Starting phenix.real_space_refine
on Tue Mar  3 12:18:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6wm0_21846/03_2026/6wm0_21846.map"
  }
  resolution = 3.52
  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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     K       5      8.98       5
     S      14      5.16       5
     C    2740      2.51       5
     N     666      2.21       5
     O     680      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4105
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2050
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 9, 'TRANS': 245}
    Chain: "B"
      Number of atoms: 2050
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 2050
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 9, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {'  K': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
  Time building chain proxies: 1.25, per 1000 atoms: 0.30
  Number of scatterers: 4105
  At special positions: 0
  Unit cell: (62.535, 76.179, 94.371, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     K       5     19.00
     S      14     16.00
     O     680      8.00
     N     666      7.00
     C    2740      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  51 " - pdb=" SG  CYS B  51 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 186.0 milliseconds
  

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  940

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      80.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 27
      removed outlier: 4.341A  pdb=" N   PHE A  14 " --> pdb=" O   SER A  10 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   VAL A  25 " --> pdb=" O   ALA A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 49
    Processing helix  chain 'A' and resid 53 through 69
      removed outlier: 3.765A  pdb=" N   LYS A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   ALA A  67 " --> pdb=" O   VAL A  63 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ASP A  69 " --> pdb=" O   SER A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 97
      removed outlier: 3.815A  pdb=" N   ALA A  93 " --> pdb=" O   MET A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 152
      removed outlier: 3.821A  pdb=" N   VAL A 116 " --> pdb=" O   ARG A 112 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   PHE A 117 " --> pdb=" O   LEU A 113 " (cutoff:3.500A)
      Proline residue:  A 124  - end of helix
      removed outlier: 3.737A  pdb=" N   THR A 128 " --> pdb=" O   PRO A 124 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER A 131 " --> pdb=" O   LEU A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 176
    Processing helix  chain 'A' and resid 177 through 187
      removed outlier: 3.724A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 202
    Processing helix  chain 'A' and resid 222 through 260
      removed outlier: 4.343A  pdb=" N   LYS A 257 " --> pdb=" O   HIS A 253 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LYS A 258 " --> pdb=" O   LYS A 254 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG A 259 " --> pdb=" O   ALA A 255 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 49
      removed outlier: 4.043A  pdb=" N   ALA B  11 " --> pdb=" O   LEU B   7 " (cutoff:3.500A)
      Proline residue:  B  29  - end of helix
      removed outlier: 3.615A  pdb=" N   LEU B  46 " --> pdb=" O   LYS B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 71
      removed outlier: 3.593A  pdb=" N   ALA B  68 " --> pdb=" O   VAL B  64 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASP B  69 " --> pdb=" O   SER B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 84 through 97
      removed outlier: 3.523A  pdb=" N   ILE B  90 " --> pdb=" O   PRO B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 152
      removed outlier: 3.867A  pdb=" N   VAL B 116 " --> pdb=" O   ARG B 112 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE B 117 " --> pdb=" O   LEU B 113 " (cutoff:3.500A)
      Proline residue:  B 124  - end of helix
      removed outlier: 3.694A  pdb=" N   THR B 128 " --> pdb=" O   PRO B 124 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   SER B 131 " --> pdb=" O   LEU B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 157 through 176
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.722A  pdb=" N   VAL B 181 " --> pdb=" O   ILE B 177 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 202
    Processing helix  chain 'B' and resid 222 through 260
      removed outlier: 3.731A  pdb=" N   LYS B 254 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   LYS B 257 " --> pdb=" O   HIS B 253 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LYS B 258 " --> pdb=" O   LYS B 254 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ARG B 259 " --> pdb=" O   ALA B 255 " (cutoff:3.500A)

