Starting phenix.real_space_refine
on Tue Feb 11 03:16:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6y5l_10701/02_2025/6y5l_10701.cif"
  }
  resolution = 3.6
  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=   0.004 sd=   0.140
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      12      5.16       5
     C    2403      2.51       5
     N     654      2.21       5
     O     786      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3855
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 531
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 531
          Classifications: {'peptide': 70}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 63}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 740
          Classifications: {'peptide': 89}
          Link IDs: {'TRANS': 88}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Restraints were copied for chains:
    C, E, D, F
  Time building chain proxies: 3.60, per 1000 atoms: 0.93
  Number of scatterers: 3855
  At special positions: 0
  Unit cell: (68.481, 71.742, 147.832, 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      12     16.00
     O     786      8.00
     N     654      7.00
     C    2403      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 281 " - pdb=" SG  CYS A 305 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 401 " - " ASN A  38 "
      " NAG C 401 " - " ASN C  38 "
      " NAG E 401 " - " ASN E  38 "
  Time building additional restraints: 0.98
  Conformation dependent library (CDL) restraints added in 409.3 milliseconds
  

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  918

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 9 sheets defined
      55.3% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'B' and resid 38 through 125
    Processing helix  chain 'D' and resid 38 through 125
    Processing helix  chain 'F' and resid 38 through 125
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26
    Processing sheet with id=AA2, first strand: chain 'A' and resid 282 through 283
    Processing sheet with id=AA3, first strand: chain 'A' and resid 294 through 295
    Processing sheet with id=AA4, first strand: chain 'C' and resid 24 through 26
    Processing sheet with id=AA5, first strand: chain 'C' and resid 282 through 283
    Processing sheet with id=AA6, first strand: chain 'C' and resid 294 through 295
    Processing sheet with id=AA7, first strand: chain 'E' and resid 24 through 26
    Processing sheet with id=AA8, first strand: chain 'E' and resid 282 through 283
    Processing sheet with id=AA9, first strand: chain 'E' and resid 294 through 295

    273 hydrogen bonds defined for protein.
    792 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: 0.95

  Time building geometry restraints manager: 1.14 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: 1270
        1.34 -     1.46: 370
        1.46 -     1.57: 2242
        1.57 -     1.69: 0
        1.69 -     1.80: 18
  Bond restraints: 3900
  Sorted by residual:
  bond pdb=" C1  NAG C 401 "
       pdb=" O5  NAG C 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.72e+00
  bond pdb=" C1  NAG E 401 "
       pdb=" O5  NAG E 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.71e+00
  bond pdb=" C1  NAG A 401 "
       pdb=" O5  NAG A 401 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.69e+00
  bond pdb=" C5  NAG E 401 "
       pdb=" O5  NAG E 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.27e+00
  bond pdb=" C5  NAG C 401 "
       pdb=" O5  NAG C 401 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  ... (remaining 3895 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 4959
        1.37 -     2.73: 272
        2.73 -     4.10: 37
        4.10 -     5.46: 0
        5.46 -     6.83: 3
  Bond angle restraints: 5271
  Sorted by residual:
  angle pdb=" N   ILE E  29 "
        pdb=" CA  ILE E  29 "
        pdb=" C   ILE E  29 "
      ideal   model   delta    sigma   weight residual
     112.96  110.20    2.76 1.00e+00 1.00e+00 7.60e+00
  angle pdb=" N   ILE C  29 "
        pdb=" CA  ILE C  29 "
        pdb=" C   ILE C  29 "
      ideal   model   delta    sigma   weight residual
     112.96  110.22    2.74 1.00e+00 1.00e+00 7.50e+00
  angle pdb=" N   ILE A  29 "
        pdb=" CA  ILE A  29 "
        pdb=" C   ILE A  29 "
      ideal   model   delta    sigma   weight residual
     112.96  110.23    2.73 1.00e+00 1.00e+00 7.47e+00
  angle pdb=" N   ALA E 317 "
        pdb=" CA  ALA E 317 "
        pdb=" C   ALA E 317 "
      ideal   model   delta    sigma   weight residual
     110.42  114.10   -3.68 1.46e+00 4.69e-01 6.35e+00
  angle pdb=" N   ALA A 317 "
        pdb=" CA  ALA A 317 "
        pdb=" C   ALA A 317 "
      ideal   model   delta    sigma   weight residual
     110.42  114.05   -3.63 1.46e+00 4.69e-01 6.18e+00
  ... (remaining 5266 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.34: 2208
       17.34 -    34.67: 204
       34.67 -    52.01: 48
       52.01 -    69.35: 6
       69.35 -    86.69: 3
  Dihedral angle restraints: 2469
    sinusoidal: 1071
      harmonic: 1398
  Sorted by residual:
  dihedral pdb=" CA  PRO C 306 "
           pdb=" C   PRO C 306 "
           pdb=" N   LYS C 307 "
           pdb=" CA  LYS C 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.72  -16.28     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  PRO A 306 "
           pdb=" C   PRO A 306 "
           pdb=" N   LYS A 307 "
           pdb=" CA  LYS A 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.76  -16.24     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" CA  PRO E 306 "
           pdb=" C   PRO E 306 "
           pdb=" N   LYS E 307 "
           pdb=" CA  LYS E 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.79  -16.21     0      5.00e+00 4.00e-02 1.05e+01
  ... (remaining 2466 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 343
       0.028 -    0.057: 154
       0.057 -    0.085: 64
       0.085 -    0.113: 40
       0.113 -    0.141: 26
  Chirality restraints: 627
  Sorted by residual:
  chirality pdb=" CA  ASP F  46 "
            pdb=" N   ASP F  46 "
            pdb=" C   ASP F  46 "
            pdb=" CB  ASP F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.00e-01
  chirality pdb=" CA  ASP B  46 "
            pdb=" N   ASP B  46 "
            pdb=" C   ASP B  46 "
            pdb=" CB  ASP B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.97e-01
  chirality pdb=" CA  ASP D  46 "
            pdb=" N   ASP D  46 "
            pdb=" C   ASP D  46 "
            pdb=" CB  ASP D  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  ... (remaining 624 not shown)

