Starting phenix.real_space_refine
on Sun Apr 27 00:57:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1z_36806/04_2025/8k1z_36806.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.074
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      32      5.16       5
     C    2706      2.51       5
     N     616      2.21       5
     O     700      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4059
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 1921
          Classifications: {'peptide': 242}
          Link IDs: {'PTRANS': 4, 'TRANS': 237}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 109
          Unusual residues: {'  K': 4, 'Y01': 3}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 106
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 106
          Unusual residues: {'  K': 1, 'Y01': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 3.46, per 1000 atoms: 0.85
  Number of scatterers: 4059
  At special positions: 0
  Unit cell: (64.9, 73.7, 89.1, 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      32     16.00
     O     700      8.00
     N     616      7.00
     C    2706      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: 1.85
  Conformation dependent library (CDL) restraints added in 541.3 milliseconds
  

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  896

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 53
      removed outlier: 5.621A  pdb=" N   ASP A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   HIS A  33 " --> pdb=" O   LEU A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 70
      removed outlier: 3.707A  pdb=" N   ARG A  60 " --> pdb=" O   SER A  56 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 71 through 75
    Processing helix  chain 'A' and resid 79 through 92
    Processing helix  chain 'A' and resid 103 through 147
      Proline residue:  A 119  - end of helix
    Processing helix  chain 'A' and resid 155 through 183
      removed outlier: 3.791A  pdb=" N   GLU A 183 " --> pdb=" O   SER A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 185 through 198
    Processing helix  chain 'A' and resid 212 through 217
    Processing helix  chain 'A' and resid 217 through 241
      removed outlier: 3.511A  pdb=" N   ASN A 240 " --> pdb=" O   GLY A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 248
      removed outlier: 3.611A  pdb=" N   THR A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3 through 53
      removed outlier: 5.619A  pdb=" N   ASP B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
      removed outlier: 5.063A  pdb=" N   HIS B  33 " --> pdb=" O   LEU B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 55 through 70
      removed outlier: 3.680A  pdb=" N   ARG B  60 " --> pdb=" O   SER B  56 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLN B  61 " --> pdb=" O   GLU B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 75
    Processing helix  chain 'B' and resid 79 through 92
    Processing helix  chain 'B' and resid 103 through 147
      Proline residue:  B 119  - end of helix
    Processing helix  chain 'B' and resid 155 through 180
    Processing helix  chain 'B' and resid 185 through 198
    Processing helix  chain 'B' and resid 212 through 217
    Processing helix  chain 'B' and resid 217 through 248
      removed outlier: 4.307A  pdb=" N   ARG B 245 " --> pdb=" O   LEU B 241 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE B 246 " --> pdb=" O   VAL B 242 " (cutoff:3.500A)

    328 hydrogen bonds defined for protein.
    972 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 673
        1.33 -     1.45: 1085
        1.45 -     1.57: 2350
        1.57 -     1.69: 0
        1.69 -     1.81: 48
  Bond restraints: 4156
  Sorted by residual:
  bond pdb=" CA  MET A 156 "
       pdb=" C   MET A 156 "
    ideal  model  delta    sigma   weight residual
    1.524  1.481  0.043 1.26e-02 6.30e+03 1.17e+01
  bond pdb=" CA  GLU B 157 "
       pdb=" C   GLU B 157 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.038 1.29e-02 6.01e+03 8.55e+00
  bond pdb=" C   GLU B 157 "
       pdb=" N   ASN B 158 "
    ideal  model  delta    sigma   weight residual
    1.335  1.296  0.039 1.36e-02 5.41e+03 8.03e+00
  bond pdb=" N   MET A 156 "
       pdb=" CA  MET A 156 "
    ideal  model  delta    sigma   weight residual
    1.459  1.425  0.034 1.20e-02 6.94e+03 7.97e+00
  bond pdb=" C   MET A 156 "
       pdb=" N   GLU A 157 "
