Starting phenix.real_space_refine
on Tue Feb 11 07:50:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7r0j_14223/02_2025/7r0j_14223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7r0j_14223/02_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_14223/02_2025/7r0j_14223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7r0j_14223/02_2025/7r0j_14223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7r0j_14223/02_2025/7r0j_14223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7r0j_14223/02_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-5592/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: 3.23, per 1000 atoms: 0.69
  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: 1.13
  Conformation dependent library (CDL) restraints added in 519.7 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: 0.66
  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: 1.37

  Time building geometry restraints manager: 1.31 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:             0.170
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.080
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.180
-------------------------------------------------------------------------------
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      :  0.008   0.115   4772  Z= 0.489
  Angle     :  1.034  14.169   6486  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 

*********************** 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  : 0.511 
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: 0.1725
  time to fit residues: 23.8945
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  : 0.833 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
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
C 281 ASN
** D   9 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 = 0.3556 r_free = 0.3556 target = 0.082128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.065223 restraints weight = 18988.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.067723 restraints weight = 11662.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.069489 restraints weight = 8299.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4772  Z= 0.216
  Angle     :  0.673   7.478   6486  Z= 0.341
  Chirality :  0.044   0.143    727
  Planarity :  0.005   0.039    825
  Dihedral  :  8.091  83.529    667
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 17.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  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: -0.74 (0.35), residues: 577
  helix: -0.94 (1.26), residues: 17
  sheet: -0.14 (0.33), residues: 250
  loop : -0.69 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.004   TRP D 229 
 HIS   0.006   0.001   HIS C 219 
 PHE   0.017   0.002   PHE D  86 
 TYR   0.013   0.002   TYR D  90 
 ARG   0.006   0.001   ARG C 312 

*********************** 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
  110 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.535 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9507 (t) cc_final: 0.9238 (t)
REVERT: C   63 TYR cc_start: 0.7013 (t80) cc_final: 0.6524 (t80)
REVERT: C  117 PHE cc_start: 0.8128 (m-80) cc_final: 0.7510 (m-80)
REVERT: C  272 TYR cc_start: 0.8506 (m-80) cc_final: 0.7761 (m-80)
REVERT: C  327 LEU cc_start: 0.9788 (mt) cc_final: 0.9580 (mt)
REVERT: C  350 THR cc_start: 0.9408 (p) cc_final: 0.9187 (t)
REVERT: C  352 MET cc_start: 0.8310 (ppp) cc_final: 0.7871 (ppp)
REVERT: D   64 ARG cc_start: 0.8835 (mmt180) cc_final: 0.8494 (mmm160)
REVERT: D  101 PHE cc_start: 0.9663 (m-80) cc_final: 0.9056 (m-80)
REVERT: D  146 LEU cc_start: 0.8796 (mt) cc_final: 0.8516 (mt)
REVERT: D  161 HIS cc_start: 0.9430 (m-70) cc_final: 0.9119 (m90)
REVERT: D  209 MET cc_start: 0.9342 (mpp) cc_final: 0.8924 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1602
  time to fit residues: 22.6306
Evaluate side-chains
  89 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 7 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   chunk 23 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   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 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D   9 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.080076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.063803 restraints weight = 19350.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.066156 restraints weight = 12056.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.067879 restraints weight = 8672.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8055
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4772  Z= 0.293
  Angle     :  0.695   8.162   6486  Z= 0.351
  Chirality :  0.043   0.137    727
  Planarity :  0.005   0.043    825
  Dihedral  :  8.114  84.023    667
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 22.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.76 %
    Favored  : 93.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  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: -0.73 (1.26), residues: 17
  sheet: -0.28 (0.32), residues: 249
  loop : -0.65 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP D 236 
 HIS   0.005   0.002   HIS C 198 
 PHE   0.027   0.003   PHE D 228 
 TYR   0.014   0.002   TYR D  90 
 ARG   0.005   0.001   ARG D 164 

*********************** 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  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9510 (t) cc_final: 0.9241 (t)
REVERT: C   63 TYR cc_start: 0.7264 (t80) cc_final: 0.7008 (t80)
REVERT: C  117 PHE cc_start: 0.8264 (m-80) cc_final: 0.7444 (m-80)
REVERT: C  272 TYR cc_start: 0.8476 (m-80) cc_final: 0.7769 (m-80)
REVERT: C  350 THR cc_start: 0.9402 (p) cc_final: 0.9151 (t)
REVERT: C  352 MET cc_start: 0.8728 (ppp) cc_final: 0.8487 (ppp)
REVERT: D   64 ARG cc_start: 0.8865 (mmt180) cc_final: 0.8653 (mmm160)
REVERT: D  101 PHE cc_start: 0.9637 (m-80) cc_final: 0.8830 (m-80)
REVERT: D  146 LEU cc_start: 0.8852 (mt) cc_final: 0.8472 (mt)
REVERT: D  209 MET cc_start: 0.9324 (mpp) cc_final: 0.8919 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1626
  time to fit residues: 21.9929
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  : 0.562 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 47 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0670
   chunk 1 optimal weight:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    2.6126

