Starting phenix.real_space_refine
on Thu Jun  5 01:18:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0j_14223/06_2025/7r0j_14223.cif"
  }
  resolution = 4.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.019 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      19      5.16       5
     C    2947      2.51       5
     N     793      2.21       5
     O     904      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4669
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 104
          Classifications: {'peptide': 13}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'TRANS': 12}
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'TPO:plan-1': 2}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 354, 2815
          Classifications: {'peptide': 354}
          Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 325}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1750
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 229, 1750
          Classifications: {'peptide': 229}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 220}
          Chain breaks: 1
  Time building chain proxies: 3.00, per 1000 atoms: 0.64
  Number of scatterers: 4669
  At special positions: 0
  Unit cell: (87.04, 99.84, 88.32, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P       6     15.00
     O     904      8.00
     N     793      7.00
     C    2947      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  26 " - pdb=" SG  CYS D  91 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 103 " - pdb=" SG  CYS D 170 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 148 " - pdb=" SG  CYS D 222 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.25
  Conformation dependent library (CDL) restraints added in 543.2 milliseconds
  

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1122

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 10 sheets defined
      4.4% alpha, 42.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.58
  Creating SS restraints...
    Processing helix  chain 'C' and resid 98 through 109
    Processing helix  chain 'C' and resid 278 through 282
    Processing helix  chain 'D' and resid 188 through 191
    Processing helix  chain 'D' and resid 213 through 217
    Processing sheet with id=AA1, first strand: chain 'A' and resid 361 through 364
    Processing sheet with id=AA2, first strand: chain 'C' and resid 76 through 87
      removed outlier: 6.573A  pdb=" N   CYS C  59 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL C  81 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN C  83 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL C  55 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL C  53 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLY C 141 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 87
      removed outlier: 6.573A  pdb=" N   CYS C  59 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   VAL C  81 " --> pdb=" O   LEU C  57 " (cutoff:3.500A)
      removed outlier: 7.085A  pdb=" N   LEU C  57 " --> pdb=" O   VAL C  81 " (cutoff:3.500A)
      removed outlier: 4.515A  pdb=" N   ASN C  83 " --> pdb=" O   VAL C  55 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   VAL C  55 " --> pdb=" O   ASN C  83 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   GLN C  85 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   VAL C  53 " --> pdb=" O   GLN C  85 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   GLY C 141 " --> pdb=" O   ARG C  62 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 183 through 188
    Processing sheet with id=AA5, first strand: chain 'C' and resid 250 through 258
      removed outlier: 3.625A  pdb=" N   CYS C 251 " --> pdb=" O   GLN C 237 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   VAL C 235 " --> pdb=" O   VAL C 253 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   MET C 255 " --> pdb=" O   ILE C 233 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ILE C 233 " --> pdb=" O   MET C 255 " (cutoff:3.500A)
      removed outlier: 4.864A  pdb=" N   GLU C 257 " --> pdb=" O   ILE C 231 " (cutoff:3.500A)
      removed outlier: 6.998A  pdb=" N   ILE C 231 " --> pdb=" O   GLU C 257 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LYS C 230 " --> pdb=" O   VAL C 328 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 321 " --> pdb=" O   PHE C 349 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 7 through 9
    Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 15
      removed outlier: 5.764A  pdb=" N   GLN D  40 " --> pdb=" O   LEU D  49 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   LEU D  49 " --> pdb=" O   GLN D  40 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 13 through 15
    Processing sheet with id=AA9, first strand: chain 'D' and resid 129 through 133
    Processing sheet with id=AB1, first strand: chain 'D' and resid 136 through 138
      removed outlier: 5.925A  pdb=" N   ARG D 164 " --> pdb=" O   TRP D 173 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   TRP D 173 " --> pdb=" O   ARG D 164 " (cutoff:3.500A)

    180 hydrogen bonds defined for protein.