    ideal  model  delta    sigma   weight residual
    1.335  1.310  0.025 1.30e-02 5.92e+03 3.81e+00
  ... (remaining 4151 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5483
        0.98 -     1.96: 114
        1.96 -     2.94: 24
        2.94 -     3.92: 12
        3.92 -     4.90: 11
  Bond angle restraints: 5644
  Sorted by residual:
  angle pdb=" N   VAL A 242 "
        pdb=" CA  VAL A 242 "
        pdb=" C   VAL A 242 "
      ideal   model   delta    sigma   weight residual
     113.71  109.72    3.99 9.50e-01 1.11e+00 1.76e+01
  angle pdb=" N   MET A 156 "
        pdb=" CA  MET A 156 "
        pdb=" C   MET A 156 "
      ideal   model   delta    sigma   weight residual
     111.14  107.73    3.41 1.08e+00 8.57e-01 9.95e+00
  angle pdb=" C   SER A 155 "
        pdb=" N   MET A 156 "
        pdb=" CA  MET A 156 "
      ideal   model   delta    sigma   weight residual
     120.44  116.32    4.12 1.36e+00 5.41e-01 9.20e+00
  angle pdb=" N   VAL A 243 "
        pdb=" CA  VAL A 243 "
        pdb=" C   VAL A 243 "
      ideal   model   delta    sigma   weight residual
     112.12  110.12    2.00 8.40e-01 1.42e+00 5.65e+00
  angle pdb=" C   LYS A   2 "
        pdb=" CA  LYS A   2 "
        pdb=" CB  LYS A   2 "
      ideal   model   delta    sigma   weight residual
     110.10  114.41   -4.31 1.90e+00 2.77e-01 5.13e+00
  ... (remaining 5639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.09: 2396
       16.09 -    32.18: 238
       32.18 -    48.27: 55
       48.27 -    64.36: 15
       64.36 -    80.44: 8
  Dihedral angle restraints: 2712
    sinusoidal: 1310
      harmonic: 1402
  Sorted by residual:
  dihedral pdb=" CG  ARG A   7 "
           pdb=" CD  ARG A   7 "
           pdb=" NE  ARG A   7 "
           pdb=" CZ  ARG A   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  130.50  -40.50     2      1.50e+01 4.44e-03 9.00e+00
  dihedral pdb=" CB  GLU B 130 "
           pdb=" CG  GLU B 130 "
           pdb=" CD  GLU B 130 "
           pdb=" OE1 GLU B 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.79  -79.79     1      3.00e+01 1.11e-03 8.78e+00
  dihedral pdb=" CB  GLU A 130 "
           pdb=" CG  GLU A 130 "
           pdb=" CD  GLU A 130 "
           pdb=" OE1 GLU A 130 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   79.69  -79.69     1      3.00e+01 1.11e-03 8.76e+00
  ... (remaining 2709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.022: 450
       0.022 -    0.043: 72
       0.043 -    0.065: 86
       0.065 -    0.087: 27
       0.087 -    0.108: 15
  Chirality restraints: 650
  Sorted by residual:
  chirality pdb=" CA  VAL B  76 "
            pdb=" N   VAL B  76 "
            pdb=" C   VAL B  76 "
            pdb=" CB  VAL B  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.94e-01
  chirality pdb=" CA  VAL A  76 "
            pdb=" N   VAL A  76 "
            pdb=" C   VAL A  76 "
            pdb=" CB  VAL A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.55   -0.11 2.00e-01 2.50e+01 2.79e-01
  chirality pdb=" CA  VAL A 206 "
            pdb=" N   VAL A 206 "
            pdb=" C   VAL A 206 "
            pdb=" CB  VAL A 206 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.54   -0.10 2.00e-01 2.50e+01 2.58e-01
  ... (remaining 647 not shown)

  Planarity restraints: 664
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A   2 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   LYS A   2 "    0.033 2.00e-02 2.50e+03
        pdb=" O   LYS A   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A   3 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 156 "   -0.008 2.00e-02 2.50e+03   1.63e-02 2.67e+00
        pdb=" C   MET B 156 "    0.028 2.00e-02 2.50e+03
        pdb=" O   MET B 156 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLU B 157 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 156 "    0.005 2.00e-02 2.50e+03   9.51e-03 9.05e-01
        pdb=" C   MET A 156 "   -0.016 2.00e-02 2.50e+03
        pdb=" O   MET A 156 "    0.006 2.00e-02 2.50e+03
        pdb=" N   GLU A 157 "    0.006 2.00e-02 2.50e+03
  ... (remaining 661 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.82: 1154
        2.82 -     3.40: 4506
        3.40 -     3.98: 7281
        3.98 -     4.56: 10210
        4.56 -     5.14: 14419
  Nonbonded interactions: 37570
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 179 "
            pdb=" O   TRP B 184 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OE1 GLN A 126 "
