Starting phenix.real_space_refine
on Fri Dec 27 12:52:54 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ja6_61291/12_2024/9ja6_61291.cif"
  }
  resolution = 4.4
  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=   0.026
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    3020      2.51       5
     N     884      2.21       5
     O     948      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 4880
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "B"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
    Chain: "D"
      Number of atoms: 1220
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1220
          Classifications: {'peptide': 147}
          Link IDs: {'PTRANS': 6, 'TRANS': 140}
  Time building chain proxies: 3.93, per 1000 atoms: 0.81
  Number of scatterers: 4880
  At special positions: 0
  Unit cell: (92, 92, 120, 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     948      8.00
     N     884      7.00
     C    3020      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: 1.35
  Conformation dependent library (CDL) restraints added in 574.7 milliseconds
  

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1136

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 0 sheets defined
      72.3% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 208 through 274
      removed outlier: 3.811A  pdb=" N   SER A 274 " --> pdb=" O   MET A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE A 303 " --> pdb=" O   ARG A 299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 318
    Processing helix  chain 'A' and resid 326 through 328
      No H-bonds generated for 'chain 'A' and resid 326 through 328'
    Processing helix  chain 'A' and resid 329 through 339
    Processing helix  chain 'A' and resid 342 through 348
    Processing helix  chain 'B' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER B 274 " --> pdb=" O   MET B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE B 303 " --> pdb=" O   ARG B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 307 through 318
    Processing helix  chain 'B' and resid 326 through 328
      No H-bonds generated for 'chain 'B' and resid 326 through 328'
    Processing helix  chain 'B' and resid 329 through 339
    Processing helix  chain 'B' and resid 342 through 348
    Processing helix  chain 'C' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER C 274 " --> pdb=" O   MET C 270 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE C 303 " --> pdb=" O   ARG C 299 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 307 through 318
    Processing helix  chain 'C' and resid 326 through 328
      No H-bonds generated for 'chain 'C' and resid 326 through 328'
    Processing helix  chain 'C' and resid 329 through 339
    Processing helix  chain 'C' and resid 342 through 348
    Processing helix  chain 'D' and resid 209 through 274
      removed outlier: 3.810A  pdb=" N   SER D 274 " --> pdb=" O   MET D 270 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 299 through 305
      removed outlier: 3.672A  pdb=" N   ILE D 303 " --> pdb=" O   ARG D 299 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 307 through 318
    Processing helix  chain 'D' and resid 326 through 328
      No H-bonds generated for 'chain 'D' and resid 326 through 328'
    Processing helix  chain 'D' and resid 329 through 339
    Processing helix  chain 'D' and resid 342 through 348

    325 hydrogen bonds defined for protein.
    975 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: 1.14

  Time building geometry restraints manager: 1.53 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1629
        1.33 -     1.45: 605
        1.45 -     1.57: 2678
        1.57 -     1.69: 0
        1.69 -     1.80: 52
  Bond restraints: 4964
  Sorted by residual:
  bond pdb=" CA  GLU A 217 "
       pdb=" C   GLU A 217 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.30e-02 5.92e+03 1.12e+01
  bond pdb=" CA  ALA C 214 "
       pdb=" C   ALA C 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.480  0.043 1.30e-02 5.92e+03 1.08e+01
  bond pdb=" CA  ALA B 214 "
       pdb=" C   ALA B 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.30e-02 5.92e+03 9.97e+00
  bond pdb=" CA  ALA A 214 "
       pdb=" C   ALA A 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.482  0.041 1.30e-02 5.92e+03 9.95e+00
  bond pdb=" CA  ALA D 214 "
       pdb=" C   ALA D 214 "
    ideal  model  delta    sigma   weight residual
    1.523  1.483  0.040 1.30e-02 5.92e+03 9.55e+00
  ... (remaining 4959 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 6483
        2.29 -     4.58: 173
        4.58 -     6.87: 21
        6.87 -     9.17: 3
        9.17 -    11.46: 4
  Bond angle restraints: 6684
  Sorted by residual:
  angle pdb=" N   ALA C 214 "
        pdb=" CA  ALA C 214 "
        pdb=" C   ALA C 214 "
      ideal   model   delta    sigma   weight residual
     111.28  105.93    5.35 1.09e+00 8.42e-01 2.41e+01
  angle pdb=" N   GLU A 217 "
        pdb=" CA  GLU A 217 "
        pdb=" C   GLU A 217 "
      ideal   model   delta    sigma   weight residual
     111.28  106.10    5.18 1.09e+00 8.42e-01 2.26e+01
  angle pdb=" N   ALA B 214 "
        pdb=" CA  ALA B 214 "
        pdb=" C   ALA B 214 "
      ideal   model   delta    sigma   weight residual
     111.28  106.50    4.78 1.09e+00 8.42e-01 1.92e+01
  angle pdb=" N   ALA A 214 "
        pdb=" CA  ALA A 214 "
        pdb=" C   ALA A 214 "
      ideal   model   delta    sigma   weight residual
     111.28  106.54    4.74 1.09e+00 8.42e-01 1.89e+01
  angle pdb=" N   GLU D 217 "
        pdb=" CA  GLU D 217 "
        pdb=" C   GLU D 217 "
      ideal   model   delta    sigma   weight residual
     111.28  107.08    4.20 1.09e+00 8.42e-01 1.48e+01
  ... (remaining 6679 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 2662
