Starting phenix.real_space_refine
on Wed Sep 17 04:16:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jj2_61515/09_2025/9jj2_61515.map"
  }
  resolution = 3.0
  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=  -0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    2540      2.51       5
     N     650      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3916
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1958
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 8, 'TRANS': 249}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 258, 1958
          Classifications: {'peptide': 258}
          Link IDs: {'PTRANS': 8, 'TRANS': 249}
          Chain breaks: 1
  Time building chain proxies: 1.37, per 1000 atoms: 0.35
  Number of scatterers: 3916
  At special positions: 0
  Unit cell: (51.46, 82.17, 100.43, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O     698      8.00
     N     650      7.00
     C    2540      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 170.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  964

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 4 sheets defined
      71.3% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 79 through 98
      removed outlier: 5.232A  pdb=" N   VAL A  85 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   PHE A  86 " --> pdb=" O   VAL A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 127
    Processing helix  chain 'A' and resid 140 through 170
      removed outlier: 3.593A  pdb=" N   LEU A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 199
      removed outlier: 3.821A  pdb=" N   MET A 180 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LEU A 182 " --> pdb=" O   GLY A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 259
    Processing helix  chain 'A' and resid 264 through 294
      removed outlier: 3.602A  pdb=" N   ILE A 268 " --> pdb=" O   ALA A 264 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
    Processing helix  chain 'A' and resid 301 through 311
    Processing helix  chain 'A' and resid 344 through 361
    Processing helix  chain 'B' and resid 81 through 98
      removed outlier: 3.879A  pdb=" N   VAL B  85 " --> pdb=" O   ALA B  81 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   GLY B  89 " --> pdb=" O   VAL B  85 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLU B  90 " --> pdb=" O   PHE B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 100 through 127
      removed outlier: 4.036A  pdb=" N   THR B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 170
      removed outlier: 3.600A  pdb=" N   LEU B 169 " --> pdb=" O   PHE B 165 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 199
      removed outlier: 3.868A  pdb=" N   MET B 180 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 259
    Processing helix  chain 'B' and resid 264 through 294
      removed outlier: 3.640A  pdb=" N   ILE B 268 " --> pdb=" O   ALA B 264 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
    Processing helix  chain 'B' and resid 301 through 311
    Processing helix  chain 'B' and resid 344 through 361
    Processing sheet with id=AA1, first strand: chain 'A' and resid 315 through 317
      removed outlier: 6.852A  pdb=" N   ALA A 338 " --> pdb=" O   ARG A 316 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ILE A 339 " --> pdb=" O   GLU A 370 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 325
      removed outlier: 7.049A  pdb=" N   HIS A 331 " --> pdb=" O   SER A 364 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   THR A 366 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   ALA A 333 " --> pdb=" O   THR A 366 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 315 through 317
      removed outlier: 3.675A  pdb=" N   ALA B 317 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ILE B 339 " --> pdb=" O   GLU B 370 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 322 through 325
      removed outlier: 7.078A  pdb=" N   HIS B 331 " --> pdb=" O   SER B 364 " (cutoff:3.500A)
      removed outlier: 8.812A  pdb=" N   THR B 366 " --> pdb=" O   HIS B 331 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   ALA B 333 " --> pdb=" O   THR B 366 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    876 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: 0.52 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1226
        1.34 -     1.46: 822
        1.46 -     1.58: 1914
        1.58 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 4008
  Sorted by residual:
  bond pdb=" C   HIS B 238 "
       pdb=" O   HIS B 238 "
    ideal  model  delta    sigma   weight residual
    1.236  1.219  0.016 1.29e-02 6.01e+03 1.63e+00
  bond pdb=" CB  ASP B 112 "
       pdb=" CG  ASP B 112 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 2.50e-02 1.60e+03 1.41e+00
  bond pdb=" CG1 ILE B 254 "