    303 hydrogen bonds defined for protein.
    909 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: 0.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1221
        1.34 -     1.46: 926
        1.46 -     1.57: 2061
        1.57 -     1.69: 0
        1.69 -     1.81: 20
  Bond restraints: 4228
  Sorted by residual:
  bond pdb=" CG1 ILE A  12 "
       pdb=" CD1 ILE A  12 "
    ideal  model  delta    sigma   weight residual
    1.513  1.476  0.037 3.90e-02 6.57e+02 8.96e-01
  bond pdb=" C   PRO A 178 "
       pdb=" N   PRO A 179 "
    ideal  model  delta    sigma   weight residual
    1.333  1.346 -0.013 1.44e-02 4.82e+03 8.38e-01
  bond pdb=" C   GLU B  28 "
       pdb=" N   PRO B  29 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.012 1.36e-02 5.41e+03 8.31e-01
  bond pdb=" CA  VAL A 213 "
       pdb=" CB  VAL A 213 "
    ideal  model  delta    sigma   weight residual
    1.533  1.544 -0.011 1.26e-02 6.30e+03 7.74e-01
  bond pdb=" CB  CYS A  51 "
       pdb=" SG  CYS A  51 "
    ideal  model  delta    sigma   weight residual
    1.808  1.780  0.028 3.30e-02 9.18e+02 7.29e-01
  ... (remaining 4223 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 5466
        1.24 -     2.48: 248
        2.48 -     3.72: 25
        3.72 -     4.96: 13
        4.96 -     6.20: 4
  Bond angle restraints: 5756
  Sorted by residual:
  angle pdb=" N   VAL A  25 "
        pdb=" CA  VAL A  25 "
        pdb=" C   VAL A  25 "
      ideal   model   delta    sigma   weight residual
     112.96  109.38    3.58 1.00e+00 1.00e+00 1.28e+01
  angle pdb=" N   PRO B 178 "
        pdb=" CA  PRO B 178 "
        pdb=" C   PRO B 178 "
      ideal   model   delta    sigma   weight residual
     110.70  113.86   -3.16 1.22e+00 6.72e-01 6.73e+00
  angle pdb=" N   PRO A 178 "
        pdb=" CA  PRO A 178 "
        pdb=" C   PRO A 178 "
      ideal   model   delta    sigma   weight residual
     110.70  113.82   -3.12 1.22e+00 6.72e-01 6.54e+00
  angle pdb=" N   PHE A  91 "
        pdb=" CA  PHE A  91 "
        pdb=" C   PHE A  91 "
      ideal   model   delta    sigma   weight residual
     111.28  109.01    2.27 1.09e+00 8.42e-01 4.34e+00
  angle pdb=" N   ILE B  96 "
        pdb=" CA  ILE B  96 "
        pdb=" C   ILE B  96 "
      ideal   model   delta    sigma   weight residual
     109.34  113.56   -4.22 2.08e+00 2.31e-01 4.12e+00
  ... (remaining 5751 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.57: 2102
       15.57 -    31.14: 224
       31.14 -    46.72: 57
       46.72 -    62.29: 9
       62.29 -    77.86: 5
  Dihedral angle restraints: 2397
    sinusoidal: 925
      harmonic: 1472
  Sorted by residual:
  dihedral pdb=" CB  CYS A  51 "
           pdb=" SG  CYS A  51 "
           pdb=" SG  CYS B  51 "
           pdb=" CB  CYS B  51 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  157.47  -64.47     1      1.00e+01 1.00e-02 5.46e+01
  dihedral pdb=" N   LYS A  42 "
           pdb=" CA  LYS A  42 "
           pdb=" CB  LYS A  42 "
           pdb=" CG  LYS A  42 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -121.51  -58.49     3      1.50e+01 4.44e-03 9.47e+00
  dihedral pdb=" CA  GLU A 187 "
           pdb=" C   GLU A 187 "
           pdb=" N   TRP A 188 "
           pdb=" CA  TRP A 188 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.77   15.23     0      5.00e+00 4.00e-02 9.28e+00
  ... (remaining 2394 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 349
       0.024 -    0.047: 148
       0.047 -    0.070: 90
       0.070 -    0.094: 38
       0.094 -    0.117: 13
  Chirality restraints: 638
  Sorted by residual:
  chirality pdb=" CA  PRO A 179 "
            pdb=" N   PRO A 179 "
            pdb=" C   PRO A 179 "
            pdb=" CB  PRO A 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.43e-01
  chirality pdb=" CA  PRO B 179 "
            pdb=" N   PRO B 179 "
            pdb=" C   PRO B 179 "
            pdb=" CB  PRO B 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.40e-01
  chirality pdb=" CA  VAL A 153 "
            pdb=" N   VAL A 153 "
            pdb=" C   VAL A 153 "
            pdb=" CB  VAL A 153 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 3.03e-01
  ... (remaining 635 not shown)