       17.14 -    34.29: 313
       34.29 -    51.43: 88
       51.43 -    68.58: 29
       68.58 -    85.72: 4
  Dihedral angle restraints: 3096
    sinusoidal: 1356
      harmonic: 1740
  Sorted by residual:
  dihedral pdb=" CA  ARG C 299 "
           pdb=" C   ARG C 299 "
           pdb=" N   ILE C 300 "
           pdb=" CA  ILE C 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.64  -17.36     0      5.00e+00 4.00e-02 1.21e+01
  dihedral pdb=" CA  ARG B 299 "
           pdb=" C   ARG B 299 "
           pdb=" N   ILE B 300 "
           pdb=" CA  ILE B 300 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CA  ARG D 299 "
           pdb=" C   ARG D 299 "
           pdb=" N   ILE D 300 "
           pdb=" CA  ILE D 300 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -162.67  -17.33     0      5.00e+00 4.00e-02 1.20e+01
  ... (remaining 3093 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 330
       0.027 -    0.054: 214
       0.054 -    0.082: 128
       0.082 -    0.109: 22
       0.109 -    0.136: 10
  Chirality restraints: 704
  Sorted by residual:
  chirality pdb=" CG  LEU D 264 "
            pdb=" CB  LEU D 264 "
            pdb=" CD1 LEU D 264 "
            pdb=" CD2 LEU D 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CG  LEU C 264 "
            pdb=" CB  LEU C 264 "
            pdb=" CD1 LEU C 264 "
            pdb=" CD2 LEU C 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.13 2.00e-01 2.50e+01 4.55e-01
  chirality pdb=" CG  LEU A 264 "
            pdb=" CB  LEU A 264 "
            pdb=" CD1 LEU A 264 "
            pdb=" CD2 LEU A 264 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.46   -0.13 2.00e-01 2.50e+01 4.51e-01
  ... (remaining 701 not shown)

  Planarity restraints: 888
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU C 216 "   -0.010 2.00e-02 2.50e+03   2.08e-02 4.35e+00
        pdb=" C   GLU C 216 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLU C 216 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLU C 217 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 216 "    0.009 2.00e-02 2.50e+03   1.85e-02 3.43e+00
        pdb=" C   GLU A 216 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLU A 216 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 217 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 213 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.73e+00
        pdb=" C   LYS B 213 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LYS B 213 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ALA B 214 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 885 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 975
        2.75 -     3.29: 5306
        3.29 -     3.82: 8175
        3.82 -     4.36: 9288
        4.36 -     4.90: 13784
  Nonbonded interactions: 37528
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP D 304 "
            pdb=" NZ  LYS D 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP B 304 "
            pdb=" NZ  LYS B 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP C 304 "
            pdb=" NZ  LYS C 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD1 ASP A 304 "
            pdb=" NZ  LYS A 331 "
     model   vdw
     2.211 3.120
  nonbonded pdb=" OD2 ASP B 304 "
            pdb=" OH  TYR B 348 "
     model   vdw
     2.249 3.040
  ... (remaining 37523 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'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.600
  Find NCS groups from input model:        0.150
  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:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6396
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      :  0.008   0.047   4964  Z= 0.512
  Angle     :  0.942  11.457   6684  Z= 0.560
  Chirality :  0.043   0.136    704
  Planarity :  0.004   0.021    888
  Dihedral  : 16.510  85.724   1960
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 19.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  9.56 %
    Allowed  :  9.74 %
    Favored  : 80.70 %
  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: -1.98 (0.32), residues: 580
  helix: -1.17 (0.22), residues: 412
  sheet:  None (None), residues: 0
  loop : -1.24 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 221 
 PHE   0.010   0.002   PHE C 275 
 TYR   0.012   0.002   TYR C 344 
 ARG   0.004   0.001   ARG D 222 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 238
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 GLU cc_start: 0.7273 (mp0) cc_final: 0.6856 (mp0)
REVERT: A  270 MET cc_start: 0.8052 (mtp) cc_final: 0.7609 (mtp)
REVERT: A  282 VAL cc_start: 0.8598 (OUTLIER) cc_final: 0.8355 (p)
REVERT: A  331 LYS cc_start: 0.8465 (mttt) cc_final: 0.8135 (mttt)
REVERT: B  220 GLU cc_start: 0.7569 (mp0) cc_final: 0.7185 (mp0)
REVERT: B  242 VAL cc_start: 0.8695 (t) cc_final: 0.8396 (t)
REVERT: B  260 MET cc_start: 0.5681 (ttp) cc_final: 0.5273 (ttp)
REVERT: B  314 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.8027 (m-10)
REVERT: B  325 ASN cc_start: 0.7286 (OUTLIER) cc_final: 0.6694 (p0)
REVERT: B  331 LYS cc_start: 0.8148 (mttt) cc_final: 0.7828 (mtpt)
REVERT: C  222 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8282 (mtt-85)
REVERT: C  242 VAL cc_start: 0.8918 (t) cc_final: 0.8717 (t)
REVERT: C  260 MET cc_start: 0.5597 (ttp) cc_final: 0.5340 (ttp)
REVERT: C  270 MET cc_start: 0.8300 (mtp) cc_final: 0.7692 (ttm)
REVERT: C  286 ASN cc_start: 0.7916 (p0) cc_final: 0.7650 (p0)
REVERT: C  304 ASP cc_start: 0.5186 (t0) cc_final: 0.4412 (t0)
REVERT: C  308 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: C  316 LYS cc_start: 0.8920 (tppp) cc_final: 0.8709 (tppp)
REVERT: C  325 ASN cc_start: 0.6600 (OUTLIER) cc_final: 0.6007 (p0)
REVERT: C  331 LYS cc_start: 0.8079 (mttt) cc_final: 0.7783 (mttt)
REVERT: D  260 MET cc_start: 0.5585 (ttp) cc_final: 0.4938 (ttp)