       pdb=" CD1 ILE B 254 "
    ideal  model  delta    sigma   weight residual
    1.513  1.469  0.044 3.90e-02 6.57e+02 1.29e+00
  bond pdb=" CB  ASP A 344 "
       pdb=" CG  ASP A 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.18e+00
  bond pdb=" CB  ASP B 344 "
       pdb=" CG  ASP B 344 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 2.50e-02 1.60e+03 1.13e+00
  ... (remaining 4003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 5302
        1.90 -     3.80: 111
        3.80 -     5.70: 31
        5.70 -     7.60: 11
        7.60 -     9.51: 9
  Bond angle restraints: 5464
  Sorted by residual:
  angle pdb=" C   SER A 115 "
        pdb=" N   MET A 116 "
        pdb=" CA  MET A 116 "
      ideal   model   delta    sigma   weight residual
     121.66  114.51    7.15 1.76e+00 3.23e-01 1.65e+01
  angle pdb=" CA  GLU B 176 "
        pdb=" CB  GLU B 176 "
        pdb=" CG  GLU B 176 "
      ideal   model   delta    sigma   weight residual
     114.10  120.63   -6.53 2.00e+00 2.50e-01 1.07e+01
  angle pdb=" CA  GLU A 142 "
        pdb=" CB  GLU A 142 "
        pdb=" CG  GLU A 142 "
      ideal   model   delta    sigma   weight residual
     114.10  119.94   -5.84 2.00e+00 2.50e-01 8.53e+00
  angle pdb=" CB  MET B 117 "
        pdb=" CG  MET B 117 "
        pdb=" SD  MET B 117 "
      ideal   model   delta    sigma   weight residual
     112.70  121.06   -8.36 3.00e+00 1.11e-01 7.77e+00
  angle pdb=" CB  GLU B 176 "
        pdb=" CG  GLU B 176 "
        pdb=" CD  GLU B 176 "
      ideal   model   delta    sigma   weight residual
     112.60  117.29   -4.69 1.70e+00 3.46e-01 7.62e+00
  ... (remaining 5459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    12.34: 1847
       12.34 -    24.69: 235
       24.69 -    37.03: 157
       37.03 -    49.37: 64
       49.37 -    61.71: 19
  Dihedral angle restraints: 2322
    sinusoidal: 830
      harmonic: 1492
  Sorted by residual:
  dihedral pdb=" CA  ASP A 340 "
           pdb=" CB  ASP A 340 "
           pdb=" CG  ASP A 340 "
           pdb=" OD1 ASP A 340 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.75   55.75     1      2.00e+01 2.50e-03 1.05e+01
  dihedral pdb=" CA  MET A 117 "
           pdb=" CB  MET A 117 "
           pdb=" CG  MET A 117 "
           pdb=" SD  MET A 117 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -119.69   59.69     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LEU A 310 "
           pdb=" CB  LEU A 310 "
           pdb=" CG  LEU A 310 "
           pdb=" CD1 LEU A 310 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.65   59.35     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2319 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 451
       0.036 -    0.072: 143
       0.072 -    0.107: 49
       0.107 -    0.143: 15
       0.143 -    0.179: 4
  Chirality restraints: 662
  Sorted by residual:
  chirality pdb=" CG  LEU B 182 "
            pdb=" CB  LEU B 182 "
            pdb=" CD1 LEU B 182 "
            pdb=" CD2 LEU B 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.41   -0.18 2.00e-01 2.50e+01 8.01e-01
  chirality pdb=" CA  MET A 116 "
            pdb=" N   MET A 116 "
            pdb=" C   MET A 116 "
            pdb=" CB  MET A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CB  VAL B 237 "
            pdb=" CA  VAL B 237 "
            pdb=" CG1 VAL B 237 "
            pdb=" CG2 VAL B 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.17e-01
  ... (remaining 659 not shown)

  Planarity restraints: 670
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 132 "    0.126 9.50e-02 1.11e+02   5.70e-02 2.64e+00
        pdb=" NE  ARG A 132 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 132 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 132 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 132 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 112 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" CG  ASP A 112 "   -0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 112 "    0.009 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 112 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 116 "    0.006 2.00e-02 2.50e+03   1.20e-02 1.44e+00
        pdb=" C   MET A 116 "   -0.021 2.00e-02 2.50e+03
        pdb=" O   MET A 116 "    0.008 2.00e-02 2.50e+03
        pdb=" N   MET A 117 "    0.007 2.00e-02 2.50e+03
  ... (remaining 667 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 2010
        2.97 -     3.45: 4221
        3.45 -     3.93: 6472
        3.93 -     4.42: 7163
        4.42 -     4.90: 11504
  Nonbonded interactions: 31370
  Sorted by model distance:
  nonbonded pdb=" O   THR B 342 "
            pdb=" OG1 THR B 342 "
     model   vdw
     2.484 3.040
  nonbonded pdb=" N   GLU B 176 "
            pdb=" OE1 GLU B 176 "
     model   vdw
     2.504 3.120
  nonbonded pdb=" N   ASP B 172 "
