 
 TYR   0.023   0.002   TYR B 313 
 PHE   0.018   0.002   PHE A 215 
 TRP   0.022   0.002   TRP B 160 
 HIS   0.007   0.001   HIS C  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 5744)
  covalent geometry    : angle       0.66134 ( 7750)
  hydrogen bonds       : bond        0.03342 (  233)
  hydrogen bonds       : angle       4.56985 (  669)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1069.96 seconds
wall clock time: 19 minutes 13.17 seconds (1153.17 seconds total)