Starting phenix.real_space_refine
on Mon Apr 28 21:14:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6b3o_7040/04_2025/6b3o_7040.cif"
  }
  resolution = 4.1
  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=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5040      2.51       5
     N    1335      2.21       5
     O    1569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 7980
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 344, 2660
          Classifications: {'peptide': 344}
          Link IDs: {'PTRANS': 13, 'TRANS': 330}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B
  Time building chain proxies: 4.81, per 1000 atoms: 0.60
  Number of scatterers: 7980
  At special positions: 0
  Unit cell: (70.72, 74.8, 202.64, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1569      8.00
     N    1335      7.00
     C    5040      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 775 " - pdb=" SG  CYS A 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 780 " - pdb=" SG  CYS A 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1082 " - pdb=" SG  CYS A1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A1132 " - pdb=" SG  CYS A1177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 775 " - pdb=" SG  CYS C 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 775 " - pdb=" SG  CYS B 797 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 780 " - pdb=" SG  CYS C 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 780 " - pdb=" SG  CYS B 786 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1082 " - pdb=" SG  CYS C1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1093 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C1132 " - pdb=" SG  CYS C1177 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1132 " - pdb=" SG  CYS B1177 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.15
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1956

  Finding SS restraints...
    Secondary structure from input PDB file:
      21 helices and 9 sheets defined
      48.0% alpha, 18.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 774 through 780
    Processing helix  chain 'A' and resid 783 through 791
    Processing helix  chain 'A' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN A 799 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 973 through 1081
    Processing helix  chain 'A' and resid 1198 through 1204
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1231 through 1245
    Processing helix  chain 'B' and resid 774 through 780
    Processing helix  chain 'B' and resid 783 through 791
    Processing helix  chain 'B' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN B 799 " --> pdb=" O   SER B 795 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 973 through 1081
    Processing helix  chain 'B' and resid 1198 through 1204
    Processing helix  chain 'B' and resid 1220 through 1224
    Processing helix  chain 'B' and resid 1231 through 1245
    Processing helix  chain 'C' and resid 774 through 780
    Processing helix  chain 'C' and resid 783 through 791
    Processing helix  chain 'C' and resid 795 through 807
      removed outlier: 4.265A  pdb=" N   ASN C 799 " --> pdb=" O   SER C 795 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 973 through 1081
    Processing helix  chain 'C' and resid 1198 through 1204
    Processing helix  chain 'C' and resid 1220 through 1224
    Processing helix  chain 'C' and resid 1231 through 1245
    Processing sheet with id=AA1, first strand: chain 'A' and resid 1097 through 1106
      removed outlier: 5.491A  pdb=" N   HIS A1098 " --> pdb=" O   TYR A1117 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR A1117 " --> pdb=" O   HIS A1098 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN A 754 " --> pdb=" O   ILE A1120 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   PHE A1122 " --> pdb=" O   PRO A 752 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR A1124 " --> pdb=" O   GLN A 750 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   GLN A 750 " --> pdb=" O   THR A1124 " (cutoff:3.500A)
      removed outlier: 9.300A  pdb=" N   ASN C1180 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   ILE A 757 " --> pdb=" O   ASN C1180 " (cutoff:3.500A)
      removed outlier: 8.197A  pdb=" N   THR C1182 " --> pdb=" O   ILE A 757 " (cutoff:3.500A)
      removed outlier: 5.919A  pdb=" N   HIS A 759 " --> pdb=" O   THR C1182 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1131 through 1132
      removed outlier: 4.238A  pdb=" N   GLY A1138 " --> pdb=" O   MET A1174 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1144 through 1149
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1180 through 1183
      removed outlier: 7.107A  pdb=" N   GLN B 750 " --> pdb=" O   THR B1124 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR B1124 " --> pdb=" O   GLN B 750 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   PHE B1122 " --> pdb=" O   PRO B 752 " (cutoff:3.500A)
      removed outlier: 6.612A  pdb=" N   ASN B 754 " --> pdb=" O   ILE B1120 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR B1117 " --> pdb=" O   HIS B1098 " (cutoff:3.500A)
      removed outlier: 5.491A  pdb=" N   HIS B1098 " --> pdb=" O   TYR B1117 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1131 through 1132
      removed outlier: 4.237A  pdb=" N   GLY B1138 " --> pdb=" O   MET B1174 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1144 through 1149
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1180 through 1183
      removed outlier: 7.107A  pdb=" N   GLN C 750 " --> pdb=" O   THR C1124 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   THR C1124 " --> pdb=" O   GLN C 750 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   PHE C1122 " --> pdb=" O   PRO C 752 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ASN C 754 " --> pdb=" O   ILE C1120 " (cutoff:3.500A)
      removed outlier: 6.359A  pdb=" N   TYR C1117 " --> pdb=" O   HIS C1098 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   HIS C1098 " --> pdb=" O   TYR C1117 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1131 through 1132
      removed outlier: 4.238A  pdb=" N   GLY C1138 " --> pdb=" O   MET C1174 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 1144 through 1149

    515 hydrogen bonds defined for protein.
