Starting phenix.real_space_refine
on Wed Sep 17 05:00:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vzn_43683/09_2025/8vzn_43683.cif"
  }
  resolution = 2.77
  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=   0.033
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      26      5.16       5
     C    3068      2.51       5
     N     748      2.21       5
     O     814      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4656
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 3246
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 15, 'TRANS': 401}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 933
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 933
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "C"
      Number of atoms: 470
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 470
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 3, 'TRANS': 58}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'CHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.42, per 1000 atoms: 0.30
  Number of scatterers: 4656
  At special positions: 0
  Unit cell: (73.87, 68.06, 118.69, 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      26     16.00
     O     814      8.00
     N     748      7.00
     C    3068      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  25 " - pdb=" SG  CYS B  99 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.05

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 177.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1090

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 3 sheets defined
      62.1% alpha, 9.2% 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 106 through 127
      removed outlier: 3.504A  pdb=" N   VAL A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 139
      removed outlier: 3.605A  pdb=" N   PHE A 135 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 158
      removed outlier: 3.628A  pdb=" N   ILE A 146 " --> pdb=" O   SER A 142 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LEU A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   SER A 150 " --> pdb=" O   ILE A 146 " (cutoff:3.500A)
      removed outlier: 4.968A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   MET A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ILE A 158 " --> pdb=" O   MET A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 171
    Processing helix  chain 'A' and resid 172 through 191
    Processing helix  chain 'A' and resid 192 through 195
      removed outlier: 3.862A  pdb=" N   LEU A 195 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 192 through 195'
    Processing helix  chain 'A' and resid 199 through 219
      removed outlier: 3.503A  pdb=" N   VAL A 215 " --> pdb=" O   SER A 211 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   PHE A 216 " --> pdb=" O   VAL A 212 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   GLY A 219 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 229
    Processing helix  chain 'A' and resid 233 through 260
      removed outlier: 3.913A  pdb=" N   ASN A 245 " --> pdb=" O   ALA A 241 " (cutoff:3.500A)
      Proline residue:  A 256  - end of helix
    Processing helix  chain 'A' and resid 268 through 295
      removed outlier: 3.588A  pdb=" N   MET A 276 " --> pdb=" O   HIS A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 3.540A  pdb=" N   ALA A 312 " --> pdb=" O   SER A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 320 through 328
      removed outlier: 3.630A  pdb=" N   ARG A 326 " --> pdb=" O   SER A 322 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   PHE A 328 " --> pdb=" O   ILE A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 353
    Processing helix  chain 'A' and resid 353 through 362
    Processing helix  chain 'A' and resid 365 through 395
    Processing helix  chain 'A' and resid 396 through 419
    Processing helix  chain 'A' and resid 423 through 453
      removed outlier: 3.824A  pdb=" N   VAL A 427 " --> pdb=" O   HIS A 423 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 442 " --> pdb=" O   MET A 438 " (cutoff:3.500A)
      Proline residue:  A 443  - end of helix
    Processing helix  chain 'A' and resid 457 through 488
    Processing helix  chain 'A' and resid 488 through 508
      removed outlier: 3.981A  pdb=" N   LEU A 496 " --> pdb=" O   GLY A 492 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 499 " --> pdb=" O   PHE A 495 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 508 " --> pdb=" O   SER A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 521
      removed outlier: 3.771A  pdb=" N   LYS A 521 " --> pdb=" O   GLN A 517 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 14
      removed outlier: 6.633A  pdb=" N   GLY B  13 " --> pdb=" O   THR B 128 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   ILE B  37 " --> pdb=" O   SER B  53 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   SER B  53 " --> pdb=" O   ILE B  37 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   TRP B  39 " --> pdb=" O   VAL B  51 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA B  43 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   GLY B  47 " --> pdb=" O   ALA B  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 22 through 26
    Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 55
      removed outlier: 6.417A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   THR C  98 " --> pdb=" O   GLN C  91 " (cutoff:3.500A)

    296 hydrogen bonds defined for protein.