    462 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: 1.31

  Time building geometry restraints manager: 1.44 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: 1499
        1.34 -     1.46: 1124
        1.46 -     1.58: 2103
        1.58 -     1.70: 22
        1.70 -     1.82: 24
  Bond restraints: 4772
  Sorted by residual:
  bond pdb=" OG1 TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.717  1.602  0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" OG1 TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.717  1.616  0.101 2.00e-02 2.50e+03 2.54e+01
  bond pdb=" C   ASN C 122 "
       pdb=" N   LEU C 123 "
    ideal  model  delta    sigma   weight residual
    1.331  1.257  0.075 1.59e-02 3.96e+03 2.21e+01
  bond pdb=" O1P TPO A 359 "
       pdb=" P   TPO A 359 "
    ideal  model  delta    sigma   weight residual
    1.525  1.609 -0.084 2.00e-02 2.50e+03 1.76e+01
  bond pdb=" O1P TPO A 360 "
       pdb=" P   TPO A 360 "
    ideal  model  delta    sigma   weight residual
    1.525  1.608 -0.083 2.00e-02 2.50e+03 1.72e+01
  ... (remaining 4767 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 6327
        2.83 -     5.67: 138
        5.67 -     8.50: 18
        8.50 -    11.34: 1
       11.34 -    14.17: 2
  Bond angle restraints: 6486
  Sorted by residual:
  angle pdb=" C   GLN D  41 "
        pdb=" N   LYS D  42 "
        pdb=" CA  LYS D  42 "
      ideal   model   delta    sigma   weight residual
     121.80  134.13  -12.33 2.44e+00 1.68e-01 2.55e+01
  angle pdb=" CB  TPO A 360 "
        pdb=" OG1 TPO A 360 "
        pdb=" P   TPO A 360 "
      ideal   model   delta    sigma   weight residual
     119.31  105.14   14.17 3.00e+00 1.11e-01 2.23e+01
  angle pdb=" N   GLY C 141 "
        pdb=" CA  GLY C 141 "
        pdb=" C   GLY C 141 "
      ideal   model   delta    sigma   weight residual
     110.74  117.04   -6.30 1.37e+00 5.33e-01 2.11e+01
  angle pdb=" N   LYS C  49 "
        pdb=" CA  LYS C  49 "
        pdb=" C   LYS C  49 "
      ideal   model   delta    sigma   weight residual
     114.31  108.80    5.51 1.29e+00 6.01e-01 1.82e+01
  angle pdb=" N   ASP C 259 "
        pdb=" CA  ASP C 259 "
        pdb=" C   ASP C 259 "
      ideal   model   delta    sigma   weight residual
     112.97  109.15    3.82 1.06e+00 8.90e-01 1.30e+01
  ... (remaining 6481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.88: 2650
       17.88 -    35.77: 205
       35.77 -    53.65: 30
       53.65 -    71.53: 5
       71.53 -    89.41: 6
  Dihedral angle restraints: 2896
    sinusoidal: 1152
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" CB  CYS D  26 "
           pdb=" SG  CYS D  26 "
           pdb=" SG  CYS D  91 "
           pdb=" CB  CYS D  91 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   49.57   43.43     1      1.00e+01 1.00e-02 2.63e+01
  dihedral pdb=" CA  ARG D 226 "
           pdb=" C   ARG D 226 "
           pdb=" N   GLN D 227 "
           pdb=" CA  GLN D 227 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.12  -21.88     0      5.00e+00 4.00e-02 1.91e+01
  dihedral pdb=" CA  LYS C  17 "
           pdb=" C   LYS C  17 "
           pdb=" N   LEU C  18 "
           pdb=" CA  LEU C  18 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.30  -21.70     0      5.00e+00 4.00e-02 1.88e+01
  ... (remaining 2893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 433
       0.035 -    0.069: 180
       0.069 -    0.103: 86
       0.103 -    0.138: 23
       0.138 -    0.172: 5
  Chirality restraints: 727
  Sorted by residual:
  chirality pdb=" CG  LEU D  76 "
            pdb=" CB  LEU D  76 "
            pdb=" CD1 LEU D  76 "
            pdb=" CD2 LEU D  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.41e-01
  chirality pdb=" CA  VAL C  81 "
            pdb=" N   VAL C  81 "
            pdb=" C   VAL C  81 "
            pdb=" CB  VAL C  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.65e-01
  chirality pdb=" CA  VAL C 220 "
            pdb=" N   VAL C 220 "
            pdb=" C   VAL C 220 "
            pdb=" CB  VAL C 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 724 not shown)

  Planarity restraints: 825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 236 "   -0.011 2.00e-02 2.50e+03   1.62e-02 6.56e+00
        pdb=" CG  TRP D 236 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 236 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 236 "    0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 236 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 236 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 236 "   -0.010 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 236 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 229 "    0.010 2.00e-02 2.50e+03   1.39e-02 4.86e+00
