Starting phenix.real_space_refine
on Sat May  2 15:17:12 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.33
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jdc_61388/05_2026/9jdc_61388.cif"
  }
  resolution = 2.33
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.067
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
     Fe      2      7.16       5
     S      32      5.16       5
     C    4394      2.51       5
     N    1176      2.21       5
     O    1284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6888
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3380
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 389}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3380
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 389}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'HEM': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 64
          Unusual residues: {'HEM': 1}
          Classifications: {'peptide': 1, 'undetermined': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.29
  Number of scatterers: 6888
  At special positions: 0
  Unit cell: (84.15, 106.25, 66.3, 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)
     Fe      2     26.01
     S      32     16.00
     O    1284      8.00
     N    1176      7.00
     C    4394      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 420.9 milliseconds
  

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 2 sheets defined
      44.5% alpha, 17.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 44
    Processing helix  chain 'A' and resid 75 through 79
    Processing helix  chain 'A' and resid 135 through 137
      No H-bonds generated for 'chain 'A' and resid 135 through 137'
    Processing helix  chain 'A' and resid 138 through 147
    Processing helix  chain 'A' and resid 156 through 167
      removed outlier: 4.168A  pdb=" N   TRP A 160 " --> pdb=" O   ASN A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
    Processing helix  chain 'A' and resid 179 through 184
      removed outlier: 3.994A  pdb=" N   MET A 184 " --> pdb=" O   PHE A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 249
    Processing helix  chain 'A' and resid 266 through 270
    Processing helix  chain 'A' and resid 309 through 314
    Processing helix  chain 'A' and resid 333 through 352
      removed outlier: 3.754A  pdb=" N   PHE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   TYR A 343 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 384 through 393
    Processing helix  chain 'A' and resid 394 through 401
      removed outlier: 6.728A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 394 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   SER A 398 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   SER A 400 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 421
      removed outlier: 3.959A  pdb=" N   TYR A 407 " --> pdb=" O   ASN A 403 " (cutoff:3.500A)
      Proline residue:  A 410  - end of helix
      Proline residue:  A 418  - end of helix
    Processing helix  chain 'A' and resid 422 through 438
      removed outlier: 3.672A  pdb=" N   GLN A 426 " --> pdb=" O   GLY A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 456
    Processing helix  chain 'A' and resid 456 through 469
      removed outlier: 3.782A  pdb=" N   GLU A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 44
      removed outlier: 3.619A  pdb=" N   ARG B  44 " --> pdb=" O   SER B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 79
    Processing helix  chain 'B' and resid 135 through 137
      No H-bonds generated for 'chain 'B' and resid 135 through 137'
    Processing helix  chain 'B' and resid 138 through 147
    Processing helix  chain 'B' and resid 156 through 167
      removed outlier: 4.046A  pdb=" N   TRP B 160 " --> pdb=" O   ASN B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 170 through 178
    Processing helix  chain 'B' and resid 179 through 184
      removed outlier: 3.995A  pdb=" N   MET B 184 " --> pdb=" O   PHE B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 237 through 250
      removed outlier: 3.584A  pdb=" N   GLY B 250 " --> pdb=" O   SER B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 270
    Processing helix  chain 'B' and resid 309 through 314
    Processing helix  chain 'B' and resid 333 through 352
      removed outlier: 3.753A  pdb=" N   PHE B 341 " --> pdb=" O   GLN B 337 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   TYR B 343 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)
      Proline residue:  B 344  - end of helix
    Processing helix  chain 'B' and resid 384 through 393
    Processing helix  chain 'B' and resid 394 through 401
      removed outlier: 6.733A  pdb=" N   SER B 397 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.374A  pdb=" N   SER B 398 " --> pdb=" O   THR B 395 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   SER B 400 " --> pdb=" O   SER B 397 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 422
      removed outlier: 3.953A  pdb=" N   TYR B 407 " --> pdb=" O   ASN B 403 " (cutoff:3.500A)
      Proline residue:  B 410  - end of helix
      Proline residue:  B 418  - end of helix
    Processing helix  chain 'B' and resid 422 through 438
      removed outlier: 3.843A  pdb=" N   GLN B 426 " --> pdb=" O   GLY B 422 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 454
      removed outlier: 3.607A  pdb=" N   LEU B 454 " --> pdb=" O   LYS B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 471
    Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 330
      removed outlier: 6.464A  pdb=" N   TRP A 255 " --> pdb=" O   LYS A 300 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LYS A 300 " --> pdb=" O   TRP A 255 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   VAL A 257 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   TYR A  60 " --> pdb=" O   LYS A 304 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 328 through 330
      removed outlier: 6.457A  pdb=" N   TRP B 255 " --> pdb=" O   LYS B 300 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   LYS B 300 " --> pdb=" O   TRP B 255 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   VAL B 257 " --> pdb=" O   VAL B 298 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   TYR B  60 " --> pdb=" O   LYS B 304 " (cutoff:3.500A)

    306 hydrogen bonds defined for protein.