    873 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.58 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 690
        1.29 -     1.42: 1370
        1.42 -     1.55: 2680
        1.55 -     1.68: 1
        1.68 -     1.81: 41
  Bond restraints: 4782
  Sorted by residual:
  bond pdb=" CA  TYR A 271 "
       pdb=" C   TYR A 271 "
    ideal  model  delta    sigma   weight residual
    1.524  1.432  0.092 1.32e-02 5.74e+03 4.81e+01
  bond pdb=" CA  ALA A 270 "
       pdb=" CB  ALA A 270 "
    ideal  model  delta    sigma   weight residual
    1.529  1.424  0.105 1.78e-02 3.16e+03 3.50e+01
  bond pdb=" C   ARG A 106 "
       pdb=" O   ARG A 106 "
    ideal  model  delta    sigma   weight residual
    1.236  1.163  0.073 1.29e-02 6.01e+03 3.18e+01
  bond pdb=" C   ILE A 126 "
       pdb=" O   ILE A 126 "
    ideal  model  delta    sigma   weight residual
    1.235  1.155  0.080 1.45e-02 4.76e+03 3.04e+01
  bond pdb=" C   LYS B 102 "
       pdb=" O   LYS B 102 "
    ideal  model  delta    sigma   weight residual
    1.234  1.168  0.067 1.22e-02 6.72e+03 3.00e+01
  ... (remaining 4777 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 5643
        2.04 -     4.07: 670
        4.07 -     6.11: 138
        6.11 -     8.14: 38
        8.14 -    10.18: 17
  Bond angle restraints: 6506
  Sorted by residual:
  angle pdb=" O   CYS A 120 "
        pdb=" C   CYS A 120 "
        pdb=" N   ASN A 121 "
      ideal   model   delta    sigma   weight residual
     122.12  114.16    7.96 1.06e+00 8.90e-01 5.64e+01
  angle pdb=" N   ALA C  33 "
        pdb=" CA  ALA C  33 "
        pdb=" C   ALA C  33 "
      ideal   model   delta    sigma   weight residual
     110.88  101.31    9.57 1.28e+00 6.10e-01 5.59e+01
  angle pdb=" C   GLN B  16 "
        pdb=" CA  GLN B  16 "
        pdb=" CB  GLN B  16 "
      ideal   model   delta    sigma   weight residual
     108.68  118.86  -10.18 1.39e+00 5.18e-01 5.36e+01
  angle pdb=" CA  TRP A 425 "
        pdb=" C   TRP A 425 "
        pdb=" O   TRP A 425 "
      ideal   model   delta    sigma   weight residual
     120.24  112.37    7.87 1.11e+00 8.12e-01 5.03e+01
  angle pdb=" N   TYR A 454 "
        pdb=" CA  TYR A 454 "
        pdb=" CB  TYR A 454 "
      ideal   model   delta    sigma   weight residual
     110.42  118.54   -8.12 1.18e+00 7.18e-01 4.74e+01
  ... (remaining 6501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 2475
       17.85 -    35.70: 210
       35.70 -    53.55: 35
       53.55 -    71.41: 13
       71.41 -    89.26: 8
  Dihedral angle restraints: 2741
    sinusoidal: 1026
      harmonic: 1715
  Sorted by residual:
  dihedral pdb=" CD  ARG B  70 "
           pdb=" NE  ARG B  70 "
           pdb=" CZ  ARG B  70 "
           pdb=" NH1 ARG B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.68  -88.68     1      1.00e+01 1.00e-02 9.38e+01
  dihedral pdb=" CD  ARG B 114 "
           pdb=" NE  ARG B 114 "
           pdb=" CZ  ARG B 114 "
           pdb=" NH1 ARG B 114 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.99  -87.99     1      1.00e+01 1.00e-02 9.26e+01
  dihedral pdb=" CD  ARG A 107 "
           pdb=" NE  ARG A 107 "
           pdb=" CZ  ARG A 107 "
           pdb=" NH1 ARG A 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.98  -86.98     1      1.00e+01 1.00e-02 9.09e+01
  ... (remaining 2738 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 459
       0.067 -    0.134: 198
       0.134 -    0.201: 59
       0.201 -    0.268: 17
       0.268 -    0.335: 3
  Chirality restraints: 736
  Sorted by residual:
  chirality pdb=" CB  VAL C  34 "
            pdb=" CA  VAL C  34 "
            pdb=" CG1 VAL C  34 "
            pdb=" CG2 VAL C  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.81e+00
  chirality pdb=" CA  SER A 104 "
            pdb=" N   SER A 104 "
            pdb=" C   SER A 104 "
            pdb=" CB  SER A 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.93e+00
  chirality pdb=" CA  LYS C  40 "
            pdb=" N   LYS C  40 "
            pdb=" C   LYS C  40 "
            pdb=" CB  LYS C  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 733 not shown)

  Planarity restraints: 795
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  70 "    1.103 9.50e-02 1.11e+02   4.94e-01 1.47e+02
        pdb=" NE  ARG B  70 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  70 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  70 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  70 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 107 "   -1.098 9.50e-02 1.11e+02   4.92e-01 1.46e+02