-------------------------------------------------------------------------------
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 198 HIS
C 219 HIS
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D   9 GLN ** 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 227 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.081934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.065800 restraints weight = 19540.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.068158 restraints weight = 12025.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.069874 restraints weight = 8588.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4772  Z= 0.230
  Angle     :  0.650   8.027   6486  Z= 0.329
  Chirality :  0.043   0.136    727
  Planarity :  0.005   0.051    825
  Dihedral  :  7.970  84.866    667
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 18.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  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: -0.54 (1.27), residues: 17
  sheet: -0.33 (0.33), residues: 240
  loop : -0.62 (0.36), residues: 320

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   0.011   0.002   TYR C  21 
 ARG   0.004   0.001   ARG D 164 

*********************** 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  : 0.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   37 VAL cc_start: 0.9500 (t) cc_final: 0.9293 (t)
REVERT: C   63 TYR cc_start: 0.7259 (t80) cc_final: 0.6861 (t80)
REVERT: C  117 PHE cc_start: 0.8339 (m-80) cc_final: 0.7562 (m-80)
REVERT: C  272 TYR cc_start: 0.8469 (m-80) cc_final: 0.7821 (m-80)
REVERT: C  350 THR cc_start: 0.9414 (p) cc_final: 0.9184 (t)
REVERT: D   64 ARG cc_start: 0.8831 (mmt180) cc_final: 0.8628 (mmm160)
REVERT: D   86 PHE cc_start: 0.8635 (m-10) cc_final: 0.8327 (m-80)
REVERT: D  101 PHE cc_start: 0.9621 (m-80) cc_final: 0.8732 (m-80)
REVERT: D  146 LEU cc_start: 0.8810 (mt) cc_final: 0.8423 (mt)
REVERT: D  161 HIS cc_start: 0.9479 (m-70) cc_final: 0.9047 (m90)
REVERT: D  209 MET cc_start: 0.9320 (mpp) cc_final: 0.8950 (mpp)
REVERT: D  216 ASP cc_start: 0.8688 (m-30) cc_final: 0.8474 (m-30)
REVERT: D  236 TRP cc_start: 0.8360 (m-10) cc_final: 0.8156 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1545
  time to fit residues: 22.1643
Evaluate side-chains
  89 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 13 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 54 optimal weight:    6.9990
   chunk 33 optimal weight:    9.9990
   chunk 3 optimal weight:    0.6980
   chunk 24 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   overall best weight:    2.0984

-------------------------------------------------------------------------------
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 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D   9 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.082263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.065748 restraints weight = 19973.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.068179 restraints weight = 12317.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.069906 restraints weight = 8784.146|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4772  Z= 0.209
  Angle     :  0.632   6.987   6486  Z= 0.318
  Chirality :  0.043   0.141    727
  Planarity :  0.004   0.051    825
  Dihedral  :  7.916  85.192    667
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  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: -0.70 (0.35), residues: 577
  helix: -0.44 (1.25), residues: 17
  sheet: -0.26 (0.32), residues: 247
  loop : -0.54 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.003   TRP D 229 
 HIS   0.004   0.001   HIS D 161 
 PHE   0.012   0.002   PHE D 228 
 TYR   0.010   0.002   TYR D 183 
 ARG   0.004   0.001   ARG C  65 