        pdb=" CG  TRP D 229 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 229 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 229 "   -0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 229 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 229 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 229 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 229 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 229 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 195 "   -0.030 5.00e-02 4.00e+02   4.56e-02 3.33e+00
        pdb=" N   PRO C 196 "    0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 196 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO C 196 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 822 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 123
        2.60 -     3.18: 4591
        3.18 -     3.75: 7627
        3.75 -     4.33: 10265
        4.33 -     4.90: 15822
  Nonbonded interactions: 38428
  Sorted by model distance:
  nonbonded pdb=" O   ASP D  85 "
            pdb=" OH  TYR D  89 "
     model   vdw
     2.029 3.040
  nonbonded pdb=" NE2 GLN D  92 "
            pdb=" O   GLN D  93 "
     model   vdw
     2.186 3.120
  nonbonded pdb=" N   GLN C 130 "
            pdb=" O   LEU C 287 "
     model   vdw
     2.188 3.120
  nonbonded pdb=" O   ALA C 263 "
            pdb=" OG  SER C 266 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" O   SER D 178 "
            pdb=" N   GLY D 182 "
     model   vdw
     2.193 3.120
  ... (remaining 38423 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:             0.210
  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:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.860
  Find NCS groups from input model:        0.040
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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      :  0.015   0.848   4776  Z= 1.288
  Angle     :  1.035  14.169   6492  Z= 0.554
  Chirality :  0.048   0.172    727
  Planarity :  0.006   0.055    825
  Dihedral  : 13.438  89.415   1765
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 37.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.84 %
    Favored  : 91.16 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.00 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.99 (0.35), residues: 577
  helix: -1.30 (1.09), residues: 17
  sheet: -0.35 (0.34), residues: 245
  loop : -0.80 (0.36), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.006   TRP D 236 
 HIS   0.007   0.002   HIS C 111 
 PHE   0.023   0.003   PHE D 228 
 TYR   0.027   0.003   TYR D  90 
 ARG   0.011   0.001   ARG C 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15981 (  164)
  hydrogen bonds       : angle       9.31468 (  462)
  SS BOND              : bond        0.00298 (    3)
  SS BOND              : angle       1.40336 (    6)
  covalent geometry    : bond        0.00781 ( 4772)
  covalent geometry    : angle       1.03410 ( 6486)
  Misc. bond           : bond        0.84753 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.505 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   28 VAL cc_start: 0.8876 (t) cc_final: 0.8454 (t)
REVERT: C   34 VAL cc_start: 0.8547 (t) cc_final: 0.8173 (t)
REVERT: C   63 TYR cc_start: 0.7302 (t80) cc_final: 0.7023 (t80)
REVERT: C   69 ASP cc_start: 0.8904 (m-30) cc_final: 0.8660 (m-30)
REVERT: C  166 LEU cc_start: 0.9118 (tt) cc_final: 0.8798 (mt)
REVERT: C  255 MET cc_start: 0.7974 (tpt) cc_final: 0.7742 (tpt)
REVERT: C  272 TYR cc_start: 0.8115 (m-80) cc_final: 0.7478 (m-80)
REVERT: D   64 ARG cc_start: 0.8462 (mmt180) cc_final: 0.8195 (mmm160)
REVERT: D  101 PHE cc_start: 0.9469 (m-80) cc_final: 0.8723 (m-80)
REVERT: D  209 MET cc_start: 0.9112 (mpp) cc_final: 0.8326 (mpp)
  outliers start: 1
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2094
  time to fit residues: 29.3605
Evaluate side-chains
  84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 43 optimal weight:    0.7980
   chunk 24 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    5.9990
   chunk 33 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 222 ASN
C 281 ASN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.081230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.064492 restraints weight = 19282.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.066968 restraints weight = 11867.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.068719 restraints weight = 8455.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8032
moved from start:          0.1852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4776  Z= 0.166
  Angle     :  0.681   7.495   6492  Z= 0.345
  Chirality :  0.044   0.151    727
  Planarity :  0.005   0.037    825
