Starting phenix.real_space_refine
on Wed Sep 17 04:57:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kbf_62223/09_2025/9kbf_62223.cif"
  }
  resolution = 3.74
  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=   0.016
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      29      5.16       5
     C    2922      2.51       5
     N     763      2.21       5
     O     873      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 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: 4587
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 162, 1298
          Classifications: {'peptide': 162}
          Link IDs: {'PTRANS': 10, 'TRANS': 151}
    Chain: "C"
      Number of atoms: 3289
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3289
          Classifications: {'peptide': 407}
          Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 385}
  Time building chain proxies: 1.33, per 1000 atoms: 0.29
  Number of scatterers: 4587
  At special positions: 0
  Unit cell: (66.42, 115.62, 113.98, 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      29     16.00
     O     873      8.00
     N     763      7.00
     C    2922      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=0, symmetry=0
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 184.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      43.6% alpha, 13.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'B' and resid 18 through 22
    Processing helix  chain 'B' and resid 24 through 34
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.549A  pdb=" N   ASP B  38 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 65
    Processing helix  chain 'B' and resid 75 through 79
      removed outlier: 3.598A  pdb=" N   GLU B  79 " --> pdb=" O   GLU B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 93
    Processing helix  chain 'B' and resid 96 through 111
    Processing helix  chain 'B' and resid 112 through 126
    Processing helix  chain 'B' and resid 131 through 139
    Processing helix  chain 'B' and resid 146 through 158
    Processing helix  chain 'C' and resid 17 through 27
      removed outlier: 3.747A  pdb=" N   PHE C  27 " --> pdb=" O   LEU C  23 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 38
      removed outlier: 3.943A  pdb=" N   TYR C  38 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 40 through 48
      removed outlier: 3.568A  pdb=" N   SER C  48 " --> pdb=" O   SER C  44 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 56
      removed outlier: 3.899A  pdb=" N   ARG C  55 " --> pdb=" O   PRO C  51 " (cutoff:3.500A)
      removed outlier: 4.145A  pdb=" N   HIS C  56 " --> pdb=" O   LEU C  52 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 51 through 56'
    Processing helix  chain 'C' and resid 64 through 72
    Processing helix  chain 'C' and resid 74 through 87
      removed outlier: 3.645A  pdb=" N   ASP C  85 " --> pdb=" O   ASP C  81 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 107
      removed outlier: 4.472A  pdb=" N   ALA C  94 " --> pdb=" O   ILE C  90 " (cutoff:3.500A)
      removed outlier: 5.598A  pdb=" N   ALA C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS C  98 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   LYS C 105 " --> pdb=" O   ASP C 101 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 111 through 118
      removed outlier: 4.644A  pdb=" N   VAL C 115 " --> pdb=" O   CYS C 111 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 123 through 135
      removed outlier: 3.520A  pdb=" N   LEU C 127 " --> pdb=" O   ARG C 123 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 139 through 149
    Processing helix  chain 'C' and resid 176 through 183
    Processing helix  chain 'C' and resid 244 through 258
    Processing helix  chain 'C' and resid 347 through 351
      removed outlier: 3.906A  pdb=" N   GLY C 350 " --> pdb=" O   GLY C 347 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 409 through 415
    Processing sheet with id=AA1, first strand: chain 'B' and resid 13 through 17
      removed outlier: 9.550A  pdb=" N   VAL B  45 " --> pdb=" O   SER B   3 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LYS B   5 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 162 through 164
    Processing sheet with id=AA3, first strand: chain 'C' and resid 173 through 174
    Processing sheet with id=AA4, first strand: chain 'C' and resid 185 through 186
    Processing sheet with id=AA5, first strand: chain 'C' and resid 224 through 226
    Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 264
    Processing sheet with id=AA7, first strand: chain 'C' and resid 284 through 285
    Processing sheet with id=AA8, first strand: chain 'C' and resid 284 through 285
      removed outlier: 3.631A  pdb=" N   TYR C 363 " --> pdb=" O   ILE C 310 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 354 through 355
      removed outlier: 3.541A  pdb=" N   CYS C 324 " --> pdb=" O   ILE C 355 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 340 through 343
      removed outlier: 3.837A  pdb=" N   VAL C 343 " --> pdb=" O   TRP C 331 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TRP C 331 " --> pdb=" O   VAL C 343 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY C 378 " --> pdb=" O   ILE C 396 " (cutoff:3.500A)

    184 hydrogen bonds defined for protein.