  Planarity restraints: 702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B 214 "    0.019 5.00e-02 4.00e+02   2.89e-02 1.34e+00
        pdb=" N   PRO B 215 "   -0.050 5.00e-02 4.00e+02
        pdb=" CA  PRO B 215 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 215 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 253 "    0.006 2.00e-02 2.50e+03   8.75e-03 1.15e+00
        pdb=" CG  HIS B 253 "   -0.018 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 253 "    0.007 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 253 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 253 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 253 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A  28 "    0.017 5.00e-02 4.00e+02   2.61e-02 1.09e+00
        pdb=" N   PRO A  29 "   -0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A  29 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  29 "    0.015 5.00e-02 4.00e+02
  ... (remaining 699 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.85: 1466
        2.85 -     3.42: 4842
        3.42 -     4.00: 7303
        4.00 -     4.57: 10768
        4.57 -     5.14: 15086
  Nonbonded interactions: 39465
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A   9 "
            pdb=" NE1 TRP B 129 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" O   LEU A 125 "
            pdb=" OG1 THR A 128 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   ALA B 158 "
            pdb=" OG1 THR B 161 "
     model   vdw
     2.355 3.040
  nonbonded pdb=" OE1 GLU A 186 "
            pdb=" OH  TYR A 219 "
     model   vdw
     2.373 3.040
  nonbonded pdb=" O   GLN B 159 "
            pdb=" OG1 THR B 163 "
     model   vdw
     2.392 3.040
  ... (remaining 39460 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 6 through 260)
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.810
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.530
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  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:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
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      :  0.003   0.042   4229  Z= 0.158
  Angle     :  0.586   6.204   5758  Z= 0.351
  Chirality :  0.038   0.117    638
  Planarity :  0.003   0.029    702
  Dihedral  : 14.115  77.859   1454
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  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 are not related in a simple way.
  whole: -0.89 (0.35), residues: 506
  helix: -0.19 (0.24), residues: 382
  sheet:  None (None), residues: 0
  loop : -1.47 (0.59), residues: 124

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 140 
 TYR   0.017   0.001   TYR B 195 
 PHE   0.008   0.001   PHE A  49 
 TRP   0.005   0.001   TRP B 230 
 HIS   0.011   0.002   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 4228)
  covalent geometry    : angle       0.58528 ( 5756)
  SS BOND              : bond        0.00254 (    1)
  SS BOND              : angle       2.00034 (    2)
  hydrogen bonds       : bond        0.13583 (  303)
  hydrogen bonds       : angle       6.21268 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ILE cc_start: 0.8533 (pt) cc_final: 0.8287 (mp)
REVERT: B  166 PHE cc_start: 0.7812 (t80) cc_final: 0.7460 (t80)
REVERT: B  199 ILE cc_start: 0.8209 (tt) cc_final: 0.7941 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.0736
  time to fit residues: 10.4009
Evaluate side-chains
  86 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 19 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
A 218 ASN
B  44 HIS
B  77 ASN
B  78 GLN
B 146 GLN
B 218 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.137719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.107512 restraints weight = 6667.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.109977 restraints weight = 3773.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.111554 restraints weight = 2740.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.112373 restraints weight = 2288.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.112658 restraints weight = 2077.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.1830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4229  Z= 0.145
  Angle     :  0.561   5.935   5758  Z= 0.298
  Chirality :  0.043   0.252    638
  Planarity :  0.004   0.031    702
  Dihedral  :  4.376  14.314    550
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 12.68 %
    Favored  : 86.15 %
  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 are not related in a simple way.
  whole:  0.85 (0.37), residues: 506
  helix:  1.26 (0.25), residues: 392
  sheet:  None (None), residues: 0
  loop : -1.82 (0.56), residues: 114