*********************** 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
  110 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7274 (t80) cc_final: 0.6904 (t80)
REVERT: C  117 PHE cc_start: 0.8282 (m-80) cc_final: 0.7641 (m-80)
REVERT: C  272 TYR cc_start: 0.8470 (m-80) cc_final: 0.7865 (m-80)
REVERT: C  290 ASP cc_start: 0.7094 (m-30) cc_final: 0.6836 (m-30)
REVERT: C  327 LEU cc_start: 0.9771 (mt) cc_final: 0.9538 (mt)
REVERT: C  350 THR cc_start: 0.9424 (p) cc_final: 0.9200 (t)
REVERT: D   64 ARG cc_start: 0.8800 (mmt180) cc_final: 0.8584 (mmm160)
REVERT: D   86 PHE cc_start: 0.8747 (m-10) cc_final: 0.8390 (m-80)
REVERT: D  101 PHE cc_start: 0.9591 (m-80) cc_final: 0.9105 (m-80)
REVERT: D  144 LEU cc_start: 0.9368 (tp) cc_final: 0.9145 (tp)
REVERT: D  146 LEU cc_start: 0.8769 (mt) cc_final: 0.8353 (mt)
REVERT: D  161 HIS cc_start: 0.9440 (m-70) cc_final: 0.8926 (m90)
REVERT: D  209 MET cc_start: 0.9371 (mpp) cc_final: 0.8838 (mpp)
REVERT: D  216 ASP cc_start: 0.8689 (m-30) cc_final: 0.8462 (m-30)
REVERT: D  236 TRP cc_start: 0.8597 (m-10) cc_final: 0.8375 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.1510
  time to fit residues: 21.6693
Evaluate side-chains
  85 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 10 optimal weight:    9.9990
   chunk 28 optimal weight:    0.0030
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 0 optimal weight:    9.9990
   chunk 46 optimal weight:    5.9990
   chunk 30 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.9998

-------------------------------------------------------------------------------
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 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 = 0.3563 r_free = 0.3563 target = 0.082754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.066367 restraints weight = 19183.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.068757 restraints weight = 11844.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.070456 restraints weight = 8451.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4772  Z= 0.197
  Angle     :  0.634   7.925   6486  Z= 0.319
  Chirality :  0.043   0.139    727
  Planarity :  0.005   0.053    825
  Dihedral  :  7.858  85.281    667
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 15.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  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 (0.35), residues: 577
  helix: -0.20 (1.27), residues: 17
  sheet: -0.28 (0.32), residues: 247
  loop : -0.48 (0.36), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP D 229 
 HIS   0.003   0.001   HIS C 198 
 PHE   0.010   0.002   PHE D 101 
 TYR   0.010   0.001   TYR D 230 
 ARG   0.003   0.000   ARG C  65 

*********************** 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
  108 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   63 TYR cc_start: 0.7269 (t80) cc_final: 0.6969 (t80)
REVERT: C  117 PHE cc_start: 0.8361 (m-80) cc_final: 0.7771 (m-80)
REVERT: C  272 TYR cc_start: 0.8480 (m-80) cc_final: 0.7860 (m-80)
REVERT: C  280 ASN cc_start: 0.9179 (p0) cc_final: 0.8931 (p0)
REVERT: C  350 THR cc_start: 0.9434 (p) cc_final: 0.9215 (t)
REVERT: D   64 ARG cc_start: 0.8839 (mmt180) cc_final: 0.8626 (mmm160)
REVERT: D   86 PHE cc_start: 0.8814 (m-10) cc_final: 0.8465 (m-80)
REVERT: D  101 PHE cc_start: 0.9563 (m-80) cc_final: 0.9026 (m-80)
REVERT: D  144 LEU cc_start: 0.9238 (tp) cc_final: 0.9001 (tp)
REVERT: D  146 LEU cc_start: 0.8752 (mt) cc_final: 0.8360 (mt)
REVERT: D  161 HIS cc_start: 0.9477 (m-70) cc_final: 0.8970 (m90)
REVERT: D  209 MET cc_start: 0.9208 (mpp) cc_final: 0.8733 (mpp)
REVERT: D  216 ASP cc_start: 0.8661 (m-30) cc_final: 0.8444 (m-30)
REVERT: D  229 TRP cc_start: 0.8343 (m100) cc_final: 0.7787 (m100)
REVERT: D  236 TRP cc_start: 0.8003 (m-10) cc_final: 0.7791 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1646
  time to fit residues: 22.9066
Evaluate side-chains
  89 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 6 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    6.9990
   chunk 51 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 44 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
C 111 HIS
** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 181 GLN
** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D  92 GLN ** 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 = 0.3461 r_free = 0.3461 target = 0.076628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.060401 restraints weight = 20168.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.062621 restraints weight = 12599.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.064198 restraints weight = 9079.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   4772  Z= 0.407
  Angle     :  0.791   8.709   6486  Z= 0.403
  Chirality :  0.045   0.201    727
  Planarity :  0.005   0.049    825
  Dihedral  :  8.380  82.956    667
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 26.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  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: -0.90 (0.35), residues: 577
  helix: -0.66 (1.20), residues: 17
  sheet: -0.39 (0.32), residues: 242
  loop : -0.68 (0.36), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.004   TRP D 236 
 HIS   0.005   0.001   HIS C 111 
 PHE   0.021   0.003   PHE D  74 
 TYR   0.019   0.003   TYR D 183 
 ARG   0.004   0.001   ARG D 224 