        pdb=" NE  ARG A 107 "    0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 107 "    0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 107 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 107 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 114 "    1.089 9.50e-02 1.11e+02   4.88e-01 1.44e+02
        pdb=" NE  ARG B 114 "   -0.067 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 114 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 114 "    0.012 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 114 "    0.015 2.00e-02 2.50e+03
  ... (remaining 792 not shown)

  Histogram of nonbonded interaction distances:
        2.33 -     2.84: 1640
        2.84 -     3.36: 4385
        3.36 -     3.87: 8138
        3.87 -     4.39: 9851
        4.39 -     4.90: 16081
  Nonbonded interactions: 40095
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 195 "
            pdb=" OH  TYR B 104 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" O   THR A 175 "
            pdb=" OG1 THR A 179 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" OH  TYR A 128 "
            pdb=" OG1 THR A 203 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   ALA A 449 "
            pdb=" OG1 THR A 453 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" N   LYS B 102 "
            pdb=" O   LYS B 102 "
     model   vdw
     2.414 2.496
  ... (remaining 40090 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.850
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.620
  Find NCS groups from input model:        0.020
  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:8.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.015   0.105   4784  Z= 0.856
  Angle     :  1.531  10.176   6510  Z= 1.057
  Chirality :  0.084   0.335    736
  Planarity :  0.039   0.494    795
  Dihedral  : 15.045  89.256   1645
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  :  8.82 %
    Favored  : 88.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.29), residues: 586
  helix: -1.97 (0.23), residues: 348
  sheet: -2.12 (0.55), residues: 67
  loop : -2.28 (0.42), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 356 
 TYR   0.019   0.003   TYR A 117 
 PHE   0.026   0.004   PHE A 436 
 TRP   0.019   0.003   TRP B 121 
 HIS   0.008   0.003   HIS B 112 

Details of bonding type rmsd
  covalent geometry    : bond        0.01507 ( 4782)
  covalent geometry    : angle       1.53143 ( 6506)
  SS BOND              : bond        0.01317 (    2)
  SS BOND              : angle       1.38911 (    4)
  hydrogen bonds       : bond        0.19791 (  296)
  hydrogen bonds       : angle       7.85925 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  102 LYS cc_start: 0.6915 (tttm) cc_final: 0.6684 (ttmm)
REVERT: A  253 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.7334 (t80)
REVERT: A  381 MET cc_start: 0.8352 (mtm) cc_final: 0.8152 (mtp)
REVERT: A  511 LYS cc_start: 0.8079 (tttt) cc_final: 0.7517 (mttp)
REVERT: B  106 TRP cc_start: 0.8598 (OUTLIER) cc_final: 0.8396 (t-100)
  outliers start: 14
  outliers final: 1
  residues processed: 87
  average time/residue: 0.6356
  time to fit residues: 57.1394
Evaluate side-chains
  64 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  295 PHE
Chi-restraints excluded: chain B residue  106 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:   10.0000
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
A 355 ASN
A 422 ASN
C  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.165270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.113851 restraints weight = 4780.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.97
r_work: 0.3107 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8437
moved from start:          0.1951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   4784  Z= 0.175
  Angle     :  0.593   7.533   6510  Z= 0.321
  Chirality :  0.042   0.159    736
  Planarity :  0.006   0.051    795
  Dihedral  :  6.027  53.133    651
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.03 %
    Favored  : 84.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.34), residues: 586
  helix:  0.40 (0.27), residues: 352
  sheet: -1.28 (0.61), residues: 65
  loop : -1.55 (0.45), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B  70 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.019   0.002   PHE A 144 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 ( 4782)