  Planarity restraints: 687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP B  46 "    0.013 2.00e-02 2.50e+03   2.54e-02 6.47e+00
        pdb=" CG  ASP B  46 "   -0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASP B  46 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP B  46 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP F  46 "   -0.013 2.00e-02 2.50e+03   2.54e-02 6.43e+00
        pdb=" CG  ASP F  46 "    0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASP F  46 "   -0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP F  46 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D  46 "    0.013 2.00e-02 2.50e+03   2.53e-02 6.38e+00
        pdb=" CG  ASP D  46 "   -0.044 2.00e-02 2.50e+03
        pdb=" OD1 ASP D  46 "    0.015 2.00e-02 2.50e+03
        pdb=" OD2 ASP D  46 "    0.016 2.00e-02 2.50e+03
  ... (remaining 684 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 53
        2.61 -     3.18: 3632
        3.18 -     3.75: 5771
        3.75 -     4.33: 7219
        4.33 -     4.90: 12244
  Nonbonded interactions: 28919
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E 281 "
            pdb=" SG  CYS E 305 "
     model   vdw
     2.032 3.760
  nonbonded pdb=" SG  CYS C 281 "
            pdb=" SG  CYS C 305 "
     model   vdw
     2.033 3.760
  nonbonded pdb=" NZ  LYS A  27 "
            pdb=" OE2 GLU B  97 "
     model   vdw
     2.161 3.120
  nonbonded pdb=" NZ  LYS E  27 "
            pdb=" OE2 GLU F  97 "
     model   vdw
     2.259 3.120
  nonbonded pdb=" NZ  LYS C  27 "
            pdb=" OE2 GLU D  97 "
     model   vdw
     2.388 3.120
  ... (remaining 28914 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
}

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=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.880
  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:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     14.230
  Find NCS groups from input model:        0.090
  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:2.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
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   0.032   3900  Z= 0.222
  Angle     :  0.701   6.830   5271  Z= 0.401
  Chirality :  0.048   0.141    627
  Planarity :  0.006   0.051    684
  Dihedral  : 14.311  86.685   1548
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.84 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  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: -2.14 (0.34), residues: 459
  helix:  0.80 (0.25), residues: 261
  sheet: -4.11 (0.66), residues: 30
  loop : -4.75 (0.34), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP D  92 
 HIS   0.005   0.002   HIS F  64 
 PHE   0.023   0.003   PHE D  63 
 TYR   0.022   0.003   TYR E 308 
 ARG   0.002   0.000   ARG F  54 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.471 
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: A  307 LYS cc_start: 0.7659 (mmmt) cc_final: 0.7178 (mtpp)
REVERT: B   51 LYS cc_start: 0.9019 (mmtt) cc_final: 0.8788 (ptpp)
REVERT: B   54 ARG cc_start: 0.8310 (mtp85) cc_final: 0.7903 (ttm110)
REVERT: B  110 LEU cc_start: 0.9037 (mt) cc_final: 0.8639 (mt)
REVERT: B  121 LYS cc_start: 0.9238 (mtpt) cc_final: 0.9020 (tmtt)
REVERT: C  307 LYS cc_start: 0.7251 (mmmt) cc_final: 0.6919 (mtpp)
REVERT: E  307 LYS cc_start: 0.7392 (mmmt) cc_final: 0.7108 (mtpp)
REVERT: E  320 MET cc_start: 0.6638 (ttm) cc_final: 0.5879 (ttm)
REVERT: D   51 LYS cc_start: 0.9065 (mmtt) cc_final: 0.8650 (ptpp)
REVERT: D   54 ARG cc_start: 0.8365 (mtp85) cc_final: 0.8128 (ttm110)
REVERT: D   58 LYS cc_start: 0.8887 (mttt) cc_final: 0.8652 (mttm)
REVERT: D  110 LEU cc_start: 0.9188 (mt) cc_final: 0.8738 (mt)
REVERT: F   54 ARG cc_start: 0.8435 (mtp85) cc_final: 0