    846 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: 1.05

  Time building geometry restraints manager: 0.86 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 2958
        1.40 -     1.57: 4078
        1.57 -     1.74: 0
        1.74 -     1.91: 52
        1.91 -     2.08: 8
  Bond restraints: 7096
  Sorted by residual:
  bond pdb=" CAH LH6 A 502 "
       pdb=" CAI LH6 A 502 "
    ideal  model  delta    sigma   weight residual
    1.338  1.528 -0.190 2.00e-02 2.50e+03 9.05e+01
  bond pdb=" CAH LH6 B 502 "
       pdb=" CAI LH6 B 502 "
    ideal  model  delta    sigma   weight residual
    1.338  1.527 -0.189 2.00e-02 2.50e+03 8.97e+01
  bond pdb=" CAJ LH6 B 502 "
       pdb=" CAK LH6 B 502 "
    ideal  model  delta    sigma   weight residual
    1.338  1.527 -0.189 2.00e-02 2.50e+03 8.92e+01
  bond pdb=" CAJ LH6 A 502 "
       pdb=" CAK LH6 A 502 "
    ideal  model  delta    sigma   weight residual
    1.338  1.527 -0.189 2.00e-02 2.50e+03 8.91e+01
  bond pdb=" CG  LH6 A 502 "
       pdb=" CD2 LH6 A 502 "
    ideal  model  delta    sigma   weight residual
    1.443  1.346  0.097 2.00e-02 2.50e+03 2.36e+01
  ... (remaining 7091 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.48: 9546
        2.48 -     4.95: 114
        4.95 -     7.43: 12
        7.43 -     9.90: 2
        9.90 -    12.38: 6
  Bond angle restraints: 9680
  Sorted by residual:
  angle pdb=" CA  LH6 B 502 "
        pdb=" N   LH6 B 502 "
        pdb=" CAG LH6 B 502 "
      ideal   model   delta    sigma   weight residual
     122.48  110.10   12.38 3.00e+00 1.11e-01 1.70e+01
  angle pdb=" CA  LH6 A 502 "
        pdb=" N   LH6 A 502 "
        pdb=" CAG LH6 A 502 "
      ideal   model   delta    sigma   weight residual
     122.48  110.15   12.33 3.00e+00 1.11e-01 1.69e+01
  angle pdb=" CAH LH6 A 502 "
        pdb=" CAI LH6 A 502 "
        pdb=" CAJ LH6 A 502 "
      ideal   model   delta    sigma   weight residual
     124.17  113.98   10.19 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" CAH LH6 B 502 "
        pdb=" CAI LH6 B 502 "
        pdb=" CAJ LH6 B 502 "
      ideal   model   delta    sigma   weight residual
     124.17  114.00   10.17 3.00e+00 1.11e-01 1.15e+01
  angle pdb=" CA  MET A 433 "
        pdb=" C   MET A 433 "
        pdb=" O   MET A 433 "
      ideal   model   delta    sigma   weight residual
     120.55  117.44    3.11 1.06e+00 8.90e-01 8.63e+00
  ... (remaining 9675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 3649
       17.08 -    34.17: 350
       34.17 -    51.25: 145
       51.25 -    68.34: 40
       68.34 -    85.42: 26
  Dihedral angle restraints: 4210
    sinusoidal: 1752
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CA  THR B  94 "
           pdb=" C   THR B  94 "
           pdb=" N   ALA B  95 "
           pdb=" CA  ALA B  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  THR A  94 "
           pdb=" C   THR A  94 "
           pdb=" N   ALA A  95 "
           pdb=" CA  ALA A  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.22  -19.78     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" CA  PHE B 185 "
           pdb=" C   PHE B 185 "
           pdb=" N   ASP B 186 "
           pdb=" CA  ASP B 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.67   19.33     0      5.00e+00 4.00e-02 1.50e+01
  ... (remaining 4207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 556
       0.031 -    0.061: 284
       0.061 -    0.092: 84
       0.092 -    0.123: 60
       0.123 -    0.153: 10
  Chirality restraints: 994
  Sorted by residual:
  chirality pdb=" CA  ILE B 128 "
            pdb=" N   ILE B 128 "
            pdb=" C   ILE B 128 "
            pdb=" CB  ILE B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.89e-01
  chirality pdb=" CA  ILE A 128 "
            pdb=" N   ILE A 128 "
            pdb=" C   ILE A 128 "
            pdb=" CB  ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CB  ILE A 128 "
            pdb=" CA  ILE A 128 "
            pdb=" CG1 ILE A 128 "
            pdb=" CG2 ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.53e-01
  ... (remaining 991 not shown)

  Planarity restraints: 1270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 128 "   -0.028 5.00e-02 4.00e+02   4.28e-02 2.93e+00
        pdb=" N   PRO B 129 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 128 "    0.028 5.00e-02 4.00e+02   4.27e-02 2.92e+00
        pdb=" N   PRO A 129 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 129 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 129 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 172 "   -0.008 2.00e-02 2.50e+03   1.60e-02 2.57e+00
        pdb=" C   HIS A 172 "    0.028 2.00e-02 2.50e+03