  covalent geometry    : angle       0.59264 ( 6506)
  SS BOND              : bond        0.00148 (    2)
  SS BOND              : angle       0.97660 (    4)
  hydrogen bonds       : bond        0.05169 (  296)
  hydrogen bonds       : angle       4.82348 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.8875 (t80) cc_final: 0.8614 (t80)
REVERT: A  253 PHE cc_start: 0.9119 (OUTLIER) cc_final: 0.8735 (m-80)
REVERT: A  297 GLU cc_start: 0.7410 (mp0) cc_final: 0.7088 (pm20)
REVERT: A  381 MET cc_start: 0.8323 (mtm) cc_final: 0.8116 (mtp)
REVERT: A  511 LYS cc_start: 0.8233 (tttt) cc_final: 0.7389 (mttp)
  outliers start: 7
  outliers final: 2
  residues processed: 71
  average time/residue: 0.6138
  time to fit residues: 45.2320
Evaluate side-chains
  66 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 18 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   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 246 GLN
A 330 ASN
A 422 ASN
C  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.164858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.113805 restraints weight = 4803.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 1.95
r_work: 0.3079 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4784  Z= 0.161
  Angle     :  0.542   6.707   6510  Z= 0.291
  Chirality :  0.041   0.152    736
  Planarity :  0.005   0.046    795
  Dihedral  :  5.040  46.107    647
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.43 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.55 (0.35), residues: 586
  helix:  1.36 (0.28), residues: 348
  sheet: -1.29 (0.64), residues: 55
  loop : -0.98 (0.46), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  41 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.017   0.002   PHE A 144 
 TRP   0.009   0.001   TRP B 108 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 4782)
  covalent geometry    : angle       0.54220 ( 6506)
  SS BOND              : bond        0.00094 (    2)
  SS BOND              : angle       0.77670 (    4)
  hydrogen bonds       : bond        0.04921 (  296)
  hydrogen bonds       : angle       4.55689 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  157 TYR cc_start: 0.8871 (t80) cc_final: 0.8622 (t80)
REVERT: A  223 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7580 (ttt90)
REVERT: A  253 PHE cc_start: 0.9140 (OUTLIER) cc_final: 0.8673 (m-80)
REVERT: A  297 GLU cc_start: 0.7484 (mp0) cc_final: 0.7214 (pm20)
REVERT: A  381 MET cc_start: 0.8295 (mtm) cc_final: 0.8072 (mtp)
REVERT: A  447 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7691 (mm-30)
REVERT: A  511 LYS cc_start: 0.8201 (tttt) cc_final: 0.7383 (mttp)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.5900
  time to fit residues: 39.7384
Evaluate side-chains
  69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  253 PHE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 37 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 49 optimal weight:   20.0000
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
A 246 GLN
A 330 ASN
A 422 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.166540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.115783 restraints weight = 4804.889|
|-----------------------------------------------------------------------------|
r_work (start): 0.3211 rms_B_bonded: 1.95
r_work: 0.3106 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4784  Z= 0.127
  Angle     :  0.502   6.510   6510  Z= 0.268
  Chirality :  0.040   0.149    736
  Planarity :  0.005   0.047    795
  Dihedral  :  4.780  45.569    647
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.23 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.35), residues: 586
  helix:  1.85 (0.28), residues: 348
  sheet: -1.10 (0.63), residues: 55
  loop : -0.75 (0.47), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.017   0.001   PHE A 144 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4782)
  covalent geometry    : angle       0.50233 ( 6506)
  SS BOND              : bond        0.00039 (    2)
  SS BOND              : angle       0.50195 (    4)
  hydrogen bonds       : bond        0.04373 (  296)
  hydrogen bonds       : angle       4.34645 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.169 
Fit side-chains
REVERT: A  157 TYR cc_start: 0.8864 (t80) cc_final: 0.8656 (t80)
REVERT: A  223 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7541 (ttt90)
REVERT: A  297 GLU cc_start: 0.7408 (mp0) cc_final: 0.7187 (pm20)
REVERT: A  381 MET cc_start: 0.8253 (mtm) cc_final: 0.8025 (mtp)