*********************** 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
  95 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: C  272 TYR cc_start: 0.8524 (m-80) cc_final: 0.7899 (m-80)
REVERT: C  327 LEU cc_start: 0.9786 (mt) cc_final: 0.9544 (mt)
REVERT: D   86 PHE cc_start: 0.9001 (m-10) cc_final: 0.8604 (m-80)
REVERT: D  101 PHE cc_start: 0.9571 (m-80) cc_final: 0.8982 (m-80)
REVERT: D  146 LEU cc_start: 0.8772 (mt) cc_final: 0.8529 (mt)
REVERT: D  209 MET cc_start: 0.9287 (mpp) cc_final: 0.8821 (mpp)
REVERT: D  229 TRP cc_start: 0.8140 (m100) cc_final: 0.7691 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1419
  time to fit residues: 17.8571
Evaluate side-chains
  68 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.547 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 24 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 49 optimal weight:    6.9990
   chunk 14 optimal weight:    8.9990
   chunk 40 optimal weight:    0.2980
   chunk 13 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    2.8586

-------------------------------------------------------------------------------
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 198 HIS
C 311 ASN
** D  92 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 = 0.3517 r_free = 0.3517 target = 0.079813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.063465 restraints weight = 19885.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.065733 restraints weight = 12333.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.067382 restraints weight = 8864.120|
|-----------------------------------------------------------------------------|
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4772  Z= 0.239
  Angle     :  0.674   7.847   6486  Z= 0.339
  Chirality :  0.043   0.145    727
  Planarity :  0.005   0.054    825
  Dihedral  :  8.161  85.398    667
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  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: -0.79 (0.35), residues: 577
  helix: -0.80 (1.16), residues: 18
  sheet: -0.31 (0.32), residues: 251
  loop : -0.60 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP D  38 
 HIS   0.002   0.001   HIS D 161 
 PHE   0.020   0.002   PHE D  74 
 TYR   0.012   0.002   TYR C 173 
 ARG   0.003   0.000   ARG C 363 

*********************** 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
  102 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8330 (m-80) cc_final: 0.7787 (m-80)
REVERT: C  272 TYR cc_start: 0.8567 (m-80) cc_final: 0.7937 (m-80)
REVERT: C  327 LEU cc_start: 0.9792 (mt) cc_final: 0.9573 (mt)
REVERT: C  350 THR cc_start: 0.9432 (p) cc_final: 0.9206 (t)
REVERT: D   74 PHE cc_start: 0.8574 (m-10) cc_final: 0.8016 (m-80)
REVERT: D   86 PHE cc_start: 0.9028 (m-10) cc_final: 0.8731 (m-80)
REVERT: D  101 PHE cc_start: 0.9545 (m-80) cc_final: 0.8966 (m-80)
REVERT: D  146 LEU cc_start: 0.8704 (mt) cc_final: 0.8390 (mt)
REVERT: D  156 TYR cc_start: 0.8532 (m-10) cc_final: 0.8173 (m-10)
REVERT: D  209 MET cc_start: 0.9279 (mpp) cc_final: 0.8947 (mpp)
REVERT: D  229 TRP cc_start: 0.7959 (m100) cc_final: 0.7717 (m100)
REVERT: D  236 TRP cc_start: 0.8424 (m-10) cc_final: 0.7997 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1488
  time to fit residues: 20.0198
Evaluate side-chains
  76 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 11 optimal weight:    7.9990
   chunk 40 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 14 optimal weight:    6.9990
   chunk 42 optimal weight:    7.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.3986

-------------------------------------------------------------------------------
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 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 = 0.3538 r_free = 0.3538 target = 0.081253 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.064424 restraints weight = 19298.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.066887 restraints weight = 11875.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.068595 restraints weight = 8441.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4772  Z= 0.230
  Angle     :  0.672   7.709   6486  Z= 0.337
  Chirality :  0.044   0.145    727
  Planarity :  0.005   0.052    825
  Dihedral  :  8.103  85.617    667
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 18.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  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: -0.88 (0.35), residues: 577
  helix: -1.37 (0.98), residues: 24
  sheet: -0.20 (0.33), residues: 235
  loop : -0.76 (0.35), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.004   TRP D 236 
 HIS   0.002   0.001   HIS D 161 
 PHE   0.024   0.002   PHE C  87 
 TYR   0.021   0.002   TYR D 183 
 ARG   0.005   0.001   ARG D 224 