    525 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: 0.66

  Time building geometry restraints manager: 0.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1489
        1.34 -     1.46: 872
        1.46 -     1.58: 2297
        1.58 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 4699
  Sorted by residual:
  bond pdb=" N   MET C 415 "
       pdb=" CA  MET C 415 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.031 1.34e-02 5.57e+03 5.42e+00
  bond pdb=" N   GLU B 161 "
       pdb=" CA  GLU B 161 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.27e-02 6.20e+03 5.10e+00
  bond pdb=" N   CYS B 160 "
       pdb=" CA  CYS B 160 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.28e-02 6.10e+03 4.54e+00
  bond pdb=" N   TRP B 159 "
       pdb=" CA  TRP B 159 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.41e-02 5.03e+03 3.91e+00
  bond pdb=" N   GLY C 416 "
       pdb=" CA  GLY C 416 "
    ideal  model  delta    sigma   weight residual
    1.451  1.476 -0.025 1.60e-02 3.91e+03 2.41e+00
  ... (remaining 4694 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 6071
        1.32 -     2.64: 242
        2.64 -     3.96: 43
        3.96 -     5.28: 9
        5.28 -     6.60: 7
  Bond angle restraints: 6372
  Sorted by residual:
  angle pdb=" C   VAL C 348 "
        pdb=" N   VAL C 349 "
        pdb=" CA  VAL C 349 "
      ideal   model   delta    sigma   weight residual
     121.97  128.21   -6.24 1.80e+00 3.09e-01 1.20e+01
  angle pdb=" N   CYS B 160 "
        pdb=" CA  CYS B 160 "
        pdb=" C   CYS B 160 "
      ideal   model   delta    sigma   weight residual
     111.82  108.03    3.79 1.16e+00 7.43e-01 1.06e+01
  angle pdb=" C   ASP B  41 "
        pdb=" N   ASP B  42 "
        pdb=" CA  ASP B  42 "
      ideal   model   delta    sigma   weight residual
     121.54  127.33   -5.79 1.91e+00 2.74e-01 9.18e+00
  angle pdb=" CA  MET C 415 "
        pdb=" C   MET C 415 "
        pdb=" O   MET C 415 "
      ideal   model   delta    sigma   weight residual
     121.87  118.46    3.41 1.16e+00 7.43e-01 8.66e+00
  angle pdb=" N   TRP B 159 "
        pdb=" CA  TRP B 159 "
        pdb=" C   TRP B 159 "
      ideal   model   delta    sigma   weight residual
     113.18  109.43    3.75 1.33e+00 5.65e-01 7.96e+00
  ... (remaining 6367 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.20: 2497
       16.20 -    32.40: 265
       32.40 -    48.60: 55
       48.60 -    64.80: 13
       64.80 -    81.00: 7
  Dihedral angle restraints: 2837
    sinusoidal: 1165
      harmonic: 1672
  Sorted by residual:
  dihedral pdb=" CA  ASP B  42 "
           pdb=" CB  ASP B  42 "
           pdb=" CG  ASP B  42 "
           pdb=" OD1 ASP B  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -88.09   58.09     1      2.00e+01 2.50e-03 1.13e+01
  dihedral pdb=" CA  ASP C 327 "
           pdb=" CB  ASP C 327 "
           pdb=" CG  ASP C 327 "
           pdb=" OD1 ASP C 327 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -87.12   57.12     1      2.00e+01 2.50e-03 1.10e+01
  dihedral pdb=" CA  ALA C  95 "
           pdb=" C   ALA C  95 "
           pdb=" N   ILE C  96 "
           pdb=" CA  ILE C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.77  -16.23     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 2834 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 543
       0.051 -    0.102: 116
       0.102 -    0.153: 31
       0.153 -    0.204: 2
       0.204 -    0.254: 1
  Chirality restraints: 693
  Sorted by residual:
  chirality pdb=" CB  VAL C 349 "
            pdb=" CA  VAL C 349 "
            pdb=" CG1 VAL C 349 "
            pdb=" CG2 VAL C 349 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.25 2.00e-01 2.50e+01 1.62e+00
  chirality pdb=" CA  CYS B 160 "
            pdb=" N   CYS B 160 "
            pdb=" C   CYS B 160 "
            pdb=" CB  CYS B 160 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  ASN C  72 "
            pdb=" N   ASN C  72 "
            pdb=" C   ASN C  72 "
            pdb=" CB  ASN C  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.22e-01
  ... (remaining 690 not shown)

  Planarity restraints: 825
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 158 "   -0.018 2.00e-02 2.50e+03   3.69e-02 1.37e+01
        pdb=" C   GLN B 158 "    0.064 2.00e-02 2.50e+03
        pdb=" O   GLN B 158 "   -0.025 2.00e-02 2.50e+03
        pdb=" N   TRP B 159 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 356 "    0.030 5.00e-02 4.00e+02   4.56e-02 3.32e+00
        pdb=" N   PRO C 357 "   -0.079 5.00e-02 4.00e+02
        pdb=" CA  PRO C 357 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 357 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP C  50 "   -0.027 5.00e-02 4.00e+02   4.11e-02 2.70e+00