REVERT: A  446 PHE cc_start: 0.8412 (m-80) cc_final: 0.8147 (m-80)
REVERT: A  447 GLU cc_start: 0.8061 (mm-30) cc_final: 0.7699 (mm-30)
REVERT: A  511 LYS cc_start: 0.8188 (tttt) cc_final: 0.7377 (mttp)
REVERT: B  101 ARG cc_start: 0.8645 (tmt170) cc_final: 0.8318 (tmt170)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.5608
  time to fit residues: 39.0712
Evaluate side-chains
  67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   67 VAL
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0770
   chunk 41 optimal weight:    9.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 246 GLN
A 330 ASN
A 422 ASN
C  28 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.165987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.115091 restraints weight = 4801.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.95
r_work: 0.3113 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4784  Z= 0.135
  Angle     :  0.505   6.548   6510  Z= 0.268
  Chirality :  0.040   0.151    736
  Planarity :  0.004   0.050    795
  Dihedral  :  4.258  15.458    645
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 14.43 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.38 (0.35), residues: 586
  helix:  1.99 (0.27), residues: 348
  sheet: -0.89 (0.64), residues: 55
  loop : -0.58 (0.48), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  41 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.016   0.001   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4782)
  covalent geometry    : angle       0.50474 ( 6506)
  SS BOND              : bond        0.00051 (    2)
  SS BOND              : angle       0.49311 (    4)
  hydrogen bonds       : bond        0.04442 (  296)
  hydrogen bonds       : angle       4.34959 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7554 (ttt90)
REVERT: A  381 MET cc_start: 0.8302 (mtm) cc_final: 0.8089 (mtp)
REVERT: A  444 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.7942 (mt)
REVERT: A  446 PHE cc_start: 0.8438 (m-80) cc_final: 0.8234 (m-80)
REVERT: A  447 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7696 (mm-30)
REVERT: A  511 LYS cc_start: 0.8185 (tttt) cc_final: 0.7378 (mttp)
  outliers start: 9
  outliers final: 5
  residues processed: 65
  average time/residue: 0.5604
  time to fit residues: 37.8181
Evaluate side-chains
  65 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 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:
A 198 HIS
A 330 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.165424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114799 restraints weight = 4853.778|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 1.93
r_work: 0.3051 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2923 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4784  Z= 0.143
  Angle     :  0.512   6.539   6510  Z= 0.271
  Chirality :  0.040   0.152    736
  Planarity :  0.004   0.051    795
  Dihedral  :  4.257  16.209    645
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 14.63 %
    Favored  : 83.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.35), residues: 586
  helix:  2.00 (0.27), residues: 349
  sheet: -0.70 (0.65), residues: 55
  loop : -0.42 (0.49), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  41 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.017   0.002   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4782)
  covalent geometry    : angle       0.51191 ( 6506)
  SS BOND              : bond        0.00063 (    2)
  SS BOND              : angle       0.47609 (    4)
  hydrogen bonds       : bond        0.04514 (  296)
  hydrogen bonds       : angle       4.33794 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7510 (ttt90)
REVERT: A  297 GLU cc_start: 0.7256 (pm20) cc_final: 0.6853 (tp30)
REVERT: A  381 MET cc_start: 0.8296 (mtm) cc_final: 0.8083 (mtp)
REVERT: A  447 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7633 (mm-30)
REVERT: A  451 GLU cc_start: 0.8913 (tp30) cc_final: 0.8699 (tp30)
REVERT: A  511 LYS cc_start: 0.8145 (tttt) cc_final: 0.7300 (mttp)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.5711
  time to fit residues: 38.5307
Evaluate side-chains
  67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 49 optimal weight:    0.0570
   chunk 39 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 26 optimal weight:    0.1980
   chunk 47 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.166426 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.116293 restraints weight = 4815.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.91