        pdb=" O   HIS A 172 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   MET A 173 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1267 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 712
        2.75 -     3.29: 6282
        3.29 -     3.82: 11802
        3.82 -     4.36: 14680
        4.36 -     4.90: 23856
  Nonbonded interactions: 57332
  Sorted by model distance:
  nonbonded pdb=" O   GLN A 354 "
            pdb=" OE1 GLN B 354 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OD2 ASP B  37 "
            pdb=" NH1 ARG B  41 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" OD2 ASP B 217 "
            pdb=" NZ  LYS B 300 "
     model   vdw
     2.364 3.120
  nonbonded pdb=" OD2 ASP A 217 "
            pdb=" NZ  LYS A 300 "
     model   vdw
     2.367 3.120
  nonbonded pdb=" NH1 ARG B  50 "
            pdb=" O2D HEM B 501 "
     model   vdw
     2.376 3.120
  ... (remaining 57327 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.510
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.510
  Find NCS groups from input model:        0.110
  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:7.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
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      :  0.007   0.190   7098  Z= 0.341
  Angle     :  0.675  12.380   9680  Z= 0.315
  Chirality :  0.045   0.153    994
  Planarity :  0.005   0.043   1270
  Dihedral  : 18.052  85.420   2610
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 4.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 18.94 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.28), residues: 832
  helix:  1.02 (0.30), residues: 300
  sheet:  0.47 (0.44), residues: 138
  loop : -1.00 (0.28), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.010   0.001   TYR A 193 
 PHE   0.011   0.002   PHE A 178 
 TRP   0.008   0.001   TRP A 414 
 HIS   0.003   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00689 ( 7096)
  covalent geometry    : angle       0.67537 ( 9680)
  hydrogen bonds       : bond        0.14406 (  306)
  hydrogen bonds       : angle       6.74568 (  846)
  Misc. bond           : bond        0.07162 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.5138 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 94
  average time/residue: 0.8890
  time to fit residues: 86.4733
Evaluate side-chains
  94 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:   10.0000
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
B 156 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.113587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.095546 restraints weight = 7055.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.28
r_work: 0.2936 rms_B_bonded: 1.62 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.0596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7098  Z= 0.226
  Angle     :  0.741  13.892   9680  Z= 0.364
  Chirality :  0.052   0.237    994
  Planarity :  0.006   0.049   1270
  Dihedral  : 10.367  87.340    955
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 14.85 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.28), residues: 832
  helix:  1.29 (0.30), residues: 298
  sheet:  0.58 (0.43), residues: 138
  loop : -1.05 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 105 
 TYR   0.010   0.002   TYR B 286 
 PHE   0.020   0.003   PHE A 178 
 TRP   0.010   0.002   TRP A 161 
 HIS   0.004   0.001   HIS A 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 7096)
  covalent geometry    : angle       0.74142 ( 9680)
  hydrogen bonds       : bond        0.07050 (  306)
  hydrogen bonds       : angle       5.92253 (  846)
  Misc. bond           : bond        0.02558 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   30 GLU cc_start: 0.4929 (OUTLIER) cc_final: 0.4699 (tm-30)
REVERT: A  224 GLN cc_start: 0.7406 (OUTLIER) cc_final: 0.7039 (pp30)
REVERT: A  295 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.7717 (pm20)
REVERT: A  300 LYS cc_start: 0.8737 (ttmm) cc_final: 0.8377 (ttmm)
REVERT: A  305 LYS cc_start: 0.8357 (pttp) cc_final: 0.8084 (pttm)
REVERT: A  308 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8395 (mt-10)
REVERT: B  295 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7629 (pm20)
REVERT: B  300 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8378 (ttmm)
REVERT: B  308 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8413 (mt-10)
  outliers start: 24
  outliers final: 7
  residues processed: 112
  average time/residue: 0.8615
  time to fit residues: 99.8176
Evaluate side-chains
  111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 GLU
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  308 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Chi-restraints excluded: chain B residue  468 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 57 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 82 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    8.9990