        pdb=" N   PRO C  51 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO C  51 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C  51 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 822 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 397
        2.74 -     3.28: 4598
        3.28 -     3.82: 7739
        3.82 -     4.36: 8909
        4.36 -     4.90: 15241
  Nonbonded interactions: 36884
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 298 "
            pdb=" O   PRO C 301 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" O   LYS B 130 "
            pdb=" ND2 ASN C  35 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" OE1 GLN C 185 "
            pdb=" OH  TYR C 207 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OD1 ASP C  85 "
            pdb=" NH2 ARG C 147 "
     model   vdw
     2.309 3.120
  nonbonded pdb=" O   MET C 114 "
            pdb=" OG  SER C 117 "
     model   vdw
     2.323 3.040
  ... (remaining 36879 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.890
  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:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.570
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
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      :  0.004   0.037   4699  Z= 0.198
  Angle     :  0.639   6.603   6372  Z= 0.351
  Chirality :  0.047   0.254    693
  Planarity :  0.005   0.046    825
  Dihedral  : 14.543  80.996   1757
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.78 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -1.16 (0.35), residues: 565
  helix: -0.62 (0.32), residues: 220
  sheet: -1.10 (0.54), residues: 96
  loop : -0.56 (0.41), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 332 
 TYR   0.010   0.002   TYR C 142 
 PHE   0.012   0.002   PHE C 306 
 TRP   0.018   0.002   TRP B 159 
 HIS   0.006   0.001   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 4699)
  covalent geometry    : angle       0.63913 ( 6372)
  hydrogen bonds       : bond        0.16134 (  182)
  hydrogen bonds       : angle       7.99074 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  158 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7946 (tm-30)
REVERT: C   40 SER cc_start: 0.8457 (t) cc_final: 0.8257 (m)
REVERT: C  100 TRP cc_start: 0.8636 (m100) cc_final: 0.7667 (m100)
REVERT: C  101 ASP cc_start: 0.7780 (t70) cc_final: 0.7148 (t0)
REVERT: C  270 ARG cc_start: 0.8276 (mtt-85) cc_final: 0.8021 (ttm-80)
REVERT: C  274 ASP cc_start: 0.7487 (t70) cc_final: 0.6590 (t70)
REVERT: C  325 GLN cc_start: 0.7425 (tt0) cc_final: 0.6909 (tt0)
REVERT: C  406 PHE cc_start: 0.8156 (p90) cc_final: 0.7844 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 165
  average time/residue: 0.0931
  time to fit residues: 18.6247
Evaluate side-chains
  103 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
C  49 HIS
C 152 GLN
C 267 GLN
C 325 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.152202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.122729 restraints weight = 7468.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.125399 restraints weight = 5392.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.127158 restraints weight = 4299.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.128263 restraints weight = 3691.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.129252 restraints weight = 3333.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   4699  Z= 0.191
  Angle     :  0.629   6.282   6372  Z= 0.325
  Chirality :  0.045   0.144    693
  Planarity :  0.004   0.036    825
  Dihedral  :  4.419  18.597    620
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  : 12.16 %
    Favored  : 86.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.82 (0.35), residues: 565
  helix: -0.13 (0.34), residues: 227
  sheet: -1.46 (0.58), residues: 77
  loop : -0.46 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 147 
 TYR   0.011   0.001   TYR C 380 
 PHE   0.012   0.002   PHE C 249 
 TRP   0.008   0.002   TRP C 248 
 HIS   0.004   0.001   HIS C  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 4699)
  covalent geometry    : angle       0.62900 ( 6372)
  hydrogen bonds       : bond        0.03564 (  182)
  hydrogen bonds       : angle       5.90048 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   81 ARG cc_start: 0.8102 (ptp-110) cc_final: 0.7594 (mtm110)
REVERT: B  158 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7146 (tm-30)
REVERT: C   15 SER cc_start: 0.8556 (p) cc_final: 0.8176 (t)
REVERT: C  229 MET cc_start: 0.7244 (tmm) cc_final: 0.6713 (tmm)
  outliers start: 6
  outliers final: 5
  residues processed: 111
  average time/residue: 0.0705
  time to fit residues: 10.1711
Evaluate side-chains
  104 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  152 GLN
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 29 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