r_work: 0.3084 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4784  Z= 0.125
  Angle     :  0.496   6.488   6510  Z= 0.261
  Chirality :  0.040   0.150    736
  Planarity :  0.004   0.052    795
  Dihedral  :  4.125  15.645    645
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 15.83 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.35), residues: 586
  helix:  2.10 (0.27), residues: 353
  sheet: -0.55 (0.65), residues: 55
  loop : -0.49 (0.49), residues: 178

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 326 
 TYR   0.025   0.001   TYR A 117 
 PHE   0.016   0.001   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4782)
  covalent geometry    : angle       0.49588 ( 6506)
  SS BOND              : bond        0.00049 (    2)
  SS BOND              : angle       0.41466 (    4)
  hydrogen bonds       : bond        0.04225 (  296)
  hydrogen bonds       : angle       4.27326 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.122 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7524 (ttt90)
REVERT: A  297 GLU cc_start: 0.7418 (pm20) cc_final: 0.6897 (tp30)
REVERT: A  381 MET cc_start: 0.8272 (mtm) cc_final: 0.8050 (mtp)
REVERT: A  444 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8041 (mt)
REVERT: A  511 LYS cc_start: 0.8127 (tttt) cc_final: 0.7280 (mttp)
  outliers start: 7
  outliers final: 5
  residues processed: 64
  average time/residue: 0.6350
  time to fit residues: 42.0352
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  444 LEU
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 49 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 12 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 48 optimal weight:    6.9990
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
C  28 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.165168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.114273 restraints weight = 4899.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 1.95
r_work: 0.3053 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.2973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4784  Z= 0.148
  Angle     :  0.520   6.540   6510  Z= 0.274
  Chirality :  0.041   0.153    736
  Planarity :  0.005   0.053    795
  Dihedral  :  4.218  16.534    645
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.03 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.36), residues: 586
  helix:  2.03 (0.27), residues: 352
  sheet: -0.47 (0.65), residues: 55
  loop : -0.33 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.017   0.002   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4782)
  covalent geometry    : angle       0.51985 ( 6506)
  SS BOND              : bond        0.00058 (    2)
  SS BOND              : angle       0.42199 (    4)
  hydrogen bonds       : bond        0.04559 (  296)
  hydrogen bonds       : angle       4.33709 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7531 (ttt90)
REVERT: A  297 GLU cc_start: 0.7432 (pm20) cc_final: 0.6882 (tp30)
REVERT: A  381 MET cc_start: 0.8300 (mtm) cc_final: 0.8087 (mtp)
REVERT: A  451 GLU cc_start: 0.8932 (tp30) cc_final: 0.8713 (tp30)
REVERT: A  511 LYS cc_start: 0.8136 (tttt) cc_final: 0.7262 (mttp)
  outliers start: 7
  outliers final: 5
  residues processed: 64
  average time/residue: 0.6244
  time to fit residues: 41.5147
Evaluate side-chains
  67 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 55 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.165581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.114811 restraints weight = 4809.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 1.93
r_work: 0.3084 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4784  Z= 0.142
  Angle     :  0.512   6.505   6510  Z= 0.269
  Chirality :  0.041   0.162    736
  Planarity :  0.005   0.053    795
  Dihedral  :  4.188  16.094    645
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.03 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.36), residues: 586
  helix:  2.06 (0.27), residues: 352
  sheet: -0.36 (0.65), residues: 55
  loop : -0.31 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.016   0.001   PHE A 144 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 4782)
  covalent geometry    : angle       0.51199 ( 6506)
  SS BOND              : bond        0.00049 (    2)
  SS BOND              : angle       0.38999 (    4)
  hydrogen bonds       : bond        0.04455 (  296)