   chunk 6 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
B 156 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.098165 restraints weight = 6917.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3078 rms_B_bonded: 1.27
r_work: 0.2975 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8744
moved from start:          0.0584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7098  Z= 0.146
  Angle     :  0.621  10.900   9680  Z= 0.302
  Chirality :  0.046   0.161    994
  Planarity :  0.005   0.046   1270
  Dihedral  :  9.140  82.634    955
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 15.94 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.28), residues: 832
  helix:  1.55 (0.30), residues: 298
  sheet:  0.48 (0.42), residues: 142
  loop : -0.99 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.008   0.001   TYR B 193 
 PHE   0.016   0.002   PHE B 178 
 TRP   0.010   0.001   TRP A 414 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 7096)
  covalent geometry    : angle       0.62126 ( 9680)
  hydrogen bonds       : bond        0.05207 (  306)
  hydrogen bonds       : angle       5.49222 (  846)
  Misc. bond           : bond        0.01602 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  224 GLN cc_start: 0.7348 (OUTLIER) cc_final: 0.6994 (pp30)
REVERT: A  295 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.7538 (pm20)
REVERT: A  300 LYS cc_start: 0.8740 (ttmm) cc_final: 0.8350 (ttmm)
REVERT: B  295 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7591 (pm20)
REVERT: B  300 LYS cc_start: 0.8746 (ttmm) cc_final: 0.8349 (ttmm)
REVERT: B  305 LYS cc_start: 0.8530 (pttp) cc_final: 0.8174 (pttp)
  outliers start: 18
  outliers final: 3
  residues processed: 109
  average time/residue: 0.8809
  time to fit residues: 99.2652
Evaluate side-chains
  101 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  224 GLN
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 82 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 47 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.101737 restraints weight = 7043.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.28
r_work: 0.3022 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2915 rms_B_bonded: 2.77 restraints_weight: 0.2500
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.0796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7098  Z= 0.105
  Angle     :  0.542   7.916   9680  Z= 0.261
  Chirality :  0.043   0.146    994
  Planarity :  0.004   0.043   1270
  Dihedral  :  7.356  76.748    952
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 16.89 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.29), residues: 832
  helix:  1.82 (0.30), residues: 300
  sheet:  0.58 (0.43), residues: 142
  loop : -0.91 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.008   0.001   TYR A 193 
 PHE   0.009   0.001   PHE B 178 
 TRP   0.010   0.001   TRP A 414 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 7096)
  covalent geometry    : angle       0.54249 ( 9680)
  hydrogen bonds       : bond        0.03809 (  306)
  hydrogen bonds       : angle       5.07471 (  846)
  Misc. bond           : bond        0.03337 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.282 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.7370 (pm20)
REVERT: A  300 LYS cc_start: 0.8689 (ttmm) cc_final: 0.8348 (ttmm)
REVERT: A  348 GLU cc_start: 0.7853 (tp30) cc_final: 0.7432 (tp30)
REVERT: B  300 LYS cc_start: 0.8692 (ttmm) cc_final: 0.8351 (ttmm)
REVERT: B  348 GLU cc_start: 0.7866 (tp30) cc_final: 0.7437 (tp30)
  outliers start: 17
  outliers final: 5
  residues processed: 105
  average time/residue: 0.8448
  time to fit residues: 91.8694
Evaluate side-chains
  100 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain B residue   73 CYS
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 14 optimal weight:    7.9990
   chunk 63 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 67 optimal weight:    4.9990
   chunk 58 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
A 245 GLN
B 156 ASN
B 245 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.096064 restraints weight = 7016.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.28
r_work: 0.2952 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2841 rms_B_bonded: 2.72 restraints_weight: 0.2500
r_work (final): 0.2841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.0712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7098  Z= 0.184
  Angle     :  0.678  12.347   9680  Z= 0.331
  Chirality :  0.049   0.190    994
  Planarity :  0.006   0.049   1270
  Dihedral  :  9.223  86.568    952
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.21 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.28), residues: 832