    1485 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: 2.80

  Time building geometry restraints manager: 2.53 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1541
        1.31 -     1.43: 2005
        1.43 -     1.56: 4488
        1.56 -     1.68: 42
        1.68 -     1.81: 48
  Bond restraints: 8124
  Sorted by residual:
  bond pdb=" CB  HIS A 759 "
       pdb=" CG  HIS A 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.11e+01
  bond pdb=" CB  HIS C 759 "
       pdb=" CG  HIS C 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.10e+01
  bond pdb=" CB  HIS B 759 "
       pdb=" CG  HIS B 759 "
    ideal  model  delta    sigma   weight residual
    1.497  1.397  0.100 1.40e-02 5.10e+03 5.09e+01
  bond pdb=" CB  PHE C 796 "
       pdb=" CG  PHE C 796 "
    ideal  model  delta    sigma   weight residual
    1.502  1.356  0.146 2.30e-02 1.89e+03 4.05e+01
  bond pdb=" CB  PHE B 796 "
       pdb=" CG  PHE B 796 "
    ideal  model  delta    sigma   weight residual
    1.502  1.356  0.146 2.30e-02 1.89e+03 4.04e+01
  ... (remaining 8119 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 9484
        2.58 -     5.16: 1374
        5.16 -     7.73: 149
        7.73 -    10.31: 24
       10.31 -    12.89: 3
  Bond angle restraints: 11034
  Sorted by residual:
  angle pdb=" N   TYR B1161 "
        pdb=" CA  TYR B1161 "
        pdb=" C   TYR B1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.68  -12.89 1.53e+00 4.27e-01 7.10e+01
  angle pdb=" N   TYR A1161 "
        pdb=" CA  TYR A1161 "
        pdb=" C   TYR A1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.66  -12.87 1.53e+00 4.27e-01 7.08e+01
  angle pdb=" N   TYR C1161 "
        pdb=" CA  TYR C1161 "
        pdb=" C   TYR C1161 "
      ideal   model   delta    sigma   weight residual
     108.79  121.62  -12.83 1.53e+00 4.27e-01 7.03e+01
  angle pdb=" N   ILE C1120 "
        pdb=" CA  ILE C1120 "
        pdb=" C   ILE C1120 "
      ideal   model   delta    sigma   weight residual
     113.53  106.94    6.59 9.80e-01 1.04e+00 4.52e+01
  angle pdb=" N   ILE B1120 "
        pdb=" CA  ILE B1120 "
        pdb=" C   ILE B1120 "
      ideal   model   delta    sigma   weight residual
     113.53  106.95    6.58 9.80e-01 1.04e+00 4.50e+01
  ... (remaining 11029 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 4710
       15.46 -    30.91: 144
       30.91 -    46.37: 27
       46.37 -    61.82: 36
       61.82 -    77.28: 18
  Dihedral angle restraints: 4935
    sinusoidal: 1917
      harmonic: 3018
  Sorted by residual:
  dihedral pdb=" CB  CYS C 775 "
           pdb=" SG  CYS C 775 "
           pdb=" SG  CYS C 797 "
           pdb=" CB  CYS C 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.77  -65.77     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" CB  CYS A 775 "
           pdb=" SG  CYS A 775 "
           pdb=" SG  CYS A 797 "
           pdb=" CB  CYS A 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.74  -65.74     1      1.00e+01 1.00e-02 5.66e+01
  dihedral pdb=" CB  CYS B 775 "
           pdb=" SG  CYS B 775 "
           pdb=" SG  CYS B 797 "
           pdb=" CB  CYS B 797 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  158.72  -65.72     1      1.00e+01 1.00e-02 5.65e+01
  ... (remaining 4932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.074: 704
       0.074 -    0.149: 364
       0.149 -    0.223: 156
       0.223 -    0.297: 39
       0.297 -    0.372: 9
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CA  GLU A1081 "
            pdb=" N   GLU A1081 "
            pdb=" C   GLU A1081 "
            pdb=" CB  GLU A1081 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  LYS B1078 "
            pdb=" N   LYS B1078 "
            pdb=" C   LYS B1078 "
            pdb=" CB  LYS B1078 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  chirality pdb=" CA  GLU B1081 "
            pdb=" N   GLU B1081 "
            pdb=" C   GLU B1081 "
            pdb=" CB  GLU B1081 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.14    0.37 2.00e-01 2.50e+01 3.45e+00
  ... (remaining 1269 not shown)

  Planarity restraints: 1446
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1155 "   -0.045 2.00e-02 2.50e+03   2.72e-02 1.29e+01
        pdb=" CG  PHE A1155 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1155 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1155 "    0.022 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1155 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1155 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1155 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C1155 "    0.045 2.00e-02 2.50e+03   2.70e-02 1.28e+01