REVERT: D  270 MET cc_start: 0.8373 (mtp) cc_final: 0.7419 (mmm)
REVERT: D  286 ASN cc_start: 0.7794 (p0) cc_final: 0.7526 (p0)
REVERT: D  304 ASP cc_start: 0.5297 (t0) cc_final: 0.4719 (t0)
REVERT: D  314 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.8047 (m-10)
  outliers start: 52
  outliers final: 18
  residues processed: 271
  average time/residue: 0.2193
  time to fit residues: 70.5154
Evaluate side-chains
  250 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 226
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
C 231 ASN
D 231 ASN
D 267 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   4964  Z= 0.180
  Angle     :  0.562   6.190   6684  Z= 0.307
  Chirality :  0.040   0.146    704
  Planarity :  0.005   0.045    888
  Dihedral  :  4.104  18.022    668
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.86 %
    Favored  : 95.96 %
  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:  1.63 (0.35), residues: 580
  helix:  1.61 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop : -0.15 (0.54), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 330 
 PHE   0.008   0.001   PHE C 284 
 TYR   0.008   0.001   TYR B 314 
 ARG   0.005   0.001   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 224
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  220 GLU cc_start: 0.7565 (mp0) cc_final: 0.7123 (mp0)
REVERT: A  222 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7448 (mtp85)
REVERT: A  329 LEU cc_start: 0.8642 (mt) cc_final: 0.8435 (mt)
REVERT: B  218 ASP cc_start: 0.4211 (m-30) cc_final: 0.3412 (m-30)
REVERT: B  227 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8045 (mm-30)
REVERT: B  249 ASP cc_start: 0.7362 (t70) cc_final: 0.7042 (t0)
REVERT: B  260 MET cc_start: 0.5958 (ttp) cc_final: 0.5558 (ttp)
REVERT: B  270 MET cc_start: 0.8166 (mtp) cc_final: 0.7663 (mtp)
REVERT: B  304 ASP cc_start: 0.6599 (t0) cc_final: 0.6202 (t0)
REVERT: B  316 LYS cc_start: 0.8977 (mmtp) cc_final: 0.8631 (mmtp)
REVERT: B  322 TYR cc_start: 0.5877 (p90) cc_final: 0.5605 (p90)
REVERT: C  222 ARG cc_start: 0.8654 (mtt-85) cc_final: 0.8352 (mtt-85)
REVERT: C  226 ASP cc_start: 0.7961 (t0) cc_final: 0.7705 (t0)
REVERT: C  227 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8234 (mm-30)
REVERT: C  242 VAL cc_start: 0.8879 (t) cc_final: 0.8656 (t)
REVERT: C  246 MET cc_start: 0.8088 (mtp) cc_final: 0.7602 (mtp)
REVERT: C  249 ASP cc_start: 0.7140 (t70) cc_final: 0.6911 (t70)
REVERT: C  260 MET cc_start: 0.6010 (ttp) cc_final: 0.5138 (ttp)
REVERT: C  268 ASN cc_start: 0.6528 (m-40) cc_final: 0.6291 (m-40)
REVERT: C  269 ASN cc_start: 0.8198 (m-40) cc_final: 0.7927 (m-40)
REVERT: C  270 MET cc_start: 0.8020 (mtp) cc_final: 0.7565 (ttm)
REVERT: C  282 VAL cc_start: 0.8969 (t) cc_final: 0.8308 (p)
REVERT: C  304 ASP cc_start: 0.6376 (t0) cc_final: 0.5377 (t0)
REVERT: C  316 LYS cc_start: 0.8766 (tppp) cc_final: 0.8409 (tppp)
REVERT: C  334 LEU cc_start: 0.8692 (tp) cc_final: 0.8449 (tp)
REVERT: C  344 TYR cc_start: 0.8188 (t80) cc_final: 0.7970 (t80)
REVERT: D  242 VAL cc_start: 0.8648 (t) cc_final: 0.8406 (t)
REVERT: D  245 ASP cc_start: 0.8550 (m-30) cc_final: 0.8319 (m-30)
REVERT: D  260 MET cc_start: 0.5877 (ttp) cc_final: 0.5171 (ttp)
REVERT: D  268 ASN cc_start: 0.6689 (m-40) cc_final: 0.6399 (m-40)
REVERT: D  270 MET cc_start: 0.8246 (mtp) cc_final: 0.7389 (ttm)
REVERT: D  316 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8623 (mmtp)
REVERT: D  331 LYS cc_start: 0.8581 (mttt) cc_final: 0.8284 (mttt)
  outliers start: 1
  outliers final: 0
  residues processed: 225
  average time/residue: 0.2242
  time to fit residues: 60.0939
Evaluate side-chains
  213 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 28 optimal weight:    0.0980
   chunk 15 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0040
   chunk 55 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 243 GLN
B 243 GLN
C 243 GLN
C 248 ASN
C 310 ASN
C 327 GLN
D 243 GLN
D 327 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6627
moved from start:          0.4979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   4964  Z= 0.149
  Angle     :  0.507   6.161   6684  Z= 0.290
  Chirality :  0.038   0.144    704
  Planarity :  0.004   0.039    888
  Dihedral  :  3.761  21.582    668
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.81 (0.36), residues: 580
  helix:  2.54 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.16 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 221 
 PHE   0.010   0.001   PHE C 284 
 TYR   0.006   0.001   TYR A 318 
 ARG   0.002   0.000   ARG A 247 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7046 (mm-30)
REVERT: A  270 MET cc_start: 0.8167 (mtp) cc_final: 0.7784 (mtp)
REVERT: A  309 GLU cc_start: 0.7663 (pp20) cc_final: 0.7159 (pp20)
REVERT: A  310 ASN cc_start: 0.7660 (m-40) cc_final: 0.7048 (m-40)
REVERT: B  227 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7975 (mm-30)
REVERT: B  260 MET cc_start: 0.5841 (ttp) cc_final: 0.5545 (ttp)
REVERT: B  262 MET cc_start: 0.5427 (tmm) cc_final: 0.5186 (tmm)
REVERT: B  269 ASN cc_start: 0.8511 (m-40) cc_final: 0.8116 (m110)
REVERT: B  316 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8478 (mmtp)
REVERT: B  322 TYR cc_start: 0.5838 (p90) cc_final: 0.5450 (p90)
REVERT: B  331 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8336 (mttt)
REVERT: C  222 ARG cc_start: 0.8536 (mtt-85) cc_final: 0.8259 (mtt-85)
REVERT: C  226 ASP cc_start: 0.7949 (t0) cc_final: 0.7661 (t0)
REVERT: C  242 VAL cc_start: 0.8934 (t) cc_final: 0.8665 (t)
REVERT: C  246 MET cc_start: 0.8167 (mtp) cc_final: 0.7836 (mtp)
REVERT: C  249 ASP cc_start: 0.7045 (t70) cc_final: 0.6748 (t70)
REVERT: C  260 MET cc_start: 0.6007 (ttp) cc_final: 0.5443 (ttp)
REVERT: C  268 ASN cc_start: 0.6420 (m-40) cc_final: 0.6105 (m-40)