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 140 
 TYR   0.015   0.001   TYR B 195 
 PHE   0.032   0.001   PHE A 147 
 TRP   0.009   0.001   TRP A 188 
 HIS   0.011   0.002   HIS A  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 4228)
  covalent geometry    : angle       0.56024 ( 5756)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       1.92591 (    2)
  hydrogen bonds       : bond        0.04238 (  303)
  hydrogen bonds       : angle       4.40883 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  166 PHE cc_start: 0.8126 (t80) cc_final: 0.7879 (t80)
REVERT: B  199 ILE cc_start: 0.8113 (tt) cc_final: 0.7791 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 103
  average time/residue: 0.0752
  time to fit residues: 9.3757
Evaluate side-chains
  87 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   89 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 14 optimal weight:    9.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 39 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  44 HIS
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  77 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.138504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.106944 restraints weight = 6623.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.109440 restraints weight = 3933.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.111042 restraints weight = 2915.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.111549 restraints weight = 2449.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.112294 restraints weight = 2279.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4229  Z= 0.139
  Angle     :  0.536   6.009   5758  Z= 0.287
  Chirality :  0.040   0.134    638
  Planarity :  0.004   0.029    702
  Dihedral  :  4.163  14.486    550
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 14.32 %
    Favored  : 83.80 %
  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 are not related in a simple way.
  whole:  1.85 (0.38), residues: 506
  helix:  1.96 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -1.31 (0.59), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 140 
 TYR   0.013   0.001   TYR B 195 
 PHE   0.040   0.001   PHE A 147 
 TRP   0.007   0.001   TRP B 188 
 HIS   0.004   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 4228)
  covalent geometry    : angle       0.53533 ( 5756)
  SS BOND              : bond        0.00228 (    1)
  SS BOND              : angle       1.85537 (    2)
  hydrogen bonds       : bond        0.03916 (  303)
  hydrogen bonds       : angle       4.11514 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 LYS cc_start: 0.9295 (ptmt) cc_final: 0.8918 (ttpp)
REVERT: B  166 PHE cc_start: 0.8094 (t80) cc_final: 0.7791 (t80)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0650
  time to fit residues: 7.8713
Evaluate side-chains
  92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  176 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 21 optimal weight:    0.0570
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 14 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.6898

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
B 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.143043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.111377 restraints weight = 6295.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.113803 restraints weight = 3783.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.115029 restraints weight = 2829.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.116218 restraints weight = 2434.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116477 restraints weight = 2207.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.2469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4229  Z= 0.122
  Angle     :  0.535   8.527   5758  Z= 0.280
  Chirality :  0.044   0.331    638
  Planarity :  0.004   0.031    702
  Dihedral  :  4.002  14.080    550
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 14.32 %
    Favored  : 83.57 %
  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 are not related in a simple way.
  whole:  2.29 (0.38), residues: 506
  helix:  2.28 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -1.16 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 140 
 TYR   0.012   0.001   TYR B 195 
 PHE   0.049   0.001   PHE A 147 
 TRP   0.007   0.001   TRP B 244 
 HIS   0.003   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4228)
  covalent geometry    : angle       0.53444 ( 5756)
  SS BOND              : bond        0.00166 (    1)
  SS BOND              : angle       1.68808 (    2)
  hydrogen bonds       : bond        0.03691 (  303)
  hydrogen bonds       : angle       4.00522 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 LYS cc_start: 0.9270 (ptmt) cc_final: 0.8927 (ttpp)
  outliers start: 9
  outliers final: 6
  residues processed: 100
  average time/residue: 0.0747
  time to fit residues: 9.1673
Evaluate side-chains
  96 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    7.9990
   chunk 48 optimal weight:    5.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.141876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.108625 restraints weight = 6342.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.110904 restraints weight = 3972.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.112002 restraints weight = 3025.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.113162 restraints weight = 2640.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.113475 restraints weight = 2413.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4229  Z= 0.164
  Angle     :  0.557   6.291   5758  Z= 0.298
  Chirality :  0.041   0.122    638
  Planarity :  0.004   0.029    702
  Dihedral  :  4.054  14.875    550
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 16.67 %
    Favored  : 81.22 %
  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 are not related in a simple way.
  whole:  2.39 (0.39), residues: 506
  helix:  2.33 (0.26), residues: 388
  sheet:  None (None), residues: 0
  loop : -1.04 (0.60), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 140 
 TYR   0.016   0.001   TYR B 195 
 PHE   0.035   0.002   PHE A 147 
 TRP   0.007   0.001   TRP B 244 
 HIS   0.003   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 4228)
  covalent geometry    : angle       0.55591 ( 5756)
  SS BOND              : bond        0.00396 (    1)
  SS BOND              : angle       2.21427 (    2)
  hydrogen bonds       : bond        0.03857 (  303)
  hydrogen bonds       : angle       4.01993 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.116 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 LYS cc_start: 0.9265 (ptmt) cc_final: 0.8879 (ttpp)
  outliers start: 9
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0716
  time to fit residues: 8.4176
Evaluate side-chains
  90 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  220 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 46 optimal weight:    0.3980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
B 146 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.145345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.110764 restraints weight = 6592.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.113176 restraints weight = 4188.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.114603 restraints weight = 3221.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115575 restraints weight = 2770.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.115970 restraints weight = 2540.678|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4229  Z= 0.133
  Angle     :  0.565   7.832   5758  Z= 0.301
  Chirality :  0.043   0.225    638
  Planarity :  0.004   0.030    702
  Dihedral  :  3.976  14.096    550
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 17.61 %
    Favored  : 80.05 %
  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 are not related in a simple way.
  whole:  2.55 (0.39), residues: 506
  helix:  2.39 (0.26), residues: 390
  sheet:  None (None), residues: 0
  loop : -0.84 (0.60), residues: 116