  Dihedral  :  8.100  83.459    667
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.35), residues: 577
  helix: -0.87 (1.27), residues: 17
  sheet: -0.23 (0.33), residues: 250
  loop : -0.70 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D 229 
 HIS   0.004   0.001   HIS C 210 
 PHE   0.015   0.002   PHE D  86 
 TYR   0.014   0.002   TYR D  90 
 ARG   0.005   0.001   ARG C 312 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04076 (  164)
  hydrogen bonds       : angle       7.17188 (  462)
  SS BOND              : bond        0.00377 (    3)
  SS BOND              : angle       1.52921 (    6)
  covalent geometry    : bond        0.00354 ( 4772)
  covalent geometry    : angle       0.67951 ( 6486)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9505 (t) cc_final: 0.9229 (t)
REVERT: C   63 TYR cc_start: 0.7057 (t80) cc_final: 0.6811 (t80)
REVERT: C  117 PHE cc_start: 0.8068 (m-80) cc_final: 0.7410 (m-80)
REVERT: C  272 TYR cc_start: 0.8473 (m-80) cc_final: 0.7709 (m-80)
REVERT: C  280 ASN cc_start: 0.9173 (p0) cc_final: 0.8962 (p0)
REVERT: C  327 LEU cc_start: 0.9774 (mt) cc_final: 0.9547 (mt)
REVERT: C  350 THR cc_start: 0.9412 (p) cc_final: 0.9185 (t)
REVERT: C  352 MET cc_start: 0.8496 (ppp) cc_final: 0.8041 (ppp)
REVERT: D   64 ARG cc_start: 0.8828 (mmt180) cc_final: 0.8471 (mmm160)
REVERT: D  101 PHE cc_start: 0.9660 (m-80) cc_final: 0.8961 (m-80)
REVERT: D  146 LEU cc_start: 0.8756 (mt) cc_final: 0.8502 (mt)
REVERT: D  209 MET cc_start: 0.9354 (mpp) cc_final: 0.8931 (mpp)
REVERT: D  229 TRP cc_start: 0.8274 (m100) cc_final: 0.8036 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1737
  time to fit residues: 24.2300
Evaluate side-chains
  84 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 7 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 53 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 46 optimal weight:    4.9990
   chunk 16 optimal weight:    9.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 HIS
D 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.079562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.063438 restraints weight = 19396.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.065793 restraints weight = 12080.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.067472 restraints weight = 8645.754|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4776  Z= 0.211
  Angle     :  0.685   8.014   6492  Z= 0.349
  Chirality :  0.043   0.135    727
  Planarity :  0.005   0.042    825
  Dihedral  :  8.133  84.367    667
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 21.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.35), residues: 577
  helix: -0.81 (1.26), residues: 17
  sheet: -0.33 (0.32), residues: 249
  loop : -0.70 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.003   TRP D 236 
 HIS   0.005   0.001   HIS C 353 
 PHE   0.026   0.003   PHE D 228 
 TYR   0.012   0.002   TYR C 113 
 ARG   0.005   0.001   ARG D 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04355 (  164)
  hydrogen bonds       : angle       7.12678 (  462)
  SS BOND              : bond        0.00368 (    3)
  SS BOND              : angle       1.25828 (    6)
  covalent geometry    : bond        0.00435 ( 4772)
  covalent geometry    : angle       0.68452 ( 6486)
  Misc. bond           : bond        0.00023 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9504 (t) cc_final: 0.9249 (t)
REVERT: C   63 TYR cc_start: 0.7253 (t80) cc_final: 0.6900 (t80)
REVERT: C  117 PHE cc_start: 0.8254 (m-80) cc_final: 0.7435 (m-80)
REVERT: C  272 TYR cc_start: 0.8469 (m-80) cc_final: 0.7762 (m-80)
REVERT: C  350 THR cc_start: 0.9398 (p) cc_final: 0.9151 (t)
REVERT: C  352 MET cc_start: 0.8752 (ppp) cc_final: 0.8461 (ppp)
REVERT: D   64 ARG cc_start: 0.8843 (mmt180) cc_final: 0.8638 (mmm160)
REVERT: D  101 PHE cc_start: 0.9613 (m-80) cc_final: 0.8807 (m-80)
REVERT: D  146 LEU cc_start: 0.8839 (mt) cc_final: 0.8453 (mt)
REVERT: D  209 MET cc_start: 0.9317 (mpp) cc_final: 0.8915 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1699
  time to fit residues: 22.9032
Evaluate side-chains
  81 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 47 optimal weight:   20.0000
   chunk 8 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0870
   chunk 1 optimal weight:    9.9990
   chunk 44 optimal weight:    6.9990
   chunk 15 optimal weight:    0.7980
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.9764

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
C 219 HIS
C 311 ASN
D   9 GLN
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.082514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.066361 restraints weight = 19233.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.068771 restraints weight = 11834.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.070451 restraints weight = 8419.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7999