            pdb=" OD1 ASP B 172 "
     model   vdw
     2.528 3.120
  nonbonded pdb=" N   ASP A 172 "
            pdb=" OD1 ASP A 172 "
     model   vdw
     2.533 3.120
  nonbonded pdb=" N   GLU A 142 "
            pdb=" OE1 GLU A 142 "
     model   vdw
     2.540 3.120
  ... (remaining 31365 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.960
  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:             0.020
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.370
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4008  Z= 0.168
  Angle     :  0.795   9.505   5464  Z= 0.378
  Chirality :  0.043   0.179    662
  Planarity :  0.004   0.057    670
  Dihedral  : 17.558  61.715   1358
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 46.15 %
    Favored  : 52.40 %
  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 aren not related in a simple way.
  whole:  2.59 (0.38), residues: 508
  helix:  2.80 (0.26), residues: 344
  sheet: -1.08 (0.80), residues: 52
  loop : -0.37 (0.61), residues: 112

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 132 
 TYR   0.014   0.001   TYR B  95 
 PHE   0.007   0.001   PHE A 302 
 TRP   0.004   0.001   TRP A 324 
 HIS   0.004   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 4008)
  covalent geometry    : angle       0.79525 ( 5464)
  hydrogen bonds       : bond        0.11674 (  295)
  hydrogen bonds       : angle       6.29828 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A  351 GLU cc_start: 0.8745 (tp30) cc_final: 0.8234 (tp30)
REVERT: B  116 MET cc_start: 0.4244 (mtp) cc_final: 0.3930 (mtt)
REVERT: B  351 GLU cc_start: 0.8476 (tp30) cc_final: 0.8114 (tp30)
  outliers start: 6
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2947
  time to fit residues: 32.6889
Evaluate side-chains
  109 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  191 ASN
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  291 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0170
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   overall best weight:    0.6422

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.118566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.093513 restraints weight = 7513.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 2.99
r_work: 0.3128 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4008  Z= 0.128
  Angle     :  0.639   8.480   5464  Z= 0.294
  Chirality :  0.040   0.138    662
  Planarity :  0.004   0.029    670
  Dihedral  :  5.985  57.040    562
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  7.21 %
    Allowed  : 35.58 %
    Favored  : 57.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.92 (0.39), residues: 508
  helix:  3.06 (0.26), residues: 348
  sheet: -1.20 (0.82), residues: 52
  loop : -0.30 (0.64), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 132 
 TYR   0.006   0.001   TYR B  95 
 PHE   0.010   0.001   PHE B 196 
 TRP   0.008   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4008)
  covalent geometry    : angle       0.63902 ( 5464)
  hydrogen bonds       : bond        0.04220 (  295)
  hydrogen bonds       : angle       4.52733 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 113
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  263 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7887 (ttpp)
REVERT: A  351 GLU cc_start: 0.8782 (tp30) cc_final: 0.8286 (tp30)
REVERT: B  116 MET cc_start: 0.4296 (mtp) cc_final: 0.3980 (mtt)
REVERT: B  180 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8027 (mtm)
REVERT: B  254 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8851 (mp)
REVERT: B  351 GLU cc_start: 0.8639 (tp30) cc_final: 0.8192 (tp30)
  outliers start: 30
  outliers final: 14
  residues processed: 129
  average time/residue: 0.3168
  time to fit residues: 43.0020
Evaluate side-chains
  122 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  344 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  344 ASP
Chi-restraints excluded: chain B residue  372 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 46 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   chunk 34 optimal weight:    0.5980
   chunk 7 optimal weight:    0.8980
   chunk 32 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.119841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.095516 restraints weight = 7441.870|
|-----------------------------------------------------------------------------|
r_work (start): 0.3301 rms_B_bonded: 2.91
r_work: 0.3144 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4008  Z= 0.124
  Angle     :  0.646   8.086   5464  Z= 0.295
  Chirality :  0.040   0.146    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.768  54.649    555
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  6.73 %
    Allowed  : 34.62 %
    Favored  : 58.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.92 (0.38), residues: 508