C 303 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.152984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.123537 restraints weight = 7373.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126177 restraints weight = 5314.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.127962 restraints weight = 4236.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.128837 restraints weight = 3643.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.130001 restraints weight = 3314.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4699  Z= 0.155
  Angle     :  0.566   5.181   6372  Z= 0.294
  Chirality :  0.044   0.149    693
  Planarity :  0.004   0.034    825
  Dihedral  :  4.309  17.627    620
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.71 %
    Favored  : 83.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.71 (0.35), residues: 565
  helix:  0.04 (0.34), residues: 227
  sheet: -1.53 (0.57), residues: 77
  loop : -0.44 (0.40), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 270 
 TYR   0.009   0.001   TYR C 142 
 PHE   0.011   0.001   PHE C 399 
 TRP   0.008   0.001   TRP B  88 
 HIS   0.002   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4699)
  covalent geometry    : angle       0.56614 ( 6372)
  hydrogen bonds       : bond        0.03191 (  182)
  hydrogen bonds       : angle       5.47312 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   97 GLN cc_start: 0.7641 (mm-40) cc_final: 0.7389 (mm-40)
REVERT: B   99 THR cc_start: 0.8297 (p) cc_final: 0.7852 (t)
REVERT: B  125 ASN cc_start: 0.8708 (m-40) cc_final: 0.8480 (m-40)
REVERT: C   15 SER cc_start: 0.8540 (p) cc_final: 0.8166 (t)
REVERT: C  229 MET cc_start: 0.7314 (tmm) cc_final: 0.6766 (tmm)
REVERT: C  274 ASP cc_start: 0.7274 (t70) cc_final: 0.6792 (t0)
REVERT: C  401 MET cc_start: 0.8185 (mmm) cc_final: 0.7919 (mmt)
  outliers start: 8
  outliers final: 7
  residues processed: 108
  average time/residue: 0.0595
  time to fit residues: 8.7503
Evaluate side-chains
  99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 53 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 303 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.153092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.123572 restraints weight = 7374.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.126089 restraints weight = 5336.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.127882 restraints weight = 4307.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.128850 restraints weight = 3681.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.129873 restraints weight = 3334.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.3042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4699  Z= 0.144
  Angle     :  0.557   5.254   6372  Z= 0.290
  Chirality :  0.044   0.151    693
  Planarity :  0.004   0.036    825
  Dihedral  :  4.289  18.905    620
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.90 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.52 (0.36), residues: 565
  helix:  0.28 (0.35), residues: 225
  sheet: -1.46 (0.59), residues: 77
  loop : -0.40 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 270 
 TYR   0.018   0.001   TYR C 252 
 PHE   0.010   0.001   PHE C 399 
 TRP   0.008   0.001   TRP C 248 
 HIS   0.009   0.001   HIS C 303 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 4699)
  covalent geometry    : angle       0.55691 ( 6372)
  hydrogen bonds       : bond        0.02963 (  182)
  hydrogen bonds       : angle       5.26825 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 THR cc_start: 0.8240 (p) cc_final: 0.7770 (t)
REVERT: B  125 ASN cc_start: 0.8718 (m-40) cc_final: 0.8498 (m-40)
REVERT: C   15 SER cc_start: 0.8566 (p) cc_final: 0.8182 (t)
REVERT: C  229 MET cc_start: 0.7283 (tmm) cc_final: 0.6775 (tmm)
REVERT: C  274 ASP cc_start: 0.7242 (t70) cc_final: 0.6775 (t0)
  outliers start: 11
  outliers final: 8
  residues processed: 102
  average time/residue: 0.0601
  time to fit residues: 8.3218
Evaluate side-chains
  96 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue  160 LEU
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9980
   chunk 46 optimal weight:    0.0030
   chunk 20 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 53 optimal weight:    0.6980
   overall best weight:    0.6590

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.167233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.133400 restraints weight = 7802.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.137477 restraints weight = 4847.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.140258 restraints weight = 3560.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.142218 restraints weight = 2909.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.143082 restraints weight = 2522.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4699  Z= 0.152
  Angle     :  0.553   5.560   6372  Z= 0.287