            pdb=" ND2 ASN A 240 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" OD2 ASP B  58 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OG  SER A 179 "
            pdb=" O   TRP A 184 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD2 ASP A  58 "
            pdb=" OH  TYR B  52 "
     model   vdw
     2.313 3.040
  ... (remaining 37565 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 2 through 248 or resid 301 through 304))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.600
  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:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     15.350
  Find NCS groups from input model:        0.140
  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:3.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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      :  0.002   0.043   4156  Z= 0.148
  Angle     :  0.420   4.902   5644  Z= 0.247
  Chirality :  0.032   0.108    650
  Planarity :  0.002   0.019    664
  Dihedral  : 13.664  80.444   1816
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  5.04 (0.38), residues: 476
  helix:  3.84 (0.25), residues: 394
  sheet:  None (None), residues: 0
  loop :  0.42 (0.71), residues: 82

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 184 
 HIS   0.001   0.000   HIS A  98 
 PHE   0.004   0.000   PHE B 109 
 TYR   0.007   0.001   TYR B  18 
 ARG   0.001   0.000   ARG B 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13129 (  328)
  hydrogen bonds       : angle       3.98302 (  972)
  covalent geometry    : bond        0.00213 ( 4156)
  covalent geometry    : angle       0.42000 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 PHE cc_start: 0.6915 (m-80) cc_final: 0.6458 (t80)
REVERT: A   42 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8046 (tppt)
REVERT: A   47 ARG cc_start: 0.7749 (ttp80) cc_final: 0.7485 (ttp80)
REVERT: A  111 MET cc_start: 0.7869 (mtm) cc_final: 0.7653 (mtp)
REVERT: A  135 PHE cc_start: 0.7010 (t80) cc_final: 0.5929 (m-10)
REVERT: B   16 PHE cc_start: 0.6839 (m-80) cc_final: 0.6434 (t80)
REVERT: B   42 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8030 (tppt)
REVERT: B   47 ARG cc_start: 0.7655 (ttp80) cc_final: 0.7448 (ttp80)
REVERT: B  111 MET cc_start: 0.7910 (mtm) cc_final: 0.7710 (mtp)
REVERT: B  135 PHE cc_start: 0.7018 (t80) cc_final: 0.5917 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.3305
  time to fit residues: 40.3462
Evaluate side-chains
  80 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 12 optimal weight:    0.6980
   chunk 24 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.4042 r_free = 0.4042 target = 0.193178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.145729 restraints weight = 4211.356|
|-----------------------------------------------------------------------------|
r_work (start): 0.3527 rms_B_bonded: 2.34
r_work: 0.3185 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.3066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4156  Z= 0.182
  Angle     :  0.610   6.813   5644  Z= 0.320
  Chirality :  0.040   0.145    650
  Planarity :  0.004   0.043    664
  Dihedral  :  5.531  37.850    952
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  9.07 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.98 (0.40), residues: 476
  helix:  3.72 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.54 (0.85), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 184 
 HIS   0.002   0.001   HIS B  72 
 PHE   0.014   0.002   PHE B 223 
 TYR   0.027   0.002   TYR A  85 
 ARG   0.006   0.001   ARG B 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04921 (  328)
  hydrogen bonds       : angle       3.21021 (  972)
  covalent geometry    : bond        0.00415 ( 4156)
  covalent geometry    : angle       0.60973 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 PHE cc_start: 0.7673 (m-80) cc_final: 0.6429 (t80)
REVERT: A   47 ARG cc_start: 0.7851 (ttp80) cc_final: 0.7404 (ttp80)
REVERT: A  135 PHE cc_start: 0.7310 (t80) cc_final: 0.6128 (m-10)
REVERT: A  173 ILE cc_start: 0.8297 (mt) cc_final: 0.8078 (mt)
REVERT: A  215 GLN cc_start: 0.7471 (mt0) cc_final: 0.7252 (mt0)
REVERT: B   16 PHE cc_start: 0.7605 (m-80) cc_final: 0.6406 (t80)
REVERT: B   38 GLU cc_start: 0.8027 (tp30) cc_final: 0.7795 (tp30)
REVERT: B   42 LYS cc_start: 0.8271 (ttmm) cc_final: 0.8050 (tppt)