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 143 
 TYR   0.014   0.001   TYR B 195 
 PHE   0.034   0.001   PHE A 147 
 TRP   0.008   0.001   TRP B 244 
 HIS   0.002   0.001   HIS B 253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4228)
  covalent geometry    : angle       0.56363 ( 5756)
  SS BOND              : bond        0.00238 (    1)
  SS BOND              : angle       1.83589 (    2)
  hydrogen bonds       : bond        0.03661 (  303)
  hydrogen bonds       : angle       3.97179 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 8
  residues processed: 95
  average time/residue: 0.0627
  time to fit residues: 7.2961
Evaluate side-chains
  93 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  165 ILE
Chi-restraints excluded: chain B residue  220 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** 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 = 0.3797 r_free = 0.3797 target = 0.141216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.107325 restraints weight = 6609.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.109661 restraints weight = 4042.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.111090 restraints weight = 3059.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.111820 restraints weight = 2622.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112384 restraints weight = 2418.038|
|-----------------------------------------------------------------------------|
r_work (final): 0.3413
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4229  Z= 0.135
  Angle     :  0.591  11.299   5758  Z= 0.306
  Chirality :  0.045   0.347    638
  Planarity :  0.004   0.030    702
  Dihedral  :  3.919  13.798    550
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 18.31 %
    Favored  : 79.34 %
  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 are not related in a simple way.
  whole:  2.81 (0.39), residues: 506
  helix:  2.47 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.18 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 259 
 TYR   0.013   0.001   TYR B 195 
 PHE   0.034   0.001   PHE A 147 
 TRP   0.010   0.001   TRP B 244 
 HIS   0.002   0.001   HIS A  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 4228)
  covalent geometry    : angle       0.59065 ( 5756)
  SS BOND              : bond        0.00230 (    1)
  SS BOND              : angle       1.77294 (    2)
  hydrogen bonds       : bond        0.03585 (  303)
  hydrogen bonds       : angle       3.96010 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 GLN cc_start: 0.8337 (tp40) cc_final: 0.7962 (tp40)
  outliers start: 10
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0711
  time to fit residues: 8.5376
Evaluate side-chains
  92 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  165 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 34 optimal weight:    0.2980
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   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 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 GLN ** 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 = 0.3849 r_free = 0.3849 target = 0.146359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.111727 restraints weight = 6501.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.114144 restraints weight = 4114.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.115514 restraints weight = 3146.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116619 restraints weight = 2714.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116619 restraints weight = 2479.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4229  Z= 0.131
  Angle     :  0.625  13.895   5758  Z= 0.322
  Chirality :  0.046   0.392    638
  Planarity :  0.004   0.038    702
  Dihedral  :  3.869  13.420    550
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.72 %
    Favored  : 78.17 %
  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 are not related in a simple way.
  whole:  2.91 (0.39), residues: 506
  helix:  2.54 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.13 (0.65), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 259 
 TYR   0.012   0.001   TYR B 195 
 PHE   0.064   0.002   PHE B 147 
 TRP   0.011   0.001   TRP B 244 
 HIS   0.003   0.001   HIS B  30 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 4228)
  covalent geometry    : angle       0.62446 ( 5756)
  SS BOND              : bond        0.00174 (    1)
  SS BOND              : angle       1.61398 (    2)
  hydrogen bonds       : bond        0.03476 (  303)
  hydrogen bonds       : angle       3.93929 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   54 GLN cc_start: 0.8237 (tp40) cc_final: 0.7986 (tp40)
  outliers start: 9
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0739
  time to fit residues: 8.5210
Evaluate side-chains
  95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Chi-restraints excluded: chain B residue  165 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:    0.0270
   chunk 14 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 20 optimal weight:    0.0970
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.5840