REVERT: C  269 ASN cc_start: 0.8236 (m-40) cc_final: 0.7744 (m-40)
REVERT: C  270 MET cc_start: 0.8045 (mtp) cc_final: 0.7550 (ttm)
REVERT: C  304 ASP cc_start: 0.6351 (t0) cc_final: 0.5433 (t0)
REVERT: C  313 ARG cc_start: 0.8331 (mtp85) cc_final: 0.7970 (mtp85)
REVERT: C  316 LYS cc_start: 0.8701 (tppp) cc_final: 0.8239 (tppp)
REVERT: C  331 LYS cc_start: 0.8770 (mtpt) cc_final: 0.8318 (mttt)
REVERT: C  344 TYR cc_start: 0.8142 (t80) cc_final: 0.7881 (t80)
REVERT: D  242 VAL cc_start: 0.8637 (t) cc_final: 0.8378 (t)
REVERT: D  244 ARG cc_start: 0.7899 (ttm170) cc_final: 0.7479 (ttm170)
REVERT: D  245 ASP cc_start: 0.8540 (m-30) cc_final: 0.8313 (m-30)
REVERT: D  260 MET cc_start: 0.5706 (ttp) cc_final: 0.5035 (ttp)
REVERT: D  266 ARG cc_start: 0.7965 (ttp-170) cc_final: 0.7662 (ptm-80)
REVERT: D  270 MET cc_start: 0.8093 (mtp) cc_final: 0.7318 (ttm)
REVERT: D  310 ASN cc_start: 0.8594 (m110) cc_final: 0.7773 (m110)
REVERT: D  316 LYS cc_start: 0.8911 (mmtp) cc_final: 0.8491 (mmtp)
REVERT: D  331 LYS cc_start: 0.8672 (mttt) cc_final: 0.8383 (mtpt)
REVERT: D  334 LEU cc_start: 0.8813 (tp) cc_final: 0.8536 (tp)
REVERT: D  344 TYR cc_start: 0.8201 (t80) cc_final: 0.7949 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 216
  average time/residue: 0.2482
  time to fit residues: 62.8833
Evaluate side-chains
  212 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 34 optimal weight:    0.2980
   chunk 51 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 45 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
B 310 ASN
C 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6708
moved from start:          0.5688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4964  Z= 0.143
  Angle     :  0.488   5.846   6684  Z= 0.279
  Chirality :  0.037   0.136    704
  Planarity :  0.004   0.035    888
  Dihedral  :  3.632  19.986    668
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  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:  3.26 (0.37), residues: 580
  helix:  2.84 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.43 (0.57), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 211 
 PHE   0.004   0.000   PHE A 284 
 TYR   0.009   0.001   TYR C 318 
 ARG   0.003   0.000   ARG C 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.591 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.7955 (mtt-85) cc_final: 0.7312 (mtp85)
REVERT: A  242 VAL cc_start: 0.8956 (p) cc_final: 0.8527 (p)
REVERT: A  260 MET cc_start: 0.6210 (ttp) cc_final: 0.5305 (ttp)
REVERT: A  262 MET cc_start: 0.5517 (tmm) cc_final: 0.5212 (tmm)
REVERT: A  270 MET cc_start: 0.8056 (mtp) cc_final: 0.7646 (mtp)
REVERT: A  316 LYS cc_start: 0.8640 (mtmm) cc_final: 0.8432 (mtmm)
REVERT: B  246 MET cc_start: 0.7959 (mtm) cc_final: 0.7502 (mtm)
REVERT: B  260 MET cc_start: 0.6006 (ttp) cc_final: 0.5765 (ttp)
REVERT: B  269 ASN cc_start: 0.8482 (m-40) cc_final: 0.7990 (m-40)
REVERT: B  282 VAL cc_start: 0.8896 (t) cc_final: 0.8620 (p)
REVERT: B  316 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8436 (mmtp)
REVERT: B  322 TYR cc_start: 0.6134 (p90) cc_final: 0.5648 (p90)
REVERT: B  331 LYS cc_start: 0.8840 (mttt) cc_final: 0.8484 (mtpt)
REVERT: B  332 ARG cc_start: 0.8403 (tpp-160) cc_final: 0.8179 (mmt-90)
REVERT: C  222 ARG cc_start: 0.8583 (mtt-85) cc_final: 0.8232 (mtt-85)
REVERT: C  226 ASP cc_start: 0.8019 (t0) cc_final: 0.7751 (t0)
REVERT: C  242 VAL cc_start: 0.8907 (t) cc_final: 0.8471 (t)
REVERT: C  246 MET cc_start: 0.8175 (mtp) cc_final: 0.7870 (mtp)
REVERT: C  249 ASP cc_start: 0.7141 (t70) cc_final: 0.6841 (t70)
REVERT: C  260 MET cc_start: 0.6076 (ttp) cc_final: 0.5688 (ttp)
REVERT: C  269 ASN cc_start: 0.8142 (m-40) cc_final: 0.7733 (m-40)
REVERT: C  304 ASP cc_start: 0.6304 (t0) cc_final: 0.5540 (t0)
REVERT: C  313 ARG cc_start: 0.8346 (mtp85) cc_final: 0.8039 (mtp85)
REVERT: C  316 LYS cc_start: 0.8609 (tppp) cc_final: 0.8045 (tppp)
REVERT: C  344 TYR cc_start: 0.8128 (t80) cc_final: 0.7841 (t80)
REVERT: D  242 VAL cc_start: 0.8576 (t) cc_final: 0.8312 (t)
REVERT: D  244 ARG cc_start: 0.7887 (ttm170) cc_final: 0.7539 (ttm170)
REVERT: D  245 ASP cc_start: 0.8574 (m-30) cc_final: 0.8250 (m-30)
REVERT: D  260 MET cc_start: 0.5888 (ttp) cc_final: 0.5057 (ttp)
REVERT: D  266 ARG cc_start: 0.8042 (ttp-170) cc_final: 0.7772 (ptm-80)
REVERT: D  316 LYS cc_start: 0.8879 (mmtp) cc_final: 0.8361 (mmtp)
REVERT: D  327 GLN cc_start: 0.6398 (mp-120) cc_final: 0.6150 (mp10)
REVERT: D  334 LEU cc_start: 0.8814 (tp) cc_final: 0.8598 (tp)
REVERT: D  344 TYR cc_start: 0.8179 (t80) cc_final: 0.7883 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.2501
  time to fit residues: 62.9009
Evaluate side-chains
  213 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 27 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 18 optimal weight:    0.4980
   chunk 10 optimal weight:    0.2980
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 252 ASN
B 231 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6705
moved from start:          0.6251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   4964  Z= 0.138
  Angle     :  0.480   6.739   6684  Z= 0.278
  Chirality :  0.038   0.131    704
  Planarity :  0.004   0.034    888
  Dihedral  :  3.633  19.965    668
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  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:  3.52 (0.36), residues: 580
  helix:  3.19 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.59 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP B 211 
 PHE   0.007   0.000   PHE C 284 
 TYR   0.009   0.001   TYR D 314 
 ARG   0.004   0.000   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7311 (mm-30)
REVERT: A  242 VAL cc_start: 0.8965 (p) cc_final: 0.8573 (p)
REVERT: A  260 MET cc_start: 0.6276 (ttp) cc_final: 0.5411 (ttp)
REVERT: A  262 MET cc_start: 0.5602 (tmm) cc_final: 0.5247 (tmm)