  helix:  1.56 (0.30), residues: 298
  sheet:  0.69 (0.43), residues: 138
  loop : -1.04 (0.28), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 105 
 TYR   0.011   0.002   TYR A 449 
 PHE   0.021   0.002   PHE B 178 
 TRP   0.009   0.002   TRP B 161 
 HIS   0.003   0.001   HIS B 211 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 7096)
  covalent geometry    : angle       0.67753 ( 9680)
  hydrogen bonds       : bond        0.06066 (  306)
  hydrogen bonds       : angle       5.57766 (  846)
  Misc. bond           : bond        0.01316 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7573 (pm20)
REVERT: A  300 LYS cc_start: 0.8744 (ttmm) cc_final: 0.8403 (ttmm)
REVERT: B  295 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7577 (pm20)
REVERT: B  300 LYS cc_start: 0.8765 (ttmm) cc_final: 0.8421 (ttmm)
  outliers start: 14
  outliers final: 4
  residues processed: 107
  average time/residue: 0.8821
  time to fit residues: 97.6684
Evaluate side-chains
  102 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 79 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 67 optimal weight:    5.9990
   chunk 23 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 76 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B 156 ASN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.116058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.098032 restraints weight = 7014.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 1.27
r_work: 0.2971 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2863 rms_B_bonded: 2.73 restraints_weight: 0.2500
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.0662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7098  Z= 0.147
  Angle     :  0.623  10.925   9680  Z= 0.302
  Chirality :  0.046   0.160    994
  Planarity :  0.005   0.048   1270
  Dihedral  :  8.610  83.144    952
  Min Nonbonded Distance : 2.626

Molprobity Statistics.
  All-atom Clashscore : 2.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.21 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.28), residues: 832
  helix:  1.63 (0.30), residues: 298
  sheet:  0.56 (0.42), residues: 142
  loop : -1.02 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.009   0.001   TYR A 193 
 PHE   0.017   0.002   PHE A 178 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 7096)
  covalent geometry    : angle       0.62275 ( 9680)
  hydrogen bonds       : bond        0.05184 (  306)
  hydrogen bonds       : angle       5.39884 (  846)
  Misc. bond           : bond        0.01120 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7522 (pm20)
REVERT: A  300 LYS cc_start: 0.8729 (ttmm) cc_final: 0.8377 (ttmm)
REVERT: B  295 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.7525 (pm20)
REVERT: B  300 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8382 (ttmm)
REVERT: B  419 ARG cc_start: 0.8186 (ttp80) cc_final: 0.7833 (ttp80)
  outliers start: 15
  outliers final: 4
  residues processed: 106
  average time/residue: 0.8930
  time to fit residues: 97.9670
Evaluate side-chains
  102 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0470
   chunk 4 optimal weight:    0.0070
   chunk 75 optimal weight:    0.5980
   chunk 42 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7300

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

Flipped N/Q/H residues before XYZ refinement:
A 156 ASN
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 156 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.119593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.101473 restraints weight = 6983.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3120 rms_B_bonded: 1.28
r_work: 0.3018 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2911 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.0819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7098  Z= 0.106
  Angle     :  0.546   7.964   9680  Z= 0.263
  Chirality :  0.044   0.148    994
  Planarity :  0.004   0.044   1270
  Dihedral  :  7.359  77.438    952
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 16.76 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.29), residues: 832
  helix:  1.85 (0.30), residues: 300
  sheet:  0.60 (0.43), residues: 142
  loop : -0.89 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  41 
 TYR   0.008   0.001   TYR A 193 
 PHE   0.009   0.001   PHE B 178 
 TRP   0.010   0.001   TRP A 414 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7096)
  covalent geometry    : angle       0.54633 ( 9680)
  hydrogen bonds       : bond        0.03867 (  306)
  hydrogen bonds       : angle       5.05951 (  846)
  Misc. bond           : bond        0.03520 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.289 
Fit side-chains