  helix:  3.06 (0.26), residues: 348
  sheet: -1.26 (0.82), residues: 52
  loop : -0.29 (0.63), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 132 
 TYR   0.010   0.001   TYR B  95 
 PHE   0.014   0.001   PHE B 196 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.003   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 4008)
  covalent geometry    : angle       0.64607 ( 5464)
  hydrogen bonds       : bond        0.04029 (  295)
  hydrogen bonds       : angle       4.34010 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 112
  time to evaluate  : 0.150 
Fit side-chains
REVERT: A  112 ASP cc_start: 0.8330 (t0) cc_final: 0.8106 (t0)
REVERT: A  263 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7917 (ttpt)
REVERT: A  340 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8300 (m-30)
REVERT: A  351 GLU cc_start: 0.8786 (tp30) cc_final: 0.8271 (tp30)
REVERT: B  180 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8073 (mtm)
REVERT: B  250 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8007 (tm)
REVERT: B  254 ILE cc_start: 0.9063 (OUTLIER) cc_final: 0.8848 (mp)
REVERT: B  351 GLU cc_start: 0.8727 (tp30) cc_final: 0.8237 (tp30)
  outliers start: 28
  outliers final: 13
  residues processed: 128
  average time/residue: 0.2854
  time to fit residues: 38.5879
Evaluate side-chains
  125 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 107
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  372 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 45 optimal weight:    0.0010
   chunk 48 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 15 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.119858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.093742 restraints weight = 7490.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 3.05
r_work: 0.3158 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4008  Z= 0.120
  Angle     :  0.632   8.648   5464  Z= 0.284
  Chirality :  0.039   0.135    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.791  56.973    555
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 34.38 %
    Favored  : 58.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.91 (0.38), residues: 508
  helix:  3.08 (0.26), residues: 348
  sheet: -1.34 (0.81), residues: 52
  loop : -0.32 (0.61), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 132 
 TYR   0.004   0.001   TYR A  95 
 PHE   0.012   0.001   PHE B 196 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.003   0.000   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4008)
  covalent geometry    : angle       0.63248 ( 5464)
  hydrogen bonds       : bond        0.03898 (  295)
  hydrogen bonds       : angle       4.24012 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  263 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7936 (ttpt)
REVERT: A  340 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8233 (m-30)
REVERT: A  351 GLU cc_start: 0.8832 (tp30) cc_final: 0.8360 (tp30)
REVERT: B  180 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8184 (mtm)
REVERT: B  250 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8121 (tm)
REVERT: B  254 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (mp)
REVERT: B  340 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7991 (m-30)
REVERT: B  351 GLU cc_start: 0.8815 (tp30) cc_final: 0.8358 (tp30)
  outliers start: 29
  outliers final: 14
  residues processed: 129
  average time/residue: 0.3029
  time to fit residues: 41.2646
Evaluate side-chains
  122 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  110 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue   84 PHE
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.119286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.094546 restraints weight = 7503.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 2.89
r_work: 0.3150 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4008  Z= 0.138
  Angle     :  0.663   8.902   5464  Z= 0.300
  Chirality :  0.040   0.132    662
  Planarity :  0.003   0.037    670
  Dihedral  :  4.869  58.887    555
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  6.25 %
    Allowed  : 36.30 %
    Favored  : 57.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.93 (0.38), residues: 508
  helix:  3.12 (0.26), residues: 348
  sheet: -1.43 (0.80), residues: 52
  loop : -0.37 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 132 
 TYR   0.004   0.001   TYR A  95 
 PHE   0.008   0.001   PHE B 273 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4008)
  covalent geometry    : angle       0.66315 ( 5464)
  hydrogen bonds       : bond        0.04033 (  295)
  hydrogen bonds       : angle       4.23735 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  105 ASP cc_start: 0.8199 (m-30) cc_final: 0.7946 (m-30)