REVERT: A  270 MET cc_start: 0.7934 (mtp) cc_final: 0.7557 (mtp)
REVERT: A  316 LYS cc_start: 0.8624 (mtmm) cc_final: 0.8336 (mtmm)
REVERT: B  246 MET cc_start: 0.7965 (mtm) cc_final: 0.7469 (mtm)
REVERT: B  267 ASN cc_start: 0.6119 (t0) cc_final: 0.5697 (t0)
REVERT: B  269 ASN cc_start: 0.8406 (m-40) cc_final: 0.7927 (m-40)
REVERT: B  282 VAL cc_start: 0.8917 (t) cc_final: 0.8548 (p)
REVERT: B  304 ASP cc_start: 0.6895 (t0) cc_final: 0.6520 (t0)
REVERT: B  310 ASN cc_start: 0.8681 (m110) cc_final: 0.8425 (m110)
REVERT: B  316 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8329 (mmtp)
REVERT: B  331 LYS cc_start: 0.8845 (mttt) cc_final: 0.8022 (ttmm)
REVERT: B  332 ARG cc_start: 0.8404 (tpp-160) cc_final: 0.8154 (mmt-90)
REVERT: C  222 ARG cc_start: 0.8533 (mtt-85) cc_final: 0.8181 (mtt-85)
REVERT: C  229 LEU cc_start: 0.9006 (mt) cc_final: 0.8793 (mt)
REVERT: C  242 VAL cc_start: 0.8895 (t) cc_final: 0.8404 (t)
REVERT: C  246 MET cc_start: 0.8137 (mtp) cc_final: 0.7814 (mtp)
REVERT: C  249 ASP cc_start: 0.7014 (t70) cc_final: 0.6744 (t70)
REVERT: C  270 MET cc_start: 0.7865 (mtp) cc_final: 0.7469 (mtp)
REVERT: C  304 ASP cc_start: 0.6383 (t0) cc_final: 0.5040 (t0)
REVERT: C  316 LYS cc_start: 0.8526 (tppp) cc_final: 0.7909 (tppp)
REVERT: C  331 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8029 (ttmt)
REVERT: C  332 ARG cc_start: 0.8552 (tpp-160) cc_final: 0.8349 (mmt-90)
REVERT: C  344 TYR cc_start: 0.8075 (t80) cc_final: 0.7806 (t80)
REVERT: D  242 VAL cc_start: 0.8580 (t) cc_final: 0.8245 (t)
REVERT: D  244 ARG cc_start: 0.7871 (ttm170) cc_final: 0.7536 (ttm170)
REVERT: D  245 ASP cc_start: 0.8536 (m-30) cc_final: 0.8216 (m-30)
REVERT: D  260 MET cc_start: 0.5809 (ttp) cc_final: 0.5150 (ttp)
REVERT: D  304 ASP cc_start: 0.6740 (t0) cc_final: 0.6187 (t0)
REVERT: D  309 GLU cc_start: 0.8424 (pp20) cc_final: 0.8188 (pp20)
REVERT: D  316 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8346 (mmtp)
REVERT: D  327 GLN cc_start: 0.6390 (mp-120) cc_final: 0.6171 (mp10)
REVERT: D  331 LYS cc_start: 0.8830 (mttt) cc_final: 0.8073 (ttmt)
REVERT: D  334 LEU cc_start: 0.8769 (tp) cc_final: 0.8532 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.2504
  time to fit residues: 64.3628
Evaluate side-chains
  215 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 6 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 231 ASN
C 231 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.6682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   4964  Z= 0.146
  Angle     :  0.506   4.845   6684  Z= 0.294
  Chirality :  0.039   0.149    704
  Planarity :  0.004   0.034    888
  Dihedral  :  3.698  20.575    668
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.65 %
    Favored  : 98.35 %
  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:  3.48 (0.36), residues: 580
  helix:  3.21 (0.25), residues: 384
  sheet:  None (None), residues: 0
  loop :  0.45 (0.50), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 211 
 PHE   0.005   0.000   PHE C 284 
 TYR   0.013   0.001   TYR A 314 
 ARG   0.004   0.000   ARG B 228 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7428 (mm-30)
REVERT: A  242 VAL cc_start: 0.9080 (p) cc_final: 0.8796 (m)
REVERT: A  260 MET cc_start: 0.6422 (ttp) cc_final: 0.5998 (ttp)
REVERT: A  270 MET cc_start: 0.7996 (mtp) cc_final: 0.7571 (mtp)
REVERT: A  316 LYS cc_start: 0.8618 (mtmm) cc_final: 0.8357 (mtmm)
REVERT: B  246 MET cc_start: 0.8004 (mtm) cc_final: 0.7518 (mtm)
REVERT: B  269 ASN cc_start: 0.8392 (m-40) cc_final: 0.8035 (m-40)
REVERT: B  304 ASP cc_start: 0.7038 (t0) cc_final: 0.6615 (t0)
REVERT: B  316 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8284 (mmtp)
REVERT: B  322 TYR cc_start: 0.6227 (p90) cc_final: 0.5208 (p90)
REVERT: B  331 LYS cc_start: 0.8917 (mttt) cc_final: 0.8081 (ttmm)
REVERT: B  332 ARG cc_start: 0.8469 (tpp-160) cc_final: 0.8164 (mmt-90)
REVERT: C  222 ARG cc_start: 0.8582 (mtt-85) cc_final: 0.8181 (mtt-85)
REVERT: C  242 VAL cc_start: 0.8931 (t) cc_final: 0.8418 (t)
REVERT: C  246 MET cc_start: 0.8111 (mtp) cc_final: 0.7835 (mtp)
REVERT: C  249 ASP cc_start: 0.7121 (t70) cc_final: 0.6894 (t70)
REVERT: C  257 VAL cc_start: 0.8437 (t) cc_final: 0.8131 (t)
REVERT: C  304 ASP cc_start: 0.6413 (t0) cc_final: 0.5353 (t0)
REVERT: C  316 LYS cc_start: 0.8514 (tppp) cc_final: 0.7868 (tppp)
REVERT: C  331 LYS cc_start: 0.8858 (mttm) cc_final: 0.8282 (ttmt)
REVERT: C  344 TYR cc_start: 0.8067 (t80) cc_final: 0.7767 (t80)
REVERT: D  242 VAL cc_start: 0.8575 (t) cc_final: 0.8220 (t)
REVERT: D  244 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7525 (ttm170)
REVERT: D  245 ASP cc_start: 0.8539 (m-30) cc_final: 0.8245 (m-30)
REVERT: D  249 ASP cc_start: 0.7030 (t70) cc_final: 0.6442 (t70)
REVERT: D  260 MET cc_start: 0.5841 (ttp) cc_final: 0.5276 (ttp)
REVERT: D  269 ASN cc_start: 0.8206 (m-40) cc_final: 0.7913 (m-40)
REVERT: D  304 ASP cc_start: 0.6684 (t0) cc_final: 0.6255 (t0)
REVERT: D  309 GLU cc_start: 0.8463 (pp20) cc_final: 0.8200 (pp20)
REVERT: D  316 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8257 (mmtp)
REVERT: D  331 LYS cc_start: 0.8840 (mttt) cc_final: 0.8103 (ttmt)
REVERT: D  334 LEU cc_start: 0.8711 (tp) cc_final: 0.8441 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2745
  time to fit residues: 67.4104
Evaluate side-chains
  207 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    0.3980
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.7215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   4964  Z= 0.154
  Angle     :  0.513   5.932   6684  Z= 0.298
  Chirality :  0.039   0.135    704
  Planarity :  0.004   0.033    888
  Dihedral  :  3.687  18.439    668
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  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:  3.22 (0.35), residues: 580