  Chirality :  0.043   0.155    693
  Planarity :  0.004   0.035    825
  Dihedral  :  4.247  19.400    620
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.88 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.35 (0.36), residues: 565
  helix:  0.45 (0.35), residues: 226
  sheet: -1.41 (0.60), residues: 77
  loop : -0.31 (0.40), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 270 
 TYR   0.019   0.001   TYR C 252 
 PHE   0.010   0.001   PHE C 399 
 TRP   0.009   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 4699)
  covalent geometry    : angle       0.55309 ( 6372)
  hydrogen bonds       : bond        0.02890 (  182)
  hydrogen bonds       : angle       5.12948 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: B   99 THR cc_start: 0.8463 (p) cc_final: 0.7982 (t)
REVERT: B  125 ASN cc_start: 0.8716 (m-40) cc_final: 0.8468 (m-40)
REVERT: C   15 SER cc_start: 0.8687 (p) cc_final: 0.8444 (t)
REVERT: C  229 MET cc_start: 0.7630 (tmm) cc_final: 0.6993 (tmm)
REVERT: C  274 ASP cc_start: 0.7332 (t70) cc_final: 0.6759 (t0)
REVERT: C  333 ILE cc_start: 0.6950 (OUTLIER) cc_final: 0.6615 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0553
  time to fit residues: 7.4067
Evaluate side-chains
  95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue  134 ILE
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  333 ILE
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 41 optimal weight:    0.3980
   chunk 54 optimal weight:    0.1980
   chunk 11 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
C 206 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.165464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.134787 restraints weight = 7850.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.138539 restraints weight = 5010.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.141218 restraints weight = 3730.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.143036 restraints weight = 3043.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.144241 restraints weight = 2642.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4699  Z= 0.132
  Angle     :  0.535   5.293   6372  Z= 0.280
  Chirality :  0.043   0.156    693
  Planarity :  0.004   0.034    825
  Dihedral  :  4.174  19.533    620
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.25 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.27 (0.36), residues: 565
  helix:  0.58 (0.35), residues: 226
  sheet: -1.08 (0.58), residues: 81
  loop : -0.42 (0.41), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  55 
 TYR   0.008   0.001   TYR C 142 
 PHE   0.009   0.001   PHE C 399 
 TRP   0.009   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4699)
  covalent geometry    : angle       0.53477 ( 6372)
  hydrogen bonds       : bond        0.02684 (  182)
  hydrogen bonds       : angle       4.99969 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 ASN cc_start: 0.8796 (m-40) cc_final: 0.8550 (m-40)
REVERT: C   15 SER cc_start: 0.8647 (p) cc_final: 0.8422 (t)
REVERT: C  229 MET cc_start: 0.7520 (tmm) cc_final: 0.6943 (tmm)
REVERT: C  274 ASP cc_start: 0.7333 (OUTLIER) cc_final: 0.6743 (t0)
REVERT: C  333 ILE cc_start: 0.7090 (OUTLIER) cc_final: 0.6705 (mp)
  outliers start: 13
  outliers final: 7
  residues processed: 93
  average time/residue: 0.0526
  time to fit residues: 6.8823
Evaluate side-chains
  93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  274 ASP
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  333 ILE
Chi-restraints excluded: chain C residue  394 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 8 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 18 optimal weight:    0.3980
   chunk 49 optimal weight:    9.9990
   chunk 19 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.165608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.133644 restraints weight = 7779.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.137735 restraints weight = 4833.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.140471 restraints weight = 3527.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.142356 restraints weight = 2870.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.143628 restraints weight = 2491.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.3433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4699  Z= 0.142
  Angle     :  0.546   7.214   6372  Z= 0.286
  Chirality :  0.043   0.162    693
  Planarity :  0.004   0.033    825
  Dihedral  :  4.156  20.135    620
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 20.00 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.25 (0.36), residues: 565
  helix:  0.62 (0.35), residues: 226
  sheet: -1.29 (0.56), residues: 82
  loop : -0.36 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  55 
 TYR   0.008   0.001   TYR C 142 
 PHE   0.021   0.001   PHE C 399 