REVERT: B   47 ARG cc_start: 0.7822 (ttp80) cc_final: 0.7439 (ttp80)
REVERT: B  135 PHE cc_start: 0.7287 (t80) cc_final: 0.6107 (m-10)
REVERT: B  173 ILE cc_start: 0.8441 (mt) cc_final: 0.8240 (mt)
  outliers start: 8
  outliers final: 2
  residues processed: 98
  average time/residue: 0.4099
  time to fit residues: 48.8093
Evaluate side-chains
  82 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 80
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 5 optimal weight:    7.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.190532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.142424 restraints weight = 4227.253|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 2.31
r_work: 0.3063 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4156  Z= 0.145
  Angle     :  0.547   6.647   5644  Z= 0.287
  Chirality :  0.036   0.153    650
  Planarity :  0.003   0.017    664
  Dihedral  :  5.026  36.668    952
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 14.46 %
    Favored  : 83.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.91 (0.39), residues: 476
  helix:  3.67 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.51 (0.85), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 184 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.010   0.001   PHE B 246 
 TYR   0.015   0.001   TYR B  85 
 ARG   0.003   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04280 (  328)
  hydrogen bonds       : angle       3.05554 (  972)
  covalent geometry    : bond        0.00327 ( 4156)
  covalent geometry    : angle       0.54747 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   42 LYS cc_start: 0.8853 (tppt) cc_final: 0.8634 (tppt)
REVERT: A  135 PHE cc_start: 0.7355 (t80) cc_final: 0.6143 (m-10)
REVERT: B   44 GLU cc_start: 0.8059 (tp30) cc_final: 0.7741 (tp30)
REVERT: B  135 PHE cc_start: 0.7294 (t80) cc_final: 0.6087 (m-10)
REVERT: B  173 ILE cc_start: 0.8418 (mt) cc_final: 0.8200 (mt)
  outliers start: 8
  outliers final: 7
  residues processed: 89
  average time/residue: 0.2283
  time to fit residues: 23.9135
Evaluate side-chains
  89 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 82
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 17 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.0370
   chunk 22 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4656

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.190842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.144191 restraints weight = 4243.060|
|-----------------------------------------------------------------------------|
r_work (start): 0.3452 rms_B_bonded: 2.16
r_work: 0.3130 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4156  Z= 0.123
  Angle     :  0.527   7.946   5644  Z= 0.271
  Chirality :  0.036   0.167    650
  Planarity :  0.002   0.015    664
  Dihedral  :  4.801  36.710    952
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 14.46 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.80 (0.39), residues: 476
  helix:  3.63 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop :  0.25 (0.83), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.009   0.001   PHE B 246 
 TYR   0.011   0.001   TYR B  85 
 ARG   0.003   0.000   ARG A  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  328)
  hydrogen bonds       : angle       2.95438 (  972)
  covalent geometry    : bond        0.00261 ( 4156)
  covalent geometry    : angle       0.52695 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 GLU cc_start: 0.8029 (tp30) cc_final: 0.7745 (tp30)
REVERT: A   44 GLU cc_start: 0.7727 (tp30) cc_final: 0.7517 (tp30)
REVERT: A   70 GLU cc_start: 0.7557 (pt0) cc_final: 0.7354 (pt0)
REVERT: A  135 PHE cc_start: 0.7349 (t80) cc_final: 0.6140 (m-10)
REVERT: B   44 GLU cc_start: 0.7706 (tp30) cc_final: 0.7503 (tp30)
REVERT: B  135 PHE cc_start: 0.7313 (t80) cc_final: 0.6128 (m-10)
REVERT: B  173 ILE cc_start: 0.8514 (mt) cc_final: 0.8310 (mt)
  outliers start: 11
  outliers final: 9
  residues processed: 90
  average time/residue: 0.2185
  time to fit residues: 23.0859
Evaluate side-chains
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 15 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.187493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.140731 restraints weight = 4348.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.25
r_work: 0.3114 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.4009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4156  Z= 0.138