  helix:  2.83 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.35 (0.55), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP B 211 
 PHE   0.008   0.001   PHE D 350 
 TYR   0.017   0.001   TYR A 314 
 ARG   0.005   0.000   ARG C 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 0.609 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: A  242 VAL cc_start: 0.9061 (p) cc_final: 0.8561 (p)
REVERT: A  260 MET cc_start: 0.6480 (ttp) cc_final: 0.6219 (ttp)
REVERT: A  270 MET cc_start: 0.7899 (mtp) cc_final: 0.7522 (mtp)
REVERT: A  314 TYR cc_start: 0.7692 (m-10) cc_final: 0.7301 (m-10)
REVERT: A  316 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8343 (mtmm)
REVERT: A  344 TYR cc_start: 0.7555 (t80) cc_final: 0.7349 (t80)
REVERT: B  246 MET cc_start: 0.8030 (mtm) cc_final: 0.7508 (mtm)
REVERT: B  269 ASN cc_start: 0.8312 (m-40) cc_final: 0.7804 (m-40)
REVERT: B  282 VAL cc_start: 0.8927 (t) cc_final: 0.8561 (p)
REVERT: B  304 ASP cc_start: 0.7090 (t0) cc_final: 0.6705 (t0)
REVERT: B  316 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8158 (mmtp)
REVERT: B  331 LYS cc_start: 0.8936 (mttt) cc_final: 0.8081 (ttmm)
REVERT: C  218 ASP cc_start: 0.4803 (m-30) cc_final: 0.4336 (m-30)
REVERT: C  222 ARG cc_start: 0.8588 (mtt-85) cc_final: 0.8269 (mtt-85)
REVERT: C  229 LEU cc_start: 0.9020 (mt) cc_final: 0.8791 (mt)
REVERT: C  242 VAL cc_start: 0.8953 (t) cc_final: 0.8432 (t)
REVERT: C  246 MET cc_start: 0.8101 (mtp) cc_final: 0.7857 (mtp)
REVERT: C  249 ASP cc_start: 0.7121 (t70) cc_final: 0.6776 (t70)
REVERT: C  257 VAL cc_start: 0.8454 (t) cc_final: 0.8137 (t)
REVERT: C  260 MET cc_start: 0.6001 (ttp) cc_final: 0.5699 (ttp)
REVERT: C  270 MET cc_start: 0.7857 (mtp) cc_final: 0.7495 (mtp)
REVERT: C  304 ASP cc_start: 0.6432 (t0) cc_final: 0.6196 (t0)
REVERT: C  316 LYS cc_start: 0.8472 (tppp) cc_final: 0.7794 (tppp)
REVERT: C  333 GLN cc_start: 0.8276 (tt0) cc_final: 0.8072 (tt0)
REVERT: C  344 TYR cc_start: 0.8042 (t80) cc_final: 0.7737 (t80)
REVERT: D  232 LEU cc_start: 0.8801 (mt) cc_final: 0.8590 (mt)
REVERT: D  242 VAL cc_start: 0.8598 (t) cc_final: 0.8235 (t)
REVERT: D  244 ARG cc_start: 0.7866 (ttm170) cc_final: 0.7511 (ttm170)
REVERT: D  245 ASP cc_start: 0.8561 (m-30) cc_final: 0.8268 (m-30)
REVERT: D  260 MET cc_start: 0.5834 (ttp) cc_final: 0.5275 (ttp)
REVERT: D  270 MET cc_start: 0.8055 (mtp) cc_final: 0.7410 (ttm)
REVERT: D  309 GLU cc_start: 0.8503 (pp20) cc_final: 0.8204 (pp20)
REVERT: D  314 TYR cc_start: 0.8200 (m-10) cc_final: 0.7859 (m-10)
REVERT: D  316 LYS cc_start: 0.8825 (mmtp) cc_final: 0.8208 (mmtp)
REVERT: D  331 LYS cc_start: 0.8810 (mttt) cc_final: 0.7913 (ttmt)
REVERT: D  334 LEU cc_start: 0.8614 (tp) cc_final: 0.8236 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2703
  time to fit residues: 66.6385
Evaluate side-chains
  211 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 5 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 51 optimal weight:    0.0060
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.6198

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

Flipped N/Q/H residues before XYZ refinement:
A 310 ASN
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6762
moved from start:          0.7529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4964  Z= 0.146
  Angle     :  0.511   5.350   6684  Z= 0.296
  Chirality :  0.039   0.147    704
  Planarity :  0.004   0.036    888
  Dihedral  :  3.735  17.619    668
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.29 %
    Favored  : 98.71 %
  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:  3.31 (0.36), residues: 580
  helix:  2.88 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.42 (0.56), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 211 
 PHE   0.010   0.001   PHE C 350 
 TYR   0.013   0.001   TYR A 314 
 ARG   0.005   0.000   ARG C 255 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  222 ARG cc_start: 0.8506 (ptm160) cc_final: 0.8085 (ptp-170)
REVERT: A  227 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7591 (mm-30)
REVERT: A  242 VAL cc_start: 0.9071 (p) cc_final: 0.8494 (p)
REVERT: A  260 MET cc_start: 0.6488 (ttp) cc_final: 0.6202 (ttp)
REVERT: A  270 MET cc_start: 0.7904 (mtp) cc_final: 0.7489 (mtp)
REVERT: A  314 TYR cc_start: 0.7713 (m-10) cc_final: 0.7220 (m-10)
REVERT: A  316 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8226 (mtmm)
REVERT: A  344 TYR cc_start: 0.7570 (t80) cc_final: 0.7355 (t80)
REVERT: B  222 ARG cc_start: 0.8406 (mtm110) cc_final: 0.7979 (mtm110)
REVERT: B  246 MET cc_start: 0.7991 (mtm) cc_final: 0.7483 (mtm)
REVERT: B  257 VAL cc_start: 0.8561 (t) cc_final: 0.8357 (t)
REVERT: B  267 ASN cc_start: 0.5721 (t0) cc_final: 0.5447 (t0)
REVERT: B  269 ASN cc_start: 0.8312 (m-40) cc_final: 0.7791 (m-40)
REVERT: B  282 VAL cc_start: 0.8920 (t) cc_final: 0.8555 (p)
REVERT: B  316 LYS cc_start: 0.8715 (mmtp) cc_final: 0.8194 (mmtp)
REVERT: B  322 TYR cc_start: 0.6332 (p90) cc_final: 0.5615 (p90)
REVERT: B  331 LYS cc_start: 0.8935 (mttt) cc_final: 0.8006 (ttmm)
REVERT: C  218 ASP cc_start: 0.4815 (m-30) cc_final: 0.4442 (m-30)
REVERT: C  222 ARG cc_start: 0.8598 (mtt-85) cc_final: 0.8244 (mtt-85)
REVERT: C  229 LEU cc_start: 0.9052 (mt) cc_final: 0.8794 (mt)
REVERT: C  242 VAL cc_start: 0.8944 (t) cc_final: 0.8401 (t)
REVERT: C  246 MET cc_start: 0.8072 (mtp) cc_final: 0.7838 (mtp)
REVERT: C  249 ASP cc_start: 0.7200 (t70) cc_final: 0.6808 (t70)
REVERT: C  257 VAL cc_start: 0.8444 (t) cc_final: 0.8241 (t)
REVERT: C  260 MET cc_start: 0.5981 (ttp) cc_final: 0.5723 (ttp)
REVERT: C  270 MET cc_start: 0.7901 (mtp) cc_final: 0.7495 (mtp)
REVERT: C  279 ILE cc_start: 0.8446 (pt) cc_final: 0.8242 (pt)
REVERT: C  304 ASP cc_start: 0.6768 (t0) cc_final: 0.5665 (t0)
REVERT: C  316 LYS cc_start: 0.8433 (tppp) cc_final: 0.7793 (tppp)