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4776  Z= 0.141
  Angle     :  0.632   7.812   6492  Z= 0.318
  Chirality :  0.043   0.133    727
  Planarity :  0.005   0.051    825
  Dihedral  :  7.883  85.774    667
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.35), residues: 577
  helix: -0.89 (1.22), residues: 17
  sheet: -0.21 (0.33), residues: 243
  loop : -0.70 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP D 236 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.013   0.002   PHE D  86 
 TYR   0.013   0.002   TYR D 183 
 ARG   0.004   0.001   ARG D 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03890 (  164)
  hydrogen bonds       : angle       6.57905 (  462)
  SS BOND              : bond        0.00503 (    3)
  SS BOND              : angle       1.26761 (    6)
  covalent geometry    : bond        0.00304 ( 4772)
  covalent geometry    : angle       0.63150 ( 6486)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.468 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8386 (m-80) cc_final: 0.7655 (m-80)
REVERT: C  272 TYR cc_start: 0.8494 (m-80) cc_final: 0.7873 (m-80)
REVERT: C  327 LEU cc_start: 0.9771 (mt) cc_final: 0.9570 (mt)
REVERT: C  350 THR cc_start: 0.9424 (p) cc_final: 0.9200 (t)
REVERT: D   64 ARG cc_start: 0.8816 (mmt180) cc_final: 0.8610 (mmm160)
REVERT: D   86 PHE cc_start: 0.8659 (m-10) cc_final: 0.8321 (m-80)
REVERT: D  101 PHE cc_start: 0.9604 (m-80) cc_final: 0.8659 (m-80)
REVERT: D  146 LEU cc_start: 0.8796 (mt) cc_final: 0.8377 (mt)
REVERT: D  161 HIS cc_start: 0.9542 (m90) cc_final: 0.9283 (m-70)
REVERT: D  209 MET cc_start: 0.9343 (mpp) cc_final: 0.8787 (mpp)
REVERT: D  216 ASP cc_start: 0.8679 (m-30) cc_final: 0.8451 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1625
  time to fit residues: 23.4252
Evaluate side-chains
  87 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 27 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 52 optimal weight:    5.9990
   chunk 21 optimal weight:    2.9990
   chunk 54 optimal weight:    8.9990
   chunk 33 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.079086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.063367 restraints weight = 20484.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.065680 restraints weight = 12576.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.067371 restraints weight = 8978.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4776  Z= 0.214
  Angle     :  0.675   6.772   6492  Z= 0.342
  Chirality :  0.043   0.139    727
  Planarity :  0.005   0.050    825
  Dihedral  :  8.009  84.210    667
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 19.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.41 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.35), residues: 577
  helix: -0.43 (1.26), residues: 17
  sheet: -0.20 (0.33), residues: 239
  loop : -0.67 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D 236 
 HIS   0.004   0.001   HIS C 353 
 PHE   0.019   0.002   PHE D  74 
 TYR   0.014   0.002   TYR D 186 
 ARG   0.004   0.001   ARG D 164 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04123 (  164)
  hydrogen bonds       : angle       6.89683 (  462)
  SS BOND              : bond        0.00245 (    3)
  SS BOND              : angle       1.01210 (    6)
  covalent geometry    : bond        0.00444 ( 4772)
  covalent geometry    : angle       0.67476 ( 6486)
  Misc. bond           : bond        0.00031 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9502 (t) cc_final: 0.9295 (t)
REVERT: C   69 ASP cc_start: 0.8525 (m-30) cc_final: 0.8298 (m-30)
REVERT: C  117 PHE cc_start: 0.8276 (m-80) cc_final: 0.7521 (m-80)
REVERT: C  272 TYR cc_start: 0.8470 (m-80) cc_final: 0.7840 (m-80)
REVERT: C  350 THR cc_start: 0.9437 (p) cc_final: 0.9209 (t)
REVERT: C  352 MET cc_start: 0.8295 (ppp) cc_final: 0.8051 (ppp)
REVERT: D   64 ARG cc_start: 0.8839 (mmt180) cc_final: 0.8636 (mmm160)
REVERT: D  101 PHE cc_start: 0.9599 (m-80) cc_final: 0.9095 (m-80)
REVERT: D  144 LEU cc_start: 0.9429 (tp) cc_final: 0.9174 (tp)
REVERT: D  146 LEU cc_start: 0.8744 (mt) cc_final: 0.8390 (mt)
REVERT: D  162 TRP cc_start: 0.7999 (m100) cc_final: 0.7680 (m100)
REVERT: D  209 MET cc_start: 0.9339 (mpp) cc_final: 0.8690 (mpp)
REVERT: D  229 TRP cc_start: 0.8010 (m100) cc_final: 0.7571 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1457
  time to fit residues: 19.7495
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:   20.0000
   chunk 12 optimal weight:    0.2980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:   10.0000