        pdb=" CG  PHE C1155 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE C1155 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE C1155 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE C1155 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE C1155 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE C1155 "    0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B1155 "    0.045 2.00e-02 2.50e+03   2.70e-02 1.27e+01
        pdb=" CG  PHE B1155 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B1155 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD2 PHE B1155 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE B1155 "    0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE B1155 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B1155 "    0.026 2.00e-02 2.50e+03
  ... (remaining 1443 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 2608
        2.81 -     3.33: 8103
        3.33 -     3.85: 13493
        3.85 -     4.38: 15988
        4.38 -     4.90: 25029
  Nonbonded interactions: 65221
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A1066 "
            pdb=" OG  SER C1063 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER A1063 "
            pdb=" OG1 THR B1066 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OG  SER B1063 "
            pdb=" OG1 THR C1066 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" N   LYS B1154 "
            pdb=" O   LYS B1154 "
     model   vdw
     2.396 2.496
  nonbonded pdb=" N   LYS C1154 "
            pdb=" O   LYS C1154 "
     model   vdw
     2.396 2.496
  ... (remaining 65216 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
}

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:             4.330
  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:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.660
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  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:3.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.140
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
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      :  0.024   0.146   8136  Z= 1.356
  Angle     :  1.832  12.890  11058  Z= 1.252
  Chirality :  0.105   0.372   1272
  Planarity :  0.008   0.033   1446
  Dihedral  : 10.994  77.281   2943
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 2.28
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.06 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  0.34 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.14 (0.24), residues: 1020
  helix:  1.69 (0.21), residues: 474
  sheet:  1.16 (0.42), residues: 129
  loop : -0.44 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.013   TRP A1153 
 HIS   0.014   0.005   HIS B1098 
 PHE   0.045   0.007   PHE A1155 
 TYR   0.032   0.007   TYR B1181 
 ARG   0.008   0.001   ARG C1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16260 (  515)
  hydrogen bonds       : angle       7.74577 ( 1485)
  SS BOND              : bond        0.00681 (   12)
  SS BOND              : angle       4.70133 (   24)
  covalent geometry    : bond        0.02430 ( 8124)
  covalent geometry    : angle       1.82053 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  223 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 220
  time to evaluate  : 0.923 
Fit side-chains
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.9093 (p) cc_final: 0.8833 (t)
REVERT: A  792 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7355 (mt-10)
REVERT: A 1153 TRP cc_start: 0.7685 (m100) cc_final: 0.6965 (m100)
REVERT: A 1198 ASP cc_start: 0.7796 (t70) cc_final: 0.7427 (m-30)
REVERT: B  787 ARG cc_start: 0.5704 (tpp-160) cc_final: 0.5480 (tpt170)
REVERT: B 1089 ARG cc_start: 0.8327 (mtp180) cc_final: 0.7619 (mmm-85)
REVERT: B 1153 TRP cc_start: 0.7550 (m100) cc_final: 0.7103 (m100)
REVERT: B 1223 LYS cc_start: 0.7551 (mmtt) cc_final: 0.7281 (mmmt)
REVERT: B 1235 MET cc_start: 0.7751 (mtp) cc_final: 0.7247 (tpp)
REVERT: B 1237 ARG cc_start: 0.6565 (mtp180) cc_final: 0.6324 (mmp80)
REVERT: C 1188 PHE cc_start: 0.7023 (t80) cc_final: 0.6290 (t80)
REVERT: C 1220 ASP cc_start: 0.6912 (t0) cc_final: 0.6697 (t0)
REVERT: C 1235 MET cc_start: 0.7888 (mtp) cc_final: 0.6985 (tpp)
  outliers start: 3