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 GLN ** 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 = 0.3864 r_free = 0.3864 target = 0.147418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.112652 restraints weight = 6628.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.115046 restraints weight = 4243.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.116617 restraints weight = 3271.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.117453 restraints weight = 2806.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.117519 restraints weight = 2582.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8009
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4229  Z= 0.124
  Angle     :  0.605  12.586   5758  Z= 0.309
  Chirality :  0.045   0.371    638
  Planarity :  0.004   0.031    702
  Dihedral  :  3.784  14.082    550
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 20.42 %
    Favored  : 77.46 %
  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 are not related in a simple way.
  whole:  3.04 (0.39), residues: 506
  helix:  2.64 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.14 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 259 
 TYR   0.011   0.001   TYR B 195 
 PHE   0.039   0.001   PHE B 147 
 TRP   0.014   0.001   TRP B 244 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4228)
  covalent geometry    : angle       0.60494 ( 5756)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       1.43870 (    2)
  hydrogen bonds       : bond        0.03435 (  303)
  hydrogen bonds       : angle       3.88757 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 9
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0750
  time to fit residues: 9.0262
Evaluate side-chains
  95 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 47 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 25 optimal weight:    0.0010
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 159 GLN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.146820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.112287 restraints weight = 6450.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.114589 restraints weight = 4168.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.115928 restraints weight = 3226.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116914 restraints weight = 2803.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117154 restraints weight = 2572.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4229  Z= 0.132
  Angle     :  0.632  14.926   5758  Z= 0.317
  Chirality :  0.047   0.408    638
  Planarity :  0.004   0.031    702
  Dihedral  :  3.761  12.961    550
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 19.48 %
    Favored  : 78.40 %
  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 are not related in a simple way.
  whole:  3.09 (0.38), residues: 506
  helix:  2.69 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.20 (0.62), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 259 
 TYR   0.012   0.001   TYR B 195 
 PHE   0.042   0.001   PHE B 147 
 TRP   0.015   0.001   TRP B 244 
 HIS   0.004   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 4228)
  covalent geometry    : angle       0.63179 ( 5756)
  SS BOND              : bond        0.00159 (    1)
  SS BOND              : angle       1.53293 (    2)
  hydrogen bonds       : bond        0.03451 (  303)
  hydrogen bonds       : angle       3.90974 (  909)

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

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

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1012 Ramachandran restraints generated.
    506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  159 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7474 (pp30)
  outliers start: 9
  outliers final: 8
  residues processed: 96
  average time/residue: 0.0725
  time to fit residues: 8.5293
Evaluate side-chains
  98 residues out of total 426 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLN
Chi-restraints excluded: chain A residue  159 GLN
Chi-restraints excluded: chain A residue  162 CYS
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain B residue   46 LEU
Chi-restraints excluded: chain B residue   78 GLN
Chi-restraints excluded: chain B residue   85 TRP
Chi-restraints excluded: chain B residue   89 MET
Chi-restraints excluded: chain B residue  162 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0030
   overall best weight:    0.5790

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

Flipped N/Q/H residues before XYZ refinement:
** A 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 ASN
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.147422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.112361 restraints weight = 6497.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.114726 restraints weight = 4193.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.116276 restraints weight = 3246.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.116881 restraints weight = 2801.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.117112 restraints weight = 2603.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3272

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4229  Z= 0.130
  Angle     :  0.628  14.136   5758  Z= 0.319
  Chirality :  0.047   0.401    638
  Planarity :  0.004   0.043    702
  Dihedral  :  3.758  12.687    550
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 20.19 %
    Favored  : 77.93 %
  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 are not related in a simple way.
  whole:  3.11 (0.38), residues: 506
  helix:  2.71 (0.26), residues: 386
  sheet:  None (None), residues: 0
  loop : -0.16 (0.61), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 259 
 TYR   0.011   0.001   TYR B 195 
 PHE   0.040   0.001   PHE B 147 
 TRP   0.068   0.002   TRP A 244 
 HIS   0.004   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4228)
  covalent geometry    : angle       0.62781 ( 5756)
  SS BOND              : bond        0.00133 (    1)
  SS BOND              : angle       1.41029 (    2)
  hydrogen bonds       : bond        0.03435 (  303)
  hydrogen bonds       : angle       3.90282 (  909)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 803.48 seconds
wall clock time: 14 minutes 33.14 seconds (873.14 seconds total)