REVERT: A  142 GLU cc_start: 0.8465 (mp0) cc_final: 0.7983 (mp0)
REVERT: A  245 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: A  263 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7951 (ttpt)
REVERT: A  340 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8262 (m-30)
REVERT: A  351 GLU cc_start: 0.8856 (tp30) cc_final: 0.8449 (tp30)
REVERT: B  180 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8225 (mtm)
REVERT: B  250 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (tm)
REVERT: B  254 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8931 (mp)
REVERT: B  340 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7961 (m-30)
REVERT: B  351 GLU cc_start: 0.8843 (tp30) cc_final: 0.8409 (tp30)
  outliers start: 26
  outliers final: 10
  residues processed: 125
  average time/residue: 0.3108
  time to fit residues: 40.9593
Evaluate side-chains
  125 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  299 ASN
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.4980
   chunk 29 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 45 optimal weight:    0.1980
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 49 optimal weight:    0.4980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.119840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.094605 restraints weight = 7582.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.99
r_work: 0.3165 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4008  Z= 0.120
  Angle     :  0.675   8.255   5464  Z= 0.301
  Chirality :  0.039   0.128    662
  Planarity :  0.003   0.028    670
  Dihedral  :  4.835  59.481    555
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.97 %
    Allowed  : 36.06 %
    Favored  : 56.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.38), residues: 508
  helix:  3.10 (0.26), residues: 348
  sheet: -1.41 (0.81), residues: 52
  loop : -0.39 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 132 
 TYR   0.004   0.001   TYR A 357 
 PHE   0.006   0.001   PHE B 273 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.003   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4008)
  covalent geometry    : angle       0.67528 ( 5464)
  hydrogen bonds       : bond        0.03889 (  295)
  hydrogen bonds       : angle       4.20293 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.7782 (OUTLIER) cc_final: 0.7438 (t)
REVERT: A  105 ASP cc_start: 0.8139 (m-30) cc_final: 0.7851 (m-30)
REVERT: A  245 GLN cc_start: 0.8469 (tm-30) cc_final: 0.8146 (tm-30)
REVERT: A  263 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7926 (ttpt)
REVERT: A  340 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (m-30)
REVERT: A  351 GLU cc_start: 0.8858 (tp30) cc_final: 0.8451 (tp30)
REVERT: B  132 ARG cc_start: 0.8485 (mtp-110) cc_final: 0.8283 (mtp180)
REVERT: B  250 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8161 (tm)
REVERT: B  254 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8902 (mp)
REVERT: B  340 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7915 (m-30)
REVERT: B  351 GLU cc_start: 0.8856 (tp30) cc_final: 0.8392 (tp30)
  outliers start: 29
  outliers final: 10
  residues processed: 127
  average time/residue: 0.3021
  time to fit residues: 40.5089
Evaluate side-chains
  120 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 17 optimal weight:    0.1980
   chunk 39 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0020
   chunk 1 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0050
   chunk 32 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.2802

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN
B 368 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.122327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.097313 restraints weight = 7616.903|
|-----------------------------------------------------------------------------|
r_work (start): 0.3355 rms_B_bonded: 3.00
r_work: 0.3203 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1950

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4008  Z= 0.114
  Angle     :  0.683  10.406   5464  Z= 0.298
  Chirality :  0.039   0.127    662
  Planarity :  0.003   0.028    670
  Dihedral  :  3.680  14.242    550
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  6.01 %
    Allowed  : 37.74 %
    Favored  : 56.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.90 (0.38), residues: 508
  helix:  3.09 (0.26), residues: 348
  sheet: -1.35 (0.81), residues: 52
  loop : -0.38 (0.60), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 132 
 TYR   0.007   0.001   TYR B 330 
 PHE   0.029   0.001   PHE B 196 
 TRP   0.007   0.001   TRP A 324 
 HIS   0.002   0.000   HIS B 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 4008)
  covalent geometry    : angle       0.68272 ( 5464)
  hydrogen bonds       : bond        0.03742 (  295)
  hydrogen bonds       : angle       4.12573 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 115