  outliers final: 0
  residues processed: 223
  average time/residue: 0.2333
  time to fit residues: 68.0860
Evaluate side-chains
  88 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.161061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.155033 restraints weight = 9487.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.140467 restraints weight = 13648.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.140582 restraints weight = 12170.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7357
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8136  Z= 0.204
  Angle     :  0.745   8.029  11058  Z= 0.402
  Chirality :  0.044   0.189   1272
  Planarity :  0.005   0.038   1446
  Dihedral  :  5.224  23.261   1089
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.16 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.93 (0.25), residues: 1020
  helix:  3.30 (0.21), residues: 471
  sheet:  0.38 (0.42), residues: 132
  loop : -0.88 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C1153 
 HIS   0.004   0.002   HIS B 760 
 PHE   0.016   0.002   PHE C 796 
 TYR   0.015   0.002   TYR C1117 
 ARG   0.005   0.001   ARG B1033 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06791 (  515)
  hydrogen bonds       : angle       5.16819 ( 1485)
  SS BOND              : bond        0.00668 (   12)
  SS BOND              : angle       1.87936 (   24)
  covalent geometry    : bond        0.00463 ( 8124)
  covalent geometry    : angle       0.74036 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8886 (p) cc_final: 0.8432 (t)
REVERT: A  767 ARG cc_start: 0.7405 (ptt-90) cc_final: 0.6356 (ptm160)
REVERT: A 1069 LYS cc_start: 0.8379 (mttp) cc_final: 0.8164 (mttm)
REVERT: A 1084 LYS cc_start: 0.8355 (mttt) cc_final: 0.8062 (mttt)
REVERT: A 1153 TRP cc_start: 0.7289 (m100) cc_final: 0.6468 (m100)
REVERT: A 1198 ASP cc_start: 0.6543 (t70) cc_final: 0.6334 (m-30)
REVERT: A 1225 ASN cc_start: 0.7519 (m-40) cc_final: 0.6415 (p0)
REVERT: B  992 ASN cc_start: 0.7281 (t0) cc_final: 0.6760 (m110)
REVERT: B 1084 LYS cc_start: 0.8076 (mttt) cc_final: 0.7686 (mttt)
REVERT: B 1153 TRP cc_start: 0.6731 (m100) cc_final: 0.6273 (m100)
REVERT: B 1237 ARG cc_start: 0.6985 (mtp180) cc_final: 0.6552 (mmp80)
REVERT: C 1092 PHE cc_start: 0.8684 (t80) cc_final: 0.8434 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.2209
  time to fit residues: 45.0854
Evaluate side-chains
  102 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 6 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0970
   chunk 5 optimal weight:    0.9980
   chunk 15 optimal weight:    0.1980
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A1055 ASN
B1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.159367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.153675 restraints weight = 9838.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140296 restraints weight = 14857.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140322 restraints weight = 12419.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8136  Z= 0.184
  Angle     :  0.659   8.072  11058  Z= 0.352
  Chirality :  0.042   0.157   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.035  24.210   1089
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.65 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.61 (0.25), residues: 1020
  helix:  3.18 (0.21), residues: 471
  sheet:  0.09 (0.35), residues: 159
  loop : -1.27 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1153 
 HIS   0.004   0.001   HIS C1114 
 PHE   0.016   0.002   PHE C1207 
 TYR   0.017   0.002   TYR C1233 
 ARG   0.003   0.001   ARG B 787 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06228 (  515)
  hydrogen bonds       : angle       4.77872 ( 1485)
  SS BOND              : bond        0.00740 (   12)
  SS BOND              : angle       2.15649 (   24)
  covalent geometry    : bond        0.00416 ( 8124)
  covalent geometry    : angle       0.65166 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.897 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  766 THR cc_start: 0.8738 (p) cc_final: 0.8276 (t)
REVERT: A  767 ARG cc_start: 0.7350 (ptt-90) cc_final: 0.6691 (ptm160)
REVERT: A 1084 LYS cc_start: 0.8359 (mttt) cc_final: 0.8155 (mttt)
REVERT: A 1153 TRP cc_start: 0.7229 (m100) cc_final: 0.6488 (m100)
REVERT: A 1233 TYR cc_start: 0.6972 (t80) cc_final: 0.6757 (t80)
REVERT: A 1240 ASP cc_start: 0.7552 (t0) cc_final: 0.7141 (t0)