 TRP   0.008   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4699)
  covalent geometry    : angle       0.54632 ( 6372)
  hydrogen bonds       : bond        0.02731 (  182)
  hydrogen bonds       : angle       4.98734 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 ASN cc_start: 0.8746 (m-40) cc_final: 0.8466 (m-40)
REVERT: C   15 SER cc_start: 0.8681 (p) cc_final: 0.8471 (t)
REVERT: C  229 MET cc_start: 0.7634 (tmm) cc_final: 0.7052 (tmm)
REVERT: C  274 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.6741 (t0)
REVERT: C  333 ILE cc_start: 0.7187 (OUTLIER) cc_final: 0.6707 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0515
  time to fit residues: 6.5519
Evaluate side-chains
  91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  274 ASP
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  333 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:    0.0980
   chunk 21 optimal weight:    1.9990
   chunk 53 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.165313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133231 restraints weight = 7902.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137280 restraints weight = 4892.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.140015 restraints weight = 3580.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.141937 restraints weight = 2917.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.143189 restraints weight = 2526.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4699  Z= 0.145
  Angle     :  0.566   8.735   6372  Z= 0.290
  Chirality :  0.043   0.163    693
  Planarity :  0.003   0.034    825
  Dihedral  :  4.154  22.212    620
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 12.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 19.80 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.16 (0.36), residues: 565
  helix:  0.63 (0.35), residues: 226
  sheet: -0.94 (0.56), residues: 88
  loop : -0.33 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  55 
 TYR   0.008   0.001   TYR C 142 
 PHE   0.025   0.001   PHE C 399 
 TRP   0.008   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4699)
  covalent geometry    : angle       0.56563 ( 6372)
  hydrogen bonds       : bond        0.02707 (  182)
  hydrogen bonds       : angle       4.99015 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 ASN cc_start: 0.8770 (m-40) cc_final: 0.8484 (m-40)
REVERT: C   15 SER cc_start: 0.8677 (p) cc_final: 0.8459 (t)
REVERT: C  229 MET cc_start: 0.7606 (tmm) cc_final: 0.7065 (tmm)
REVERT: C  274 ASP cc_start: 0.7375 (OUTLIER) cc_final: 0.6776 (t0)
REVERT: C  333 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6754 (mp)
  outliers start: 13
  outliers final: 9
  residues processed: 90
  average time/residue: 0.0518
  time to fit residues: 6.6003
Evaluate side-chains
  94 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  274 ASP
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  333 ILE
Chi-restraints excluded: chain C residue  380 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 45 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.165223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.133342 restraints weight = 7732.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137346 restraints weight = 4826.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.140058 restraints weight = 3541.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.141811 restraints weight = 2892.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.143154 restraints weight = 2527.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4699  Z= 0.143
  Angle     :  0.565   8.138   6372  Z= 0.291
  Chirality :  0.043   0.164    693
  Planarity :  0.003   0.034    825
  Dihedral  :  4.152  23.532    620
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.20 %
    Favored  : 77.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.13 (0.36), residues: 565
  helix:  0.63 (0.35), residues: 226
  sheet: -0.91 (0.56), residues: 89
  loop : -0.29 (0.42), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  55 
 TYR   0.009   0.001   TYR C 142 
 PHE   0.017   0.001   PHE C 399 
 TRP   0.008   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4699)
  covalent geometry    : angle       0.56486 ( 6372)
  hydrogen bonds       : bond        0.02707 (  182)
  hydrogen bonds       : angle       4.95259 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 ASN cc_start: 0.8775 (m-40) cc_final: 0.8491 (m-40)
REVERT: C   15 SER cc_start: 0.8679 (p) cc_final: 0.8476 (t)
REVERT: C  229 MET cc_start: 0.7617 (tmm) cc_final: 0.7080 (tmm)
REVERT: C  274 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6799 (t0)
REVERT: C  333 ILE cc_start: 0.7130 (OUTLIER) cc_final: 0.6795 (mp)
REVERT: C  352 PHE cc_start: 0.8335 (m-80) cc_final: 0.7946 (m-10)
  outliers start: 13
  outliers final: 9
  residues processed: 92