   chunk 46 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.082577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.066238 restraints weight = 19052.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.068664 restraints weight = 11690.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.070384 restraints weight = 8299.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   4776  Z= 0.129
  Angle     :  0.629   7.385   6492  Z= 0.315
  Chirality :  0.043   0.137    727
  Planarity :  0.005   0.050    825
  Dihedral  :  7.909  86.027    667
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.35), residues: 577
  helix: -0.62 (1.24), residues: 17
  sheet: -0.21 (0.33), residues: 239
  loop : -0.53 (0.36), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.003   TRP D 236 
 HIS   0.002   0.001   HIS D 161 
 PHE   0.017   0.002   PHE D 228 
 TYR   0.009   0.001   TYR D  52 
 ARG   0.006   0.001   ARG D 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03622 (  164)
  hydrogen bonds       : angle       6.39734 (  462)
  SS BOND              : bond        0.00338 (    3)
  SS BOND              : angle       1.17839 (    6)
  covalent geometry    : bond        0.00278 ( 4772)
  covalent geometry    : angle       0.62820 ( 6486)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8297 (m-80) cc_final: 0.7663 (m-80)
REVERT: C  272 TYR cc_start: 0.8606 (m-80) cc_final: 0.7939 (m-80)
REVERT: C  350 THR cc_start: 0.9438 (p) cc_final: 0.9214 (t)
REVERT: D   74 PHE cc_start: 0.8133 (m-80) cc_final: 0.7907 (m-80)
REVERT: D  101 PHE cc_start: 0.9552 (m-80) cc_final: 0.9034 (m-80)
REVERT: D  146 LEU cc_start: 0.8753 (mt) cc_final: 0.8425 (mt)
REVERT: D  162 TRP cc_start: 0.7908 (m100) cc_final: 0.7699 (m100)
REVERT: D  209 MET cc_start: 0.9127 (mpp) cc_final: 0.8761 (mpp)
REVERT: D  216 ASP cc_start: 0.8632 (m-30) cc_final: 0.8405 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1635
  time to fit residues: 22.6253
Evaluate side-chains
  90 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 51 optimal weight:   10.0000
   chunk 56 optimal weight:   10.0000
   chunk 55 optimal weight:    7.9990
   chunk 32 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 HIS
** D 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.077165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.061319 restraints weight = 20686.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.063578 restraints weight = 12822.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.065159 restraints weight = 9218.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.034   4776  Z= 0.270
  Angle     :  0.753   8.500   6492  Z= 0.381
  Chirality :  0.045   0.188    727
  Planarity :  0.005   0.044    825
  Dihedral  :  8.205  83.262    667
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 24.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.35), residues: 577
  helix: -0.76 (1.21), residues: 17
  sheet: -0.39 (0.32), residues: 244
  loop : -0.65 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.005   TRP D 236 
 HIS   0.006   0.001   HIS C 362 
 PHE   0.019   0.003   PHE D  74 
 TYR   0.019   0.002   TYR D 183 
 ARG   0.005   0.001   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04498 (  164)
  hydrogen bonds       : angle       7.18471 (  462)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.97439 (    6)
  covalent geometry    : bond        0.00555 ( 4772)
  covalent geometry    : angle       0.75293 ( 6486)
  Misc. bond           : bond        0.00047 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   21 TYR cc_start: 0.8851 (m-10) cc_final: 0.8650 (m-10)
REVERT: C  272 TYR cc_start: 0.8530 (m-80) cc_final: 0.7905 (m-80)
REVERT: D   86 PHE cc_start: 0.9051 (m-10) cc_final: 0.8780 (m-80)
REVERT: D  101 PHE cc_start: 0.9583 (m-80) cc_final: 0.9030 (m-80)
REVERT: D  146 LEU cc_start: 0.8716 (mt) cc_final: 0.8464 (mt)
REVERT: D  209 MET cc_start: 0.9199 (mpp) cc_final: 0.8817 (mpp)
REVERT: D  216 ASP cc_start: 0.8732 (m-30) cc_final: 0.8532 (m-30)
REVERT: D  229 TRP cc_start: 0.8581 (m100) cc_final: 0.7910 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1632
  time to fit residues: 21.0706
Evaluate side-chains
  73 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.508 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    9.9990
   chunk 24 optimal weight:    0.0040
   chunk 5 optimal weight:    0.0970
   chunk 49 optimal weight:    8.9990
   chunk 14 optimal weight:    6.9990
   chunk 40 optimal weight:    0.2980
   chunk 13 optimal weight:    0.7980
   chunk 45 optimal weight:    5.9990
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 10 optimal weight:    9.9990
   overall best weight:    1.0392

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
C 311 ASN