REVERT: B 1084 LYS cc_start: 0.8039 (mttt) cc_final: 0.7563 (mttt)
REVERT: B 1153 TRP cc_start: 0.7081 (m100) cc_final: 0.6737 (m100)
REVERT: B 1237 ARG cc_start: 0.6841 (mtp180) cc_final: 0.6303 (mmp80)
REVERT: C 1153 TRP cc_start: 0.6985 (m100) cc_final: 0.6544 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.2006
  time to fit residues: 36.5792
Evaluate side-chains
  89 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 101 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 750 GLN
A1055 ASN
** A1170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 788 GLN
** C1170 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.150689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145110 restraints weight = 10247.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.142534 restraints weight = 15947.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141307 restraints weight = 19010.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.072   8136  Z= 0.277
  Angle     :  0.802   8.227  11058  Z= 0.427
  Chirality :  0.046   0.155   1272
  Planarity :  0.005   0.038   1446
  Dihedral  :  5.779  27.891   1089
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.24 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  :  3.84 %
    Favored  : 95.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.25), residues: 1020
  helix:  2.56 (0.21), residues: 480
  sheet: -0.40 (0.36), residues: 138
  loop : -1.62 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C1153 
 HIS   0.008   0.002   HIS A1114 
 PHE   0.030   0.003   PHE B1188 
 TYR   0.025   0.003   TYR C1181 
 ARG   0.004   0.001   ARG C1089 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06705 (  515)
  hydrogen bonds       : angle       5.05393 ( 1485)
  SS BOND              : bond        0.00842 (   12)
  SS BOND              : angle       2.17977 (   24)
  covalent geometry    : bond        0.00661 ( 8124)
  covalent geometry    : angle       0.79690 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7806 (ptt-90) cc_final: 0.7069 (ptm160)
REVERT: A  788 GLN cc_start: 0.7577 (mm-40) cc_final: 0.7374 (mm-40)
REVERT: A 1153 TRP cc_start: 0.7288 (m100) cc_final: 0.6607 (m100)
REVERT: B  791 VAL cc_start: 0.7623 (t) cc_final: 0.7385 (t)
REVERT: B 1084 LYS cc_start: 0.8184 (mttt) cc_final: 0.7776 (mttt)
REVERT: B 1153 TRP cc_start: 0.7057 (m100) cc_final: 0.6827 (m100)
REVERT: C 1029 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8543 (tm-30)
REVERT: C 1153 TRP cc_start: 0.6873 (m100) cc_final: 0.6167 (m100)
REVERT: C 1240 ASP cc_start: 0.6474 (t0) cc_final: 0.6230 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 123
  average time/residue: 0.2184
  time to fit residues: 36.8017
Evaluate side-chains
  83 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0770
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 5 optimal weight:    0.1980
   overall best weight:    0.4538

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

Flipped N/Q/H residues before XYZ refinement:
A1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.163692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.158369 restraints weight = 9969.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.145515 restraints weight = 13327.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.145218 restraints weight = 15624.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.5222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8136  Z= 0.153
  Angle     :  0.600   7.929  11058  Z= 0.321
  Chirality :  0.040   0.138   1272
  Planarity :  0.004   0.035   1446
  Dihedral  :  5.159  25.386   1089
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.84 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.25 (0.26), residues: 1020
  helix:  3.00 (0.22), residues: 474
  sheet: -0.28 (0.36), residues: 153
  loop : -1.56 (0.29), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C1206 
 HIS   0.005   0.002   HIS B 759 
 PHE   0.019   0.002   PHE A1188 
 TYR   0.012   0.002   TYR C1162 
 ARG   0.003   0.001   ARG B1050 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05977 (  515)
  hydrogen bonds       : angle       4.56536 ( 1485)
  SS BOND              : bond        0.00444 (   12)
  SS BOND              : angle       1.84905 (   24)
  covalent geometry    : bond        0.00335 ( 8124)
  covalent geometry    : angle       0.59446 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.861 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7105 (mm-40)