  Angle     :  0.536   6.266   5644  Z= 0.281
  Chirality :  0.036   0.155    650
  Planarity :  0.003   0.015    664
  Dihedral  :  4.663  33.854    952
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 14.46 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.69 (0.39), residues: 476
  helix:  3.60 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.04 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 184 
 HIS   0.001   0.000   HIS B  72 
 PHE   0.010   0.001   PHE B 223 
 TYR   0.014   0.001   TYR B  85 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04096 (  328)
  hydrogen bonds       : angle       2.99621 (  972)
  covalent geometry    : bond        0.00308 ( 4156)
  covalent geometry    : angle       0.53612 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8031 (tt)
REVERT: A   44 GLU cc_start: 0.7711 (tp30) cc_final: 0.7499 (tp30)
REVERT: A  135 PHE cc_start: 0.7390 (t80) cc_final: 0.6144 (m-10)
REVERT: B   29 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: B   44 GLU cc_start: 0.7708 (tp30) cc_final: 0.7497 (tp30)
REVERT: B  135 PHE cc_start: 0.7366 (t80) cc_final: 0.6113 (m-10)
REVERT: B  173 ILE cc_start: 0.8573 (mt) cc_final: 0.8343 (mt)
REVERT: B  227 TYR cc_start: 0.8675 (t80) cc_final: 0.8181 (t80)
  outliers start: 14
  outliers final: 9
  residues processed: 98
  average time/residue: 0.2278
  time to fit residues: 26.3938
Evaluate side-chains
  93 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 35 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 41 optimal weight:    0.4980
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.186306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.142181 restraints weight = 4281.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 2.22
r_work: 0.3052 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4156  Z= 0.141
  Angle     :  0.573   9.073   5644  Z= 0.298
  Chirality :  0.037   0.165    650
  Planarity :  0.002   0.016    664
  Dihedral  :  4.628  36.464    952
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.93 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.66 (0.39), residues: 476
  helix:  3.60 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.14 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.009   0.001   PHE A  16 
 TYR   0.013   0.001   TYR A  85 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04097 (  328)
  hydrogen bonds       : angle       3.02855 (  972)
  covalent geometry    : bond        0.00315 ( 4156)
  covalent geometry    : angle       0.57335 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8061 (tt)
REVERT: A   38 GLU cc_start: 0.8125 (tp30) cc_final: 0.7868 (tp30)
REVERT: A   44 GLU cc_start: 0.7717 (tp30) cc_final: 0.7505 (tp30)
REVERT: A   70 GLU cc_start: 0.7366 (pt0) cc_final: 0.7049 (pm20)
REVERT: A  135 PHE cc_start: 0.7407 (t80) cc_final: 0.6100 (m-10)
REVERT: A  227 TYR cc_start: 0.8695 (t80) cc_final: 0.8034 (t80)
REVERT: B   29 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8098 (tt)
REVERT: B   44 GLU cc_start: 0.7728 (tp30) cc_final: 0.7520 (tp30)
REVERT: B  135 PHE cc_start: 0.7419 (t80) cc_final: 0.6142 (m-10)
REVERT: B  227 TYR cc_start: 0.8674 (t80) cc_final: 0.8129 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.2250
  time to fit residues: 24.8118
Evaluate side-chains
  97 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   20 LEU
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 38 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 12 optimal weight:    0.2980
   chunk 17 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.6380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.185664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.140978 restraints weight = 4324.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 2.28
r_work: 0.3067 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4156  Z= 0.137
  Angle     :  0.547   6.765   5644  Z= 0.286
  Chirality :  0.036   0.152    650
  Planarity :  0.003   0.017    664
  Dihedral  :  4.638  38.043    952
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 15.93 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.74 (0.39), residues: 476
  helix:  3.65 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.14 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.026   0.001   PHE B 112 
 TYR   0.012   0.001   TYR A  85 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  328)