REVERT: A  221 ASN cc_start: 0.8245 (p0) cc_final: 0.7917 (p0)
REVERT: A  295 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7362 (pm20)
REVERT: A  300 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8323 (ttmm)
REVERT: B  295 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7442 (pm20)
REVERT: B  300 LYS cc_start: 0.8686 (ttmm) cc_final: 0.8332 (ttmm)
REVERT: B  305 LYS cc_start: 0.8549 (pttp) cc_final: 0.8151 (ptmt)
REVERT: B  419 ARG cc_start: 0.8188 (ttp80) cc_final: 0.7927 (ttm110)
  outliers start: 13
  outliers final: 4
  residues processed: 104
  average time/residue: 0.8919
  time to fit residues: 95.9425
Evaluate side-chains
  101 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 66 optimal weight:    7.9990
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 36 optimal weight:    7.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 76 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0040
   overall best weight:    1.7998

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

Flipped N/Q/H residues before XYZ refinement:
A 245 GLN
B 156 ASN
B 245 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.115093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.096993 restraints weight = 7124.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 1.28
r_work: 0.2970 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8725
moved from start:          0.0691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7098  Z= 0.154
  Angle     :  0.635  11.372   9680  Z= 0.307
  Chirality :  0.047   0.163    994
  Planarity :  0.005   0.047   1270
  Dihedral  :  8.501  84.430    952
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 2.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.49 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.28), residues: 832
  helix:  1.70 (0.30), residues: 298
  sheet:  0.58 (0.42), residues: 142
  loop : -0.98 (0.29), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 105 
 TYR   0.011   0.001   TYR A 449 
 PHE   0.019   0.002   PHE B 178 
 TRP   0.009   0.001   TRP B 161 
 HIS   0.003   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7096)
  covalent geometry    : angle       0.63498 ( 9680)
  hydrogen bonds       : bond        0.05337 (  306)
  hydrogen bonds       : angle       5.38469 (  846)
  Misc. bond           : bond        0.00329 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.267 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7554 (pm20)
REVERT: A  300 LYS cc_start: 0.8720 (ttmm) cc_final: 0.8358 (ttmm)
REVERT: B  295 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.7553 (pm20)
REVERT: B  300 LYS cc_start: 0.8698 (ttmm) cc_final: 0.8342 (ttmm)
REVERT: B  305 LYS cc_start: 0.8561 (pttp) cc_final: 0.8147 (ptmt)
  outliers start: 15
  outliers final: 6
  residues processed: 105
  average time/residue: 0.8719
  time to fit residues: 94.7870
Evaluate side-chains
  105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  408 LYS
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
B 245 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.116994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.098794 restraints weight = 7000.163|
|-----------------------------------------------------------------------------|
r_work (start): 0.3085 rms_B_bonded: 1.28
r_work: 0.2983 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 2.74 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.0717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7098  Z= 0.135
  Angle     :  0.605  10.327   9680  Z= 0.292
  Chirality :  0.045   0.149    994
  Planarity :  0.005   0.046   1270
  Dihedral  :  8.181  82.232    952
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.03 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.28), residues: 832
  helix:  1.69 (0.30), residues: 300
  sheet:  0.58 (0.43), residues: 142
  loop : -0.96 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.008   0.001   TYR B 449 
 PHE   0.016   0.002   PHE A 178 
 TRP   0.008   0.001   TRP B 161 
 HIS   0.003   0.001   HIS A 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7096)
  covalent geometry    : angle       0.60468 ( 9680)
  hydrogen bonds       : bond        0.04808 (  306)
  hydrogen bonds       : angle       5.28724 (  846)
  Misc. bond           : bond        0.01552 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A  295 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.7578 (pm20)
REVERT: A  300 LYS cc_start: 0.8716 (ttmm) cc_final: 0.8363 (ttmm)
REVERT: B  295 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7451 (pm20)
REVERT: B  300 LYS cc_start: 0.8704 (ttmm) cc_final: 0.8354 (ttmm)
REVERT: B  305 LYS cc_start: 0.8570 (pttp) cc_final: 0.8160 (ptmt)
  outliers start: 11
  outliers final: 7
  residues processed: 103
  average time/residue: 0.8958