REVERT: A 1029 GLU cc_start: 0.8787 (tm-30) cc_final: 0.8514 (tm-30)
REVERT: A 1153 TRP cc_start: 0.7459 (m100) cc_final: 0.6545 (m100)
REVERT: A 1237 ARG cc_start: 0.7133 (mmp80) cc_final: 0.6749 (mmp80)
REVERT: B  791 VAL cc_start: 0.7904 (t) cc_final: 0.7655 (t)
REVERT: B 1077 GLU cc_start: 0.7025 (tt0) cc_final: 0.6732 (tt0)
REVERT: B 1084 LYS cc_start: 0.7852 (mttt) cc_final: 0.7562 (mttt)
REVERT: B 1240 ASP cc_start: 0.7481 (t0) cc_final: 0.7073 (t0)
REVERT: C 1153 TRP cc_start: 0.7138 (m100) cc_final: 0.6240 (m100)
REVERT: C 1234 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7240 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2029
  time to fit residues: 34.1361
Evaluate side-chains
  85 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 17 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C1055 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.164343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.163353 restraints weight = 9909.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 83)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.151106 restraints weight = 14104.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.150781 restraints weight = 16002.692|
|-----------------------------------------------------------------------------|
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.5480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8136  Z= 0.168
  Angle     :  0.619   7.947  11058  Z= 0.327
  Chirality :  0.040   0.141   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.027  24.201   1089
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.14 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.32 (0.26), residues: 1020
  helix:  2.98 (0.22), residues: 474
  sheet:  0.06 (0.38), residues: 138
  loop : -1.50 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1206 
 HIS   0.004   0.002   HIS C1114 
 PHE   0.015   0.002   PHE B1188 
 TYR   0.012   0.002   TYR A1181 
 ARG   0.003   0.001   ARG C1237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05967 (  515)
  hydrogen bonds       : angle       4.53336 ( 1485)
  SS BOND              : bond        0.00344 (   12)
  SS BOND              : angle       1.95737 (   24)
  covalent geometry    : bond        0.00385 ( 8124)
  covalent geometry    : angle       0.61323 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7593 (ptt-90) cc_final: 0.6950 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7288 (m100) cc_final: 0.6438 (m100)
REVERT: A 1237 ARG cc_start: 0.7063 (mmp80) cc_final: 0.6610 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7438 (tt0) cc_final: 0.6876 (tt0)
REVERT: B 1084 LYS cc_start: 0.7926 (mttt) cc_final: 0.7611 (mttt)
REVERT: C 1092 PHE cc_start: 0.8491 (t80) cc_final: 0.8054 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1951
  time to fit residues: 33.4987
Evaluate side-chains
  89 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.849 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0770
   chunk 19 optimal weight:    0.9990
   chunk 47 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0670
   chunk 23 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 5 optimal weight:    0.0050
   chunk 53 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0470
   overall best weight:    0.1588

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.169573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162657 restraints weight = 9827.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162657 restraints weight = 14470.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.162657 restraints weight = 14470.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8136  Z= 0.120
  Angle     :  0.535   7.606  11058  Z= 0.282
  Chirality :  0.039   0.133   1272
  Planarity :  0.004   0.033   1446
  Dihedral  :  4.545  22.427   1089
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.75 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.77 (0.27), residues: 1020
  helix:  3.33 (0.23), residues: 477
  sheet:  0.38 (0.37), residues: 153
  loop : -1.40 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C1206 
 HIS   0.005   0.001   HIS C 759 
 PHE   0.016   0.002   PHE A1092 
 TYR   0.010   0.001   TYR C1162 
 ARG   0.005   0.001   ARG C1237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05486 (  515)
  hydrogen bonds       : angle       4.21034 ( 1485)
  SS BOND              : bond        0.00374 (   12)
  SS BOND              : angle       1.34883 (   24)