  time to evaluate  : 0.102 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7281 (t)
REVERT: A  105 ASP cc_start: 0.8141 (m-30) cc_final: 0.7799 (m-30)
REVERT: A  245 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: A  263 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7825 (ttpp)
REVERT: A  351 GLU cc_start: 0.8843 (tp30) cc_final: 0.8579 (tp30)
REVERT: B   87 MET cc_start: 0.8127 (ttm) cc_final: 0.7915 (ttt)
REVERT: B  132 ARG cc_start: 0.8419 (mtp-110) cc_final: 0.8201 (mtp180)
REVERT: B  250 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8129 (tm)
REVERT: B  254 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8870 (mp)
REVERT: B  340 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7979 (m-30)
REVERT: B  351 GLU cc_start: 0.8826 (tp30) cc_final: 0.8401 (tp30)
  outliers start: 25
  outliers final: 10
  residues processed: 130
  average time/residue: 0.3088
  time to fit residues: 42.2902
Evaluate side-chains
  122 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  250 LEU
Chi-restraints excluded: chain B residue  254 ILE
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  296 THR
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 35 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.1980
   chunk 16 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.121034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.096326 restraints weight = 7505.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3333 rms_B_bonded: 2.91
r_work: 0.3182 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4008  Z= 0.125
  Angle     :  0.700   9.545   5464  Z= 0.310
  Chirality :  0.040   0.142    662
  Planarity :  0.003   0.028    670
  Dihedral  :  3.681  14.034    550
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 37.50 %
    Favored  : 56.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.82 (0.38), residues: 508
  helix:  3.09 (0.26), residues: 350
  sheet: -1.52 (0.78), residues: 52
  loop : -0.68 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 132 
 TYR   0.018   0.001   TYR B  95 
 PHE   0.023   0.001   PHE A 273 
 TRP   0.006   0.001   TRP B 324 
 HIS   0.003   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 4008)
  covalent geometry    : angle       0.69986 ( 5464)
  hydrogen bonds       : bond        0.03817 (  295)
  hydrogen bonds       : angle       4.11559 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.8035 (OUTLIER) cc_final: 0.7440 (t)
REVERT: A   90 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7007 (mp0)
REVERT: A  165 PHE cc_start: 0.8590 (OUTLIER) cc_final: 0.8378 (t80)
REVERT: A  245 GLN cc_start: 0.8424 (tm-30) cc_final: 0.8113 (tm-30)
REVERT: A  263 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7866 (ttpt)
REVERT: A  340 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8281 (m-30)
REVERT: A  351 GLU cc_start: 0.8860 (tp30) cc_final: 0.8561 (tp30)
REVERT: B  340 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7954 (m-30)
REVERT: B  351 GLU cc_start: 0.8840 (tp30) cc_final: 0.8405 (tp30)
  outliers start: 27
  outliers final: 8
  residues processed: 122
  average time/residue: 0.3468
  time to fit residues: 44.4335
Evaluate side-chains
  118 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  165 PHE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  276 CYS
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.120828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.096606 restraints weight = 7592.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 2.78
r_work: 0.3210 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4008  Z= 0.150
  Angle     :  0.722  10.446   5464  Z= 0.322
  Chirality :  0.040   0.146    662
  Planarity :  0.003   0.031    670
  Dihedral  :  3.808  14.457    550
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 38.94 %
    Favored  : 55.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.77 (0.38), residues: 508
  helix:  3.07 (0.26), residues: 350
  sheet: -1.63 (0.77), residues: 52
  loop : -0.70 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 290 
 TYR   0.010   0.001   TYR B 330 
 PHE   0.031   0.001   PHE B 196 
 TRP   0.005   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 4008)
  covalent geometry    : angle       0.72162 ( 5464)
  hydrogen bonds       : bond        0.04075 (  295)
  hydrogen bonds       : angle       4.20372 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.185 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7600 (t)
REVERT: A   90 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.7085 (mp0)
REVERT: A  142 GLU cc_start: 0.8487 (mp0) cc_final: 0.8004 (mp0)
REVERT: A  245 GLN cc_start: 0.8486 (tm-30) cc_final: 0.8193 (tm-30)
REVERT: A  263 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7928 (ttpt)