  hydrogen bonds       : angle       3.01653 (  972)
  covalent geometry    : bond        0.00304 ( 4156)
  covalent geometry    : angle       0.54691 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8079 (tt)
REVERT: A   45 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7762 (tm-30)
REVERT: A   70 GLU cc_start: 0.7496 (pt0) cc_final: 0.7255 (pm20)
REVERT: A  135 PHE cc_start: 0.7478 (t80) cc_final: 0.6130 (m-10)
REVERT: A  227 TYR cc_start: 0.8709 (t80) cc_final: 0.8163 (t80)
REVERT: B   29 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8109 (tt)
REVERT: B   44 GLU cc_start: 0.7770 (tp30) cc_final: 0.7565 (tp30)
REVERT: B   70 GLU cc_start: 0.7670 (pt0) cc_final: 0.7181 (pm20)
REVERT: B  135 PHE cc_start: 0.7514 (t80) cc_final: 0.6211 (m-10)
REVERT: B  227 TYR cc_start: 0.8742 (t80) cc_final: 0.8197 (t80)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 0.2159
  time to fit residues: 23.9083
Evaluate side-chains
  100 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 35 optimal weight:    0.2980
   chunk 28 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 158 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.185784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.139323 restraints weight = 4234.352|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.03
r_work: 0.3090 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4156  Z= 0.136
  Angle     :  0.548   6.987   5644  Z= 0.288
  Chirality :  0.036   0.151    650
  Planarity :  0.002   0.016    664
  Dihedral  :  4.640  39.436    952
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.18 %
    Favored  : 80.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.82 (0.39), residues: 476
  helix:  3.71 (0.25), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.15 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 184 
 HIS   0.000   0.000   HIS A  33 
 PHE   0.025   0.001   PHE A 112 
 TYR   0.011   0.001   TYR A 113 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03991 (  328)
  hydrogen bonds       : angle       3.02450 (  972)
  covalent geometry    : bond        0.00300 ( 4156)
  covalent geometry    : angle       0.54845 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8079 (tt)
REVERT: A   38 GLU cc_start: 0.8189 (tp30) cc_final: 0.7907 (tp30)
REVERT: A  135 PHE cc_start: 0.7545 (t80) cc_final: 0.6226 (m-10)
REVERT: A  227 TYR cc_start: 0.8724 (t80) cc_final: 0.8082 (t80)
REVERT: B   29 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: B  135 PHE cc_start: 0.7586 (t80) cc_final: 0.6271 (m-10)
REVERT: B  227 TYR cc_start: 0.8745 (t80) cc_final: 0.8192 (t80)
  outliers start: 15
  outliers final: 11
  residues processed: 94
  average time/residue: 0.2160
  time to fit residues: 23.9689
Evaluate side-chains
  95 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 14 optimal weight:    0.1980
   chunk 3 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.185517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.140385 restraints weight = 4276.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 2.28
r_work: 0.3073 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4156  Z= 0.139
  Angle     :  0.579   9.363   5644  Z= 0.304
  Chirality :  0.037   0.159    650
  Planarity :  0.003   0.019    664
  Dihedral  :  4.629  40.157    952
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.91 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.87 (0.39), residues: 476
  helix:  3.75 (0.24), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.16 (0.79), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 184 
 HIS   0.001   0.000   HIS A 188 
 PHE   0.025   0.001   PHE A 112 
 TYR   0.013   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03944 (  328)
  hydrogen bonds       : angle       3.06261 (  972)
  covalent geometry    : bond        0.00306 ( 4156)
  covalent geometry    : angle       0.57918 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: A   38 GLU cc_start: 0.8185 (tp30) cc_final: 0.7925 (tp30)
REVERT: A  135 PHE cc_start: 0.7584 (t80) cc_final: 0.6253 (m-10)
REVERT: A  227 TYR cc_start: 0.8797 (t80) cc_final: 0.8186 (t80)
REVERT: B   29 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8103 (tt)
REVERT: B   38 GLU cc_start: 0.8123 (tp30) cc_final: 0.7860 (tp30)
REVERT: B   70 GLU cc_start: 0.7632 (pt0) cc_final: 0.7247 (pm20)
REVERT: B  135 PHE cc_start: 0.7647 (t80) cc_final: 0.6297 (m-10)