  time to fit residues: 95.4749
Evaluate side-chains
  105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  408 LYS
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  408 LYS
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 71 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 83 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 75 optimal weight:    0.0000
   chunk 31 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
B 156 ASN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.118779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.100723 restraints weight = 6993.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.3111 rms_B_bonded: 1.28
r_work: 0.3009 rms_B_bonded: 1.65 restraints_weight: 0.5000
r_work: 0.2901 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2901
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.0822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7098  Z= 0.113
  Angle     :  0.565   8.715   9680  Z= 0.271
  Chirality :  0.044   0.147    994
  Planarity :  0.005   0.044   1270
  Dihedral  :  7.467  78.939    952
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.17 %
    Favored  : 81.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.29), residues: 832
  helix:  1.83 (0.30), residues: 300
  sheet:  0.61 (0.43), residues: 142
  loop : -0.91 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  41 
 TYR   0.007   0.001   TYR A 193 
 PHE   0.011   0.001   PHE B 178 
 TRP   0.009   0.001   TRP A 414 
 HIS   0.002   0.001   HIS B 196 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 7096)
  covalent geometry    : angle       0.56536 ( 9680)
  hydrogen bonds       : bond        0.04090 (  306)
  hydrogen bonds       : angle       5.09427 (  846)
  Misc. bond           : bond        0.02965 (    2)

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

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

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1664 Ramachandran restraints generated.
    832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   41 ARG cc_start: 0.8385 (mtm110) cc_final: 0.8152 (mtp180)
REVERT: A  221 ASN cc_start: 0.8248 (p0) cc_final: 0.7914 (p0)
REVERT: A  295 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7490 (pm20)
REVERT: A  300 LYS cc_start: 0.8701 (ttmm) cc_final: 0.8341 (ttmm)
REVERT: A  305 LYS cc_start: 0.8562 (pttp) cc_final: 0.8150 (ptmt)
REVERT: B  295 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7442 (pm20)
REVERT: B  300 LYS cc_start: 0.8685 (ttmm) cc_final: 0.8329 (ttmm)
REVERT: B  305 LYS cc_start: 0.8571 (pttp) cc_final: 0.8168 (ptmt)
  outliers start: 11
  outliers final: 6
  residues processed: 104
  average time/residue: 0.9144
  time to fit residues: 98.2861
Evaluate side-chains
  105 residues out of total 734 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 GLU
Chi-restraints excluded: chain A residue  395 THR
Chi-restraints excluded: chain A residue  408 LYS
Chi-restraints excluded: chain A residue  433 MET
Chi-restraints excluded: chain A residue  450 LYS
Chi-restraints excluded: chain B residue  295 GLU
Chi-restraints excluded: chain B residue  395 THR
Chi-restraints excluded: chain B residue  433 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 84
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9980
   chunk 66 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 245 GLN
B 245 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.119672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.101656 restraints weight = 6986.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.28
r_work: 0.3023 rms_B_bonded: 1.66 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 2.76 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.0919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7098  Z= 0.108
  Angle     :  0.553   8.240   9680  Z= 0.264
  Chirality :  0.044   0.150    994
  Planarity :  0.004   0.042   1270
  Dihedral  :  7.236  78.339    952
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 17.98 %
    Favored  : 80.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.29), residues: 832
  helix:  1.92 (0.30), residues: 300
  sheet:  0.61 (0.43), residues: 142
  loop : -0.85 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 105 
 TYR   0.007   0.001   TYR A 193 
 PHE   0.011   0.001   PHE A 178 
 TRP   0.009   0.001   TRP A 414 
 HIS   0.002   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 7096)
  covalent geometry    : angle       0.55261 ( 9680)
  hydrogen bonds       : bond        0.03857 (  306)
  hydrogen bonds       : angle       5.01130 (  846)
  Misc. bond           : bond        0.02648 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2817.54 seconds
wall clock time: 48 minutes 41.87 seconds (2921.87 seconds total)