REVERT: C  322 TYR cc_start: 0.6611 (p90) cc_final: 0.6366 (p90)
REVERT: C  331 LYS cc_start: 0.8834 (mttt) cc_final: 0.8200 (ttmt)
REVERT: C  344 TYR cc_start: 0.8017 (t80) cc_final: 0.7750 (t80)
REVERT: D  232 LEU cc_start: 0.8797 (mt) cc_final: 0.8596 (mt)
REVERT: D  242 VAL cc_start: 0.8575 (t) cc_final: 0.8206 (t)
REVERT: D  244 ARG cc_start: 0.7853 (ttm170) cc_final: 0.7497 (ttm170)
REVERT: D  245 ASP cc_start: 0.8558 (m-30) cc_final: 0.8285 (m-30)
REVERT: D  270 MET cc_start: 0.7921 (mtp) cc_final: 0.7388 (ttm)
REVERT: D  309 GLU cc_start: 0.8505 (pp20) cc_final: 0.8199 (pp20)
REVERT: D  314 TYR cc_start: 0.8289 (m-10) cc_final: 0.7905 (m-10)
REVERT: D  316 LYS cc_start: 0.8744 (mmtp) cc_final: 0.8183 (mmtp)
REVERT: D  331 LYS cc_start: 0.8861 (mttt) cc_final: 0.8024 (ttmt)
REVERT: D  334 LEU cc_start: 0.8583 (tp) cc_final: 0.8209 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2751
  time to fit residues: 65.9621
Evaluate side-chains
  204 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 51 optimal weight:    4.9990
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
A 269 ASN
** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6801
moved from start:          0.7883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4964  Z= 0.172
  Angle     :  0.574   8.965   6684  Z= 0.332
  Chirality :  0.040   0.143    704
  Planarity :  0.004   0.036    888
  Dihedral  :  3.868  17.405    668
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.37 %
    Favored  : 99.63 %
  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:  3.19 (0.36), residues: 580
  helix:  2.78 (0.24), residues: 412
  sheet:  None (None), residues: 0
  loop :  0.44 (0.57), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 211 
 PHE   0.007   0.001   PHE C 350 
 TYR   0.010   0.001   TYR A 314 
 ARG   0.012   0.000   ARG A 222 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.769 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  232 LEU cc_start: 0.8748 (mt) cc_final: 0.8496 (mt)
REVERT: A  242 VAL cc_start: 0.9087 (p) cc_final: 0.8585 (p)
REVERT: A  260 MET cc_start: 0.6668 (ttp) cc_final: 0.6200 (ttp)
REVERT: A  262 MET cc_start: 0.5814 (tmm) cc_final: 0.5583 (tmm)
REVERT: A  314 TYR cc_start: 0.8022 (m-10) cc_final: 0.7434 (m-10)
REVERT: A  316 LYS cc_start: 0.8597 (mtmm) cc_final: 0.8252 (mtmm)
REVERT: A  329 LEU cc_start: 0.8790 (mt) cc_final: 0.8586 (mt)
REVERT: A  344 TYR cc_start: 0.7636 (t80) cc_final: 0.7394 (t80)
REVERT: B  242 VAL cc_start: 0.8749 (t) cc_final: 0.8520 (t)
REVERT: B  246 MET cc_start: 0.8043 (mtm) cc_final: 0.7496 (mtm)
REVERT: B  267 ASN cc_start: 0.5790 (t0) cc_final: 0.5284 (t0)
REVERT: B  269 ASN cc_start: 0.8306 (m-40) cc_final: 0.7744 (m-40)
REVERT: B  282 VAL cc_start: 0.8902 (t) cc_final: 0.8535 (p)
REVERT: B  310 ASN cc_start: 0.8694 (m110) cc_final: 0.8456 (m-40)
REVERT: B  316 LYS cc_start: 0.8690 (mmtp) cc_final: 0.8187 (mmtp)
REVERT: B  322 TYR cc_start: 0.6281 (p90) cc_final: 0.5632 (p90)
REVERT: B  331 LYS cc_start: 0.8942 (mttt) cc_final: 0.8088 (ttmm)
REVERT: C  218 ASP cc_start: 0.4869 (m-30) cc_final: 0.4557 (m-30)
REVERT: C  222 ARG cc_start: 0.8643 (mtt-85) cc_final: 0.8272 (mtt-85)
REVERT: C  229 LEU cc_start: 0.9054 (mt) cc_final: 0.8787 (mt)
REVERT: C  242 VAL cc_start: 0.8933 (t) cc_final: 0.8381 (t)
REVERT: C  246 MET cc_start: 0.8070 (mtp) cc_final: 0.7861 (mtp)
REVERT: C  249 ASP cc_start: 0.7184 (t70) cc_final: 0.6884 (t70)
REVERT: C  260 MET cc_start: 0.5946 (ttp) cc_final: 0.5674 (ttp)
REVERT: C  270 MET cc_start: 0.7936 (mtp) cc_final: 0.7563 (mtp)
REVERT: C  279 ILE cc_start: 0.8452 (pt) cc_final: 0.8218 (pt)
REVERT: C  316 LYS cc_start: 0.8453 (tppp) cc_final: 0.7836 (tppp)
REVERT: C  344 TYR cc_start: 0.8033 (t80) cc_final: 0.7740 (t80)
REVERT: D  242 VAL cc_start: 0.8627 (t) cc_final: 0.8217 (t)
REVERT: D  244 ARG cc_start: 0.7890 (ttm170) cc_final: 0.7562 (ttm170)
REVERT: D  245 ASP cc_start: 0.8604 (m-30) cc_final: 0.8339 (m-30)
REVERT: D  249 ASP cc_start: 0.7002 (t70) cc_final: 0.6304 (t70)
REVERT: D  270 MET cc_start: 0.7923 (mtp) cc_final: 0.7414 (ttm)
REVERT: D  309 GLU cc_start: 0.8544 (pp20) cc_final: 0.8279 (pp20)
REVERT: D  316 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8182 (mmtp)
REVERT: D  331 LYS cc_start: 0.8866 (mttt) cc_final: 0.8129 (ttmt)
REVERT: D  332 ARG cc_start: 0.8708 (tpp-160) cc_final: 0.8414 (mmt-90)
REVERT: D  334 LEU cc_start: 0.8582 (tp) cc_final: 0.8224 (tp)
REVERT: D  344 TYR cc_start: 0.8075 (t80) cc_final: 0.7714 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2714
  time to fit residues: 65.5240
Evaluate side-chains
  204 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    0.0050
   chunk 34 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 47 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 40 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 231 ASN
A 267 ASN
B 231 ASN
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 231 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 231 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6760
moved from start:          0.8032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4964  Z= 0.150
  Angle     :  0.551   5.992   6684  Z= 0.320
  Chirality :  0.040   0.136    704
  Planarity :  0.004   0.060    888
  Dihedral  :  3.827  20.422    668
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  3.26 (0.36), residues: 580
  helix:  2.91 (0.25), residues: 408
  sheet:  None (None), residues: 0
  loop :  0.29 (0.55), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 211 
 PHE   0.005   0.001   PHE A 350 
 TYR   0.019   0.001   TYR D 348 
 ARG   0.006   0.000   ARG A 222 

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

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

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1160 Ramachandran restraints generated.