REVERT: B  227 TYR cc_start: 0.8792 (t80) cc_final: 0.8269 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 90
  average time/residue: 0.2271
  time to fit residues: 24.0044
Evaluate side-chains
  88 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.1980
   chunk 43 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3970 r_free = 0.3970 target = 0.185387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.139298 restraints weight = 4274.011|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 2.21
r_work: 0.3082 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3082
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.4739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4156  Z= 0.144
  Angle     :  0.601  10.140   5644  Z= 0.315
  Chirality :  0.037   0.166    650
  Planarity :  0.002   0.017    664
  Dihedral  :  4.641  40.640    952
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.42 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.88 (0.39), residues: 476
  helix:  3.77 (0.24), residues: 400
  sheet:  None (None), residues: 0
  loop : -0.22 (0.79), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 184 
 HIS   0.001   0.000   HIS A  72 
 PHE   0.024   0.001   PHE A 112 
 TYR   0.012   0.001   TYR B  59 
 ARG   0.002   0.000   ARG B  73 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03996 (  328)
  hydrogen bonds       : angle       3.10791 (  972)
  covalent geometry    : bond        0.00318 ( 4156)
  covalent geometry    : angle       0.60089 ( 5644)

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

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

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  952 Ramachandran restraints generated.
    476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8111 (tt)
REVERT: A   38 GLU cc_start: 0.8162 (tp30) cc_final: 0.7916 (tp30)
REVERT: A  227 TYR cc_start: 0.8811 (t80) cc_final: 0.8197 (t80)
REVERT: B   29 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8096 (tt)
REVERT: B   38 GLU cc_start: 0.8166 (tp30) cc_final: 0.7853 (tp30)
REVERT: B   42 LYS cc_start: 0.8962 (tppt) cc_final: 0.8759 (tppt)
REVERT: B   70 GLU cc_start: 0.7781 (pt0) cc_final: 0.7202 (pm20)
REVERT: B  173 ILE cc_start: 0.8678 (mt) cc_final: 0.8454 (mt)
REVERT: B  227 TYR cc_start: 0.8812 (t80) cc_final: 0.8263 (t80)
  outliers start: 13
  outliers final: 11
  residues processed: 87
  average time/residue: 0.2190
  time to fit residues: 22.4873
Evaluate side-chains
  91 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 LEU
Chi-restraints excluded: chain A residue   39 GLU
Chi-restraints excluded: chain A residue   91 ILE
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  156 MET
Chi-restraints excluded: chain A residue  180 GLN
Chi-restraints excluded: chain A residue  229 LEU
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain B residue   29 LEU
Chi-restraints excluded: chain B residue   39 GLU
Chi-restraints excluded: chain B residue   91 ILE
Chi-restraints excluded: chain B residue  139 LEU
Chi-restraints excluded: chain B residue  229 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.184739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.136696 restraints weight = 4252.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 2.24
r_work: 0.3038 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.4899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4156  Z= 0.143
  Angle     :  0.591   7.726   5644  Z= 0.308
  Chirality :  0.037   0.160    650
  Planarity :  0.002   0.015    664
  Dihedral  :  4.648  41.247    952
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  3.43 %
    Allowed  : 16.91 %
    Favored  : 79.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  4.96 (0.38), residues: 476
  helix:  3.83 (0.24), residues: 398
  sheet:  None (None), residues: 0
  loop : -0.11 (0.78), residues: 78

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 184 
 HIS   0.000   0.000   HIS B  98 
 PHE   0.024   0.001   PHE A 112 
 TYR   0.012   0.001   TYR A  59 
 ARG   0.002   0.000   ARG A 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04100 (  328)
  hydrogen bonds       : angle       3.13028 (  972)
  covalent geometry    : bond        0.00319 ( 4156)
  covalent geometry    : angle       0.59065 ( 5644)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2421.35 seconds
wall clock time: 43 minutes 1.93 seconds (2581.93 seconds total)