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.083307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.066777 restraints weight = 18892.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.069256 restraints weight = 11607.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.071005 restraints weight = 8241.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4776  Z= 0.120
  Angle     :  0.656   7.708   6492  Z= 0.326
  Chirality :  0.044   0.137    727
  Planarity :  0.005   0.044    825
  Dihedral  :  7.927  86.627    667
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.35), residues: 577
  helix: -0.73 (1.21), residues: 18
  sheet: -0.26 (0.33), residues: 250
  loop : -0.55 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.004   TRP D  38 
 HIS   0.002   0.001   HIS C 210 
 PHE   0.016   0.002   PHE D 228 
 TYR   0.014   0.001   TYR D 156 
 ARG   0.004   0.000   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03570 (  164)
  hydrogen bonds       : angle       6.31531 (  462)
  SS BOND              : bond        0.00538 (    3)
  SS BOND              : angle       1.39942 (    6)
  covalent geometry    : bond        0.00262 ( 4772)
  covalent geometry    : angle       0.65539 ( 6486)
  Misc. bond           : bond        0.00005 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7087 (t80) cc_final: 0.6882 (t80)
REVERT: C   69 ASP cc_start: 0.8582 (m-30) cc_final: 0.8380 (m-30)
REVERT: C  117 PHE cc_start: 0.8095 (m-80) cc_final: 0.7782 (m-80)
REVERT: C  272 TYR cc_start: 0.8582 (m-80) cc_final: 0.7922 (m-80)
REVERT: C  350 THR cc_start: 0.9415 (p) cc_final: 0.9214 (t)
REVERT: D   74 PHE cc_start: 0.8109 (m-80) cc_final: 0.7901 (m-80)
REVERT: D   86 PHE cc_start: 0.9024 (m-10) cc_final: 0.8727 (m-80)
REVERT: D  101 PHE cc_start: 0.9524 (m-80) cc_final: 0.9017 (m-80)
REVERT: D  146 LEU cc_start: 0.8744 (mt) cc_final: 0.8376 (mt)
REVERT: D  161 HIS cc_start: 0.9526 (m90) cc_final: 0.9306 (m-70)
REVERT: D  209 MET cc_start: 0.9109 (mpp) cc_final: 0.8737 (mpp)
REVERT: D  216 ASP cc_start: 0.8720 (m-30) cc_final: 0.8387 (m-30)
REVERT: D  226 ARG cc_start: 0.8277 (tmt170) cc_final: 0.7985 (tpt-90)
REVERT: D  229 TRP cc_start: 0.8339 (m100) cc_final: 0.7956 (m100)
REVERT: D  236 TRP cc_start: 0.8210 (m-10) cc_final: 0.7951 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1487
  time to fit residues: 20.7279
Evaluate side-chains
  83 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 40 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 29 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    9.9990
   chunk 42 optimal weight:   30.0000
   chunk 20 optimal weight:    6.9990
   chunk 33 optimal weight:    6.9990
   overall best weight:    4.1588

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
C 311 ASN
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 227 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.078090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.062508 restraints weight = 19773.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.064869 restraints weight = 12007.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.066529 restraints weight = 8414.743|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.3205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   4776  Z= 0.222
  Angle     :  0.706   7.258   6492  Z= 0.356
  Chirality :  0.043   0.140    727
  Planarity :  0.005   0.042    825
  Dihedral  :  8.029  83.827    667
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 21.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.35), residues: 577
  helix: -0.46 (1.27), residues: 17
  sheet: -0.33 (0.33), residues: 248
  loop : -0.57 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.005   TRP D 229 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.021   0.002   PHE D  74 
 TYR   0.016   0.002   TYR D  39 
 ARG   0.004   0.001   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04256 (  164)
  hydrogen bonds       : angle       6.82307 (  462)
  SS BOND              : bond        0.00665 (    3)
  SS BOND              : angle       1.76365 (    6)
  covalent geometry    : bond        0.00471 ( 4772)
  covalent geometry    : angle       0.70394 ( 6486)
  Misc. bond           : bond        0.00020 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8321 (m-80) cc_final: 0.8018 (m-80)
REVERT: C  272 TYR cc_start: 0.8564 (m-80) cc_final: 0.7942 (m-80)
REVERT: C  350 THR cc_start: 0.9436 (p) cc_final: 0.9225 (t)
REVERT: D   86 PHE cc_start: 0.9105 (m-10) cc_final: 0.8817 (m-80)
REVERT: D  101 PHE cc_start: 0.9632 (m-80) cc_final: 0.9004 (m-80)
REVERT: D  146 LEU cc_start: 0.8749 (mt) cc_final: 0.8456 (mt)
REVERT: D  162 TRP cc_start: 0.7940 (m100) cc_final: 0.7730 (m100)