  average time/residue: 0.0508
  time to fit residues: 6.6802
Evaluate side-chains
  93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  274 ASP
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  333 ILE
Chi-restraints excluded: chain C residue  380 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 47 optimal weight:    0.6980
   chunk 44 optimal weight:    0.3980
   chunk 49 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0170
   chunk 35 optimal weight:    2.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.165166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.133097 restraints weight = 7777.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137108 restraints weight = 4830.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139898 restraints weight = 3551.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.141556 restraints weight = 2881.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.142999 restraints weight = 2522.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4699  Z= 0.142
  Angle     :  0.579   8.002   6372  Z= 0.297
  Chirality :  0.044   0.171    693
  Planarity :  0.003   0.036    825
  Dihedral  :  4.172  24.368    620
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 19.80 %
    Favored  : 77.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.12 (0.37), residues: 565
  helix:  0.56 (0.35), residues: 226
  sheet: -0.74 (0.57), residues: 90
  loop : -0.26 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  55 
 TYR   0.011   0.001   TYR C 142 
 PHE   0.014   0.001   PHE C 399 
 TRP   0.008   0.001   TRP C 248 
 HIS   0.002   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4699)
  covalent geometry    : angle       0.57944 ( 6372)
  hydrogen bonds       : bond        0.02718 (  182)
  hydrogen bonds       : angle       4.98991 (  525)

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

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

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1130 Ramachandran restraints generated.
    565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: B  125 ASN cc_start: 0.8764 (m-40) cc_final: 0.8483 (m-40)
REVERT: C   15 SER cc_start: 0.8697 (p) cc_final: 0.8474 (t)
REVERT: C  229 MET cc_start: 0.7619 (tmm) cc_final: 0.7101 (tmm)
REVERT: C  274 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6791 (t0)
REVERT: C  333 ILE cc_start: 0.7118 (OUTLIER) cc_final: 0.6800 (mp)
REVERT: C  352 PHE cc_start: 0.8323 (m-80) cc_final: 0.7934 (m-10)
  outliers start: 12
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0491
  time to fit residues: 6.6256
Evaluate side-chains
  93 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue  131 THR
Chi-restraints excluded: chain C residue   12 THR
Chi-restraints excluded: chain C residue   16 LEU
Chi-restraints excluded: chain C residue   37 CYS
Chi-restraints excluded: chain C residue   78 LEU
Chi-restraints excluded: chain C residue  177 VAL
Chi-restraints excluded: chain C residue  274 ASP
Chi-restraints excluded: chain C residue  303 HIS
Chi-restraints excluded: chain C residue  333 ILE
Chi-restraints excluded: chain C residue  380 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 48 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    0.3980
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
C 133 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.162795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131320 restraints weight = 7911.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.134877 restraints weight = 5203.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.137358 restraints weight = 3947.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.138985 restraints weight = 3277.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139585 restraints weight = 2897.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4699  Z= 0.198
  Angle     :  0.625   7.244   6372  Z= 0.318
  Chirality :  0.045   0.171    693
  Planarity :  0.004   0.036    825
  Dihedral  :  4.311  25.321    620
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 20.00 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.45 %
    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: -0.25 (0.36), residues: 565
  helix:  0.43 (0.35), residues: 226
  sheet: -0.99 (0.56), residues: 90
  loop : -0.22 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  55 
 TYR   0.012   0.001   TYR C 142 
 PHE   0.012   0.002   PHE C 249 
 TRP   0.009   0.001   TRP C 248 
 HIS   0.003   0.001   HIS B  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00472 ( 4699)
  covalent geometry    : angle       0.62538 ( 6372)
  hydrogen bonds       : bond        0.02921 (  182)
  hydrogen bonds       : angle       5.17636 (  525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1111.35 seconds
wall clock time: 19 minutes 53.52 seconds (1193.52 seconds total)