*********************** 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
  96 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8231 (m-80) cc_final: 0.7847 (m-80)
REVERT: C  272 TYR cc_start: 0.8600 (m-80) cc_final: 0.7941 (m-80)
REVERT: C  280 ASN cc_start: 0.9252 (p0) cc_final: 0.9040 (p0)
REVERT: D   74 PHE cc_start: 0.8547 (m-10) cc_final: 0.7974 (m-80)
REVERT: D   86 PHE cc_start: 0.9031 (m-10) cc_final: 0.8737 (m-80)
REVERT: D  101 PHE cc_start: 0.9534 (m-80) cc_final: 0.8932 (m-80)
REVERT: D  146 LEU cc_start: 0.8744 (mt) cc_final: 0.8438 (mt)
REVERT: D  209 MET cc_start: 0.9277 (mpp) cc_final: 0.8961 (mpp)
REVERT: D  229 TRP cc_start: 0.7843 (m100) cc_final: 0.7639 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1487
  time to fit residues: 18.7730
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  : 0.561 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
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 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** C 353 HIS ** 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 = 0.3566 r_free = 0.3566 target = 0.082705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.066747 restraints weight = 18988.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.068988 restraints weight = 11879.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.070614 restraints weight = 8557.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4772  Z= 0.202
  Angle     :  0.659   7.401   6486  Z= 0.328
  Chirality :  0.044   0.142    727
  Planarity :  0.005   0.052    825
  Dihedral  :  8.006  86.351    667
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 16.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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: -0.55 (0.35), residues: 577
  helix: -0.42 (1.26), residues: 18
  sheet: -0.05 (0.33), residues: 245
  loop : -0.54 (0.36), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.004   TRP D  38 
 HIS   0.003   0.001   HIS C 210 
 PHE   0.018   0.002   PHE D  74 
 TYR   0.011   0.001   TYR C  63 
 ARG   0.005   0.001   ARG D 224 

********************** 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
  104 residues out of total 512 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  117 PHE cc_start: 0.8029 (m-80) cc_final: 0.7762 (m-80)
REVERT: C  272 TYR cc_start: 0.8515 (m-80) cc_final: 0.7891 (m-80)
REVERT: C  280 ASN cc_start: 0.9219 (p0) cc_final: 0.8971 (p0)
REVERT: C  350 THR cc_start: 0.9434 (p) cc_final: 0.9224 (t)
REVERT: D   74 PHE cc_start: 0.8561 (m-10) cc_final: 0.7951 (m-80)
REVERT: D   86 PHE cc_start: 0.9029 (m-10) cc_final: 0.8749 (m-80)
REVERT: D  101 PHE cc_start: 0.9544 (m-80) cc_final: 0.8915 (m-80)
REVERT: D  146 LEU cc_start: 0.8703 (mt) cc_final: 0.8345 (mt)
REVERT: D  206 TYR cc_start: 0.7706 (m-80) cc_final: 0.7457 (m-80)
REVERT: D  209 MET cc_start: 0.9204 (mpp) cc_final: 0.8881 (mpp)
REVERT: D  226 ARG cc_start: 0.7928 (mmp-170) cc_final: 0.7725 (mmp-170)
REVERT: D  229 TRP cc_start: 0.7816 (m100) cc_final: 0.7495 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1505
  time to fit residues: 20.5368
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  : 0.555 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 8 optimal weight:    0.2980
   chunk 12 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 35 optimal weight:    6.9990
   chunk 55 optimal weight:    5.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    1.8384

-------------------------------------------------------------------------------
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 198 HIS
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 311 ASN
** D 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 238 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.082712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.066446 restraints weight = 18847.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.068824 restraints weight = 11535.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.070314 restraints weight = 8191.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4772  Z= 0.204
  Angle     :  0.665   7.201   6486  Z= 0.332
  Chirality :  0.043   0.159    727
  Planarity :  0.005   0.052    825
  Dihedral  :  7.937  85.708    667
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  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: -0.56 (0.35), residues: 577
  helix: -0.11 (1.37), residues: 18
  sheet:  0.01 (0.34), residues: 233
  loop : -0.62 (0.35), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP D 236 
 HIS   0.005   0.001   HIS C 295 
 PHE   0.024   0.002   PHE D 228 
 TYR   0.014   0.001   TYR D 183 
 ARG   0.003   0.000   ARG D 164 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1546.92 seconds
wall clock time: 28 minutes 32.64 seconds (1712.64 seconds total)