    580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8071 (mm-30)
REVERT: A  242 VAL cc_start: 0.9053 (p) cc_final: 0.8503 (p)
REVERT: A  260 MET cc_start: 0.6721 (ttp) cc_final: 0.5960 (ttp)
REVERT: A  314 TYR cc_start: 0.7858 (m-10) cc_final: 0.7484 (m-10)
REVERT: A  316 LYS cc_start: 0.8543 (mtmm) cc_final: 0.8205 (mtmm)
REVERT: A  344 TYR cc_start: 0.7650 (t80) cc_final: 0.7393 (t80)
REVERT: B  222 ARG cc_start: 0.8326 (mtm110) cc_final: 0.7938 (mtm110)
REVERT: B  242 VAL cc_start: 0.8699 (t) cc_final: 0.8488 (t)
REVERT: B  246 MET cc_start: 0.7947 (mtm) cc_final: 0.7467 (mtm)
REVERT: B  257 VAL cc_start: 0.8554 (t) cc_final: 0.8285 (t)
REVERT: B  267 ASN cc_start: 0.5519 (t0) cc_final: 0.5067 (t0)
REVERT: B  269 ASN cc_start: 0.8298 (m-40) cc_final: 0.7767 (m-40)
REVERT: B  282 VAL cc_start: 0.8921 (t) cc_final: 0.8560 (p)
REVERT: B  316 LYS cc_start: 0.8697 (mmtp) cc_final: 0.8152 (mmtp)
REVERT: B  322 TYR cc_start: 0.6266 (p90) cc_final: 0.5592 (p90)
REVERT: B  331 LYS cc_start: 0.8902 (mttt) cc_final: 0.8029 (ttmm)
REVERT: C  218 ASP cc_start: 0.4718 (m-30) cc_final: 0.4509 (m-30)
REVERT: C  222 ARG cc_start: 0.8655 (mtt-85) cc_final: 0.8170 (mtt-85)
REVERT: C  242 VAL cc_start: 0.8903 (t) cc_final: 0.8369 (t)
REVERT: C  249 ASP cc_start: 0.7138 (t70) cc_final: 0.6874 (t70)
REVERT: C  257 VAL cc_start: 0.8463 (t) cc_final: 0.8201 (t)
REVERT: C  260 MET cc_start: 0.5984 (ttp) cc_final: 0.5631 (ttp)
REVERT: C  270 MET cc_start: 0.7901 (mtp) cc_final: 0.7588 (mtp)
REVERT: C  316 LYS cc_start: 0.8363 (tppp) cc_final: 0.7722 (tppp)
REVERT: C  331 LYS cc_start: 0.8874 (mttt) cc_final: 0.8033 (ttmt)
REVERT: C  344 TYR cc_start: 0.7997 (t80) cc_final: 0.7691 (t80)
REVERT: D  242 VAL cc_start: 0.8556 (t) cc_final: 0.8177 (t)
REVERT: D  244 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7494 (ttm170)
REVERT: D  245 ASP cc_start: 0.8571 (m-30) cc_final: 0.8295 (m-30)
REVERT: D  249 ASP cc_start: 0.6957 (t70) cc_final: 0.6279 (t70)
REVERT: D  270 MET cc_start: 0.7855 (mtp) cc_final: 0.7311 (ttm)
REVERT: D  309 GLU cc_start: 0.8529 (pp20) cc_final: 0.8190 (pp20)
REVERT: D  314 TYR cc_start: 0.8224 (m-10) cc_final: 0.7910 (m-10)
REVERT: D  316 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8334 (mmtp)
REVERT: D  331 LYS cc_start: 0.8875 (mttt) cc_final: 0.8167 (ttmt)
REVERT: D  334 LEU cc_start: 0.8595 (tp) cc_final: 0.8267 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.2718
  time to fit residues: 63.4410
Evaluate side-chains
  201 residues out of total 544 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 252 ASN
** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 269 ASN
** C 268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 269 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.099488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.083973 restraints weight = 12914.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.087440 restraints weight = 6599.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.089722 restraints weight = 4070.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.8271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4964  Z= 0.167
  Angle     :  0.555   6.159   6684  Z= 0.325
  Chirality :  0.040   0.146    704
  Planarity :  0.004   0.053    888
  Dihedral  :  3.970  19.808    668
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  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:  3.07 (0.36), residues: 580
  helix:  2.74 (0.24), residues: 408
  sheet:  None (None), residues: 0
  loop :  0.31 (0.56), residues: 172

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 211 
 PHE   0.015   0.001   PHE A 275 
 TYR   0.010   0.001   TYR A 314 
 ARG   0.007   0.000   ARG A 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1824.36 seconds
wall clock time: 33 minutes 49.75 seconds (2029.75 seconds total)