REVERT: A  340 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (m-30)
REVERT: A  351 GLU cc_start: 0.8813 (tp30) cc_final: 0.8498 (tp30)
REVERT: B   87 MET cc_start: 0.8239 (ttm) cc_final: 0.7965 (ttt)
REVERT: B  340 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.7949 (m-30)
REVERT: B  351 GLU cc_start: 0.8813 (tp30) cc_final: 0.8490 (tp30)
  outliers start: 22
  outliers final: 12
  residues processed: 119
  average time/residue: 0.3116
  time to fit residues: 39.1239
Evaluate side-chains
  124 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 107
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue   84 PHE
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.0370
   chunk 46 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 37 optimal weight:    9.9990
   chunk 1 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 24 optimal weight:    0.0010
   chunk 14 optimal weight:    1.9990
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   overall best weight:    0.4064

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.121147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.095900 restraints weight = 7582.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3372 rms_B_bonded: 2.93
r_work: 0.3227 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4008  Z= 0.125
  Angle     :  0.723  10.203   5464  Z= 0.318
  Chirality :  0.040   0.137    662
  Planarity :  0.003   0.029    670
  Dihedral  :  3.757  13.929    550
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 41.11 %
    Favored  : 55.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.38), residues: 508
  helix:  3.02 (0.26), residues: 350
  sheet: -1.57 (0.78), residues: 52
  loop : -0.70 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 306 
 TYR   0.018   0.001   TYR B  95 
 PHE   0.038   0.001   PHE B 196 
 TRP   0.008   0.001   TRP A 324 
 HIS   0.002   0.000   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4008)
  covalent geometry    : angle       0.72349 ( 5464)
  hydrogen bonds       : bond        0.03932 (  295)
  hydrogen bonds       : angle       4.17821 (  876)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   80 CYS cc_start: 0.8227 (OUTLIER) cc_final: 0.7578 (t)
REVERT: A  242 ASP cc_start: 0.8518 (m-30) cc_final: 0.8069 (t70)
REVERT: A  245 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: A  263 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7916 (ttpt)
REVERT: A  340 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8299 (m-30)
REVERT: A  351 GLU cc_start: 0.8829 (tp30) cc_final: 0.8499 (tp30)
REVERT: B   87 MET cc_start: 0.8257 (ttm) cc_final: 0.7980 (ttt)
REVERT: B  340 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7946 (m-30)
REVERT: B  351 GLU cc_start: 0.8803 (tp30) cc_final: 0.8470 (tp30)
  outliers start: 13
  outliers final: 9
  residues processed: 109
  average time/residue: 0.3186
  time to fit residues: 36.6476
Evaluate side-chains
  116 residues out of total 416 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 CYS
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  263 LYS
Chi-restraints excluded: chain A residue  291 ILE
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain B residue   82 VAL
Chi-restraints excluded: chain B residue  133 THR
Chi-restraints excluded: chain B residue  196 PHE
Chi-restraints excluded: chain B residue  243 LEU
Chi-restraints excluded: chain B residue  291 ILE
Chi-restraints excluded: chain B residue  299 ASN
Chi-restraints excluded: chain B residue  340 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 29 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   chunk 37 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.121393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.096836 restraints weight = 7581.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 2.86
r_work: 0.3222 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4008  Z= 0.141
  Angle     :  0.715   9.851   5464  Z= 0.319
  Chirality :  0.041   0.138    662
  Planarity :  0.003   0.029    670
  Dihedral  :  3.759  14.119    550
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 41.35 %
    Favored  : 55.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.72 (0.38), residues: 508
  helix:  3.02 (0.26), residues: 350
  sheet: -1.59 (0.77), residues: 52
  loop : -0.69 (0.58), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 306 
 TYR   0.009   0.001   TYR B 330 
 PHE   0.040   0.001   PHE B 196 
 TRP   0.006   0.001   TRP A 324 
 HIS   0.002   0.001   HIS B 170 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 4008)
  covalent geometry    : angle       0.71473 ( 5464)
  hydrogen bonds       : bond        0.04018 (  295)
  hydrogen bonds       : angle       4.20692 (  876)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1489.12 seconds
wall clock time: 26 minutes 10.82 seconds (1570.82 seconds total)