  covalent geometry    : bond        0.00233 ( 8124)
  covalent geometry    : angle       0.53208 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7549 (ptt-90) cc_final: 0.7050 (ptm160)
REVERT: A 1153 TRP cc_start: 0.7034 (m100) cc_final: 0.6326 (m100)
REVERT: B 1084 LYS cc_start: 0.7699 (mttt) cc_final: 0.7304 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2213
  time to fit residues: 39.6317
Evaluate side-chains
  87 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.872 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 53 optimal weight:    0.0870
   chunk 31 optimal weight:    0.0980
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0670
   chunk 100 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0870
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.2074

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

Flipped N/Q/H residues before XYZ refinement:
B 750 GLN
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.170751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.164128 restraints weight = 10044.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.151859 restraints weight = 14031.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.151860 restraints weight = 12459.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.5994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   8136  Z= 0.117
  Angle     :  0.526   7.376  11058  Z= 0.278
  Chirality :  0.039   0.130   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.345  21.582   1089
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.04 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.83 (0.27), residues: 1020
  helix:  3.48 (0.23), residues: 480
  sheet:  0.17 (0.44), residues: 123
  loop : -1.34 (0.28), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C1153 
 HIS   0.003   0.001   HIS C 759 
 PHE   0.014   0.001   PHE A1092 
 TYR   0.010   0.001   TYR B1162 
 ARG   0.004   0.001   ARG C1237 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05332 (  515)
  hydrogen bonds       : angle       4.06838 ( 1485)
  SS BOND              : bond        0.00312 (   12)
  SS BOND              : angle       1.27588 (   24)
  covalent geometry    : bond        0.00237 ( 8124)
  covalent geometry    : angle       0.52288 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 1.018 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7605 (ptt-90) cc_final: 0.6991 (ptm160)
REVERT: B 1084 LYS cc_start: 0.7731 (mttt) cc_final: 0.7482 (mttt)
REVERT: B 1153 TRP cc_start: 0.6866 (m100) cc_final: 0.6621 (m100)
REVERT: C  767 ARG cc_start: 0.7632 (ptt-90) cc_final: 0.6726 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2475
  time to fit residues: 38.9717
Evaluate side-chains
  80 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.913 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 77 optimal weight:    0.7980
   chunk 85 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.151823 restraints weight = 10048.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138582 restraints weight = 14524.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.138115 restraints weight = 12548.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.5932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8136  Z= 0.174
  Angle     :  0.619   7.395  11058  Z= 0.327
  Chirality :  0.041   0.140   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.797  22.303   1089
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.53 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.39 (0.26), residues: 1020
  helix:  3.09 (0.23), residues: 480
  sheet: -0.20 (0.46), residues: 111
  loop : -1.45 (0.27), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C1153 
 HIS   0.006   0.002   HIS A1114 
 PHE   0.019   0.002   PHE A1092 
 TYR   0.018   0.002   TYR A1233 
 ARG   0.005   0.001   ARG C 787 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05748 (  515)
  hydrogen bonds       : angle       4.28203 ( 1485)
  SS BOND              : bond        0.00467 (   12)
  SS BOND              : angle       2.11671 (   24)
  covalent geometry    : bond        0.00406 ( 8124)
  covalent geometry    : angle       0.61162 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7651 (ptt-90) cc_final: 0.6993 (ptm160)
REVERT: A 1237 ARG cc_start: 0.6817 (mmp80) cc_final: 0.6408 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7417 (tt0) cc_final: 0.6844 (tt0)
REVERT: B 1084 LYS cc_start: 0.7861 (mttt) cc_final: 0.7511 (mttt)