REVERT: D  209 MET cc_start: 0.9158 (mpp) cc_final: 0.8883 (mpp)
REVERT: D  216 ASP cc_start: 0.8731 (m-30) cc_final: 0.8506 (m-30)
REVERT: D  229 TRP cc_start: 0.8199 (m100) cc_final: 0.7871 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1617
  time to fit residues: 20.3107
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 5 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 12 optimal weight:    0.0870
   chunk 2 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0870
   chunk 39 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   overall best weight:    1.6342

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

Flipped N/Q/H residues before XYZ refinement:
C 198 HIS
C 311 ASN
** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.081646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.065365 restraints weight = 19494.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.067721 restraints weight = 12124.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.069398 restraints weight = 8701.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4776  Z= 0.133
  Angle     :  0.666   7.749   6492  Z= 0.334
  Chirality :  0.043   0.135    727
  Planarity :  0.004   0.042    825
  Dihedral  :  7.911  85.890    667
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.36), residues: 577
  helix: -0.55 (1.25), residues: 18
  sheet: -0.28 (0.33), residues: 247
  loop : -0.46 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D  38 
 HIS   0.002   0.000   HIS C 210 
 PHE   0.012   0.002   PHE D 101 
 TYR   0.010   0.001   TYR D 156 
 ARG   0.004   0.000   ARG C  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03726 (  164)
  hydrogen bonds       : angle       6.32624 (  462)
  SS BOND              : bond        0.00497 (    3)
  SS BOND              : angle       1.76063 (    6)
  covalent geometry    : bond        0.00297 ( 4772)
  covalent geometry    : angle       0.66451 ( 6486)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1154 Ramachandran restraints generated.
    577 Oldfield, 0 Emsley, 577 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8178 (m-80) cc_final: 0.7804 (m-80)
REVERT: C  272 TYR cc_start: 0.8553 (m-80) cc_final: 0.7939 (m-80)
REVERT: C  327 LEU cc_start: 0.9777 (mt) cc_final: 0.9536 (mp)
REVERT: D   74 PHE cc_start: 0.8214 (m-80) cc_final: 0.7743 (m-80)
REVERT: D   86 PHE cc_start: 0.9087 (m-10) cc_final: 0.8739 (m-80)
REVERT: D  101 PHE cc_start: 0.9602 (m-80) cc_final: 0.8995 (m-80)
REVERT: D  146 LEU cc_start: 0.8743 (mt) cc_final: 0.8413 (mt)
REVERT: D  161 HIS cc_start: 0.9524 (m90) cc_final: 0.9195 (m-70)
REVERT: D  209 MET cc_start: 0.9096 (mpp) cc_final: 0.8828 (mpp)
REVERT: D  216 ASP cc_start: 0.8776 (m-30) cc_final: 0.8429 (m-30)
REVERT: D  229 TRP cc_start: 0.8025 (m100) cc_final: 0.7814 (m100)
REVERT: D  236 TRP cc_start: 0.8379 (m-10) cc_final: 0.8098 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1468
  time to fit residues: 19.1263
Evaluate side-chains
  78 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 12 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 GLN
C 198 HIS
C 311 ASN
** D  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 161 HIS
** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 238 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.077101 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.061120 restraints weight = 20450.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.063395 restraints weight = 12640.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.065100 restraints weight = 9050.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.3267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4776  Z= 0.254
  Angle     :  0.752   8.818   6492  Z= 0.381
  Chirality :  0.045   0.156    727
  Planarity :  0.005   0.041    825
  Dihedral  :  8.178  83.148    667
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 25.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.35), residues: 577
  helix: -0.72 (1.21), residues: 17
  sheet: -0.42 (0.33), residues: 247
  loop : -0.50 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.006   TRP D  38 
 HIS   0.004   0.001   HIS C 198 
 PHE   0.015   0.002   PHE D  74 
 TYR   0.014   0.002   TYR C 173 
 ARG   0.004   0.001   ARG C 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  164)
  hydrogen bonds       : angle       6.94635 (  462)
  SS BOND              : bond        0.00120 (    3)
  SS BOND              : angle       1.45800 (    6)
  covalent geometry    : bond        0.00531 ( 4772)
  covalent geometry    : angle       0.75056 ( 6486)
  Misc. bond           : bond        0.00033 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1724.08 seconds
wall clock time: 31 minutes 1.22 seconds (1861.22 seconds total)