  hydrogen bonds       : angle       4.31858 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7568 (ttt90)
REVERT: A  297 GLU cc_start: 0.7498 (pm20) cc_final: 0.6894 (tp30)
REVERT: A  381 MET cc_start: 0.8315 (mtm) cc_final: 0.8076 (mtp)
REVERT: A  446 PHE cc_start: 0.8327 (m-80) cc_final: 0.8088 (m-80)
REVERT: A  447 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7827 (mm-30)
REVERT: A  511 LYS cc_start: 0.8179 (tttt) cc_final: 0.7325 (mttp)
  outliers start: 7
  outliers final: 5
  residues processed: 67
  average time/residue: 0.6360
  time to fit residues: 44.1163
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.165086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.115040 restraints weight = 4829.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.89
r_work: 0.3090 rms_B_bonded: 2.21 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.3051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4784  Z= 0.141
  Angle     :  0.516   6.715   6510  Z= 0.270
  Chirality :  0.041   0.180    736
  Planarity :  0.005   0.053    795
  Dihedral  :  4.183  16.111    645
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 16.03 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.68 (0.36), residues: 586
  helix:  2.06 (0.27), residues: 352
  sheet: -0.25 (0.64), residues: 55
  loop : -0.30 (0.50), residues: 179

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  41 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.016   0.001   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 4782)
  covalent geometry    : angle       0.51614 ( 6506)
  SS BOND              : bond        0.00059 (    2)
  SS BOND              : angle       0.46238 (    4)
  hydrogen bonds       : bond        0.04451 (  296)
  hydrogen bonds       : angle       4.31689 (  873)

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

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

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1172 Ramachandran restraints generated.
    586 Oldfield, 0 Emsley, 586 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  223 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7519 (ttt90)
REVERT: A  297 GLU cc_start: 0.7500 (pm20) cc_final: 0.6880 (tp30)
REVERT: A  326 ARG cc_start: 0.7798 (mtm-85) cc_final: 0.7538 (ttp-110)
REVERT: A  381 MET cc_start: 0.8274 (mtm) cc_final: 0.8044 (mtp)
REVERT: A  446 PHE cc_start: 0.8293 (m-80) cc_final: 0.8090 (m-80)
REVERT: A  511 LYS cc_start: 0.8123 (tttt) cc_final: 0.7233 (mttp)
  outliers start: 6
  outliers final: 5
  residues processed: 65
  average time/residue: 0.5917
  time to fit residues: 39.9842
Evaluate side-chains
  68 residues out of total 499 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 62
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 THR
Chi-restraints excluded: chain A residue  223 ARG
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain C residue   40 LYS
Chi-restraints excluded: chain C residue   92 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 41 optimal weight:    0.2980
   chunk 1 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.165728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.115410 restraints weight = 4831.955|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.92
r_work: 0.3085 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2957 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8392
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4784  Z= 0.136
  Angle     :  0.515   7.779   6510  Z= 0.269
  Chirality :  0.041   0.196    736
  Planarity :  0.004   0.053    795
  Dihedral  :  4.155  15.998    645
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.03 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.36), residues: 586
  helix:  2.05 (0.27), residues: 355
  sheet: -0.30 (0.63), residues: 56
  loop : -0.23 (0.51), residues: 175

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 107 
 TYR   0.024   0.001   TYR A 117 
 PHE   0.016   0.001   PHE A 144 
 TRP   0.008   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  38 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4782)
  covalent geometry    : angle       0.51498 ( 6506)
  SS BOND              : bond        0.00050 (    2)
  SS BOND              : angle       0.42021 (    4)
  hydrogen bonds       : bond        0.04396 (  296)
  hydrogen bonds       : angle       4.30300 (  873)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1965.07 seconds
wall clock time: 34 minutes 16.24 seconds (2056.24 seconds total)