REVERT: C 1092 PHE cc_start: 0.8481 (t80) cc_final: 0.8087 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2109
  time to fit residues: 31.3020
Evaluate side-chains
  91 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.912 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 801 ASN
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.157033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.151493 restraints weight = 9974.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.137688 restraints weight = 14605.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.137787 restraints weight = 13003.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.6009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   8136  Z= 0.199
  Angle     :  0.665   7.531  11058  Z= 0.349
  Chirality :  0.042   0.143   1272
  Planarity :  0.004   0.034   1446
  Dihedral  :  5.205  22.004   1089
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.73 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.11 %
    Favored  : 99.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.03 (0.26), residues: 1020
  helix:  2.99 (0.23), residues: 471
  sheet: -0.91 (0.39), residues: 141
  loop : -1.63 (0.28), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A1153 
 HIS   0.007   0.002   HIS A1114 
 PHE   0.025   0.002   PHE A1092 
 TYR   0.014   0.002   TYR C1181 
 ARG   0.004   0.001   ARG C 787 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05916 (  515)
  hydrogen bonds       : angle       4.43845 ( 1485)
  SS BOND              : bond        0.00512 (   12)
  SS BOND              : angle       2.78782 (   24)
  covalent geometry    : bond        0.00474 ( 8124)
  covalent geometry    : angle       0.65323 (11034)

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

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

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2040 Ramachandran restraints generated.
    1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  767 ARG cc_start: 0.7638 (ptt-90) cc_final: 0.6898 (ptm160)
REVERT: A 1237 ARG cc_start: 0.7009 (mmp80) cc_final: 0.6445 (mmp80)
REVERT: B 1077 GLU cc_start: 0.7297 (tt0) cc_final: 0.6999 (tt0)
REVERT: B 1084 LYS cc_start: 0.7884 (mttt) cc_final: 0.7516 (mttt)
REVERT: C 1092 PHE cc_start: 0.8419 (t80) cc_final: 0.8016 (t80)
REVERT: C 1237 ARG cc_start: 0.6159 (mmp80) cc_final: 0.5811 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2652
  time to fit residues: 45.4554
Evaluate side-chains
  94 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 50 optimal weight:    0.9990
   chunk 49 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9980
   chunk 15 optimal weight:    0.2980
   chunk 84 optimal weight:    0.5980
   chunk 77 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9980
   chunk 63 optimal weight:    0.1980
   chunk 22 optimal weight:    5.9990
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
A 801 ASN
B1055 ASN
C1055 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.159194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.153671 restraints weight = 9896.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139788 restraints weight = 14297.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.139954 restraints weight = 13217.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.6163

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8136  Z= 0.141
  Angle     :  0.581   7.204  11058  Z= 0.306
  Chirality :  0.040   0.139   1272
  Planarity :  0.004   0.032   1446
  Dihedral  :  4.770  21.333   1089
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  3.82 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.29 (0.27), residues: 1020
  helix:  3.17 (0.23), residues: 474
  sheet: -0.62 (0.43), residues: 123
  loop : -1.52 (0.28), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C1153 
 HIS   0.003   0.001   HIS B1114 
 PHE   0.028   0.002   PHE A1092 
 TYR   0.020   0.002   TYR A1233 
 ARG   0.004   0.001   ARG C 787 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05647 (  515)
  hydrogen bonds       : angle       4.29167 ( 1485)
  SS BOND              : bond        0.00417 (   12)
  SS BOND              : angle       2.08914 (   24)
  covalent geometry    : bond        0.00312 ( 8124)
  covalent geometry    : angle       0.57365 (11034)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2703.24 seconds
wall clock time: 49 minutes 13.23 seconds (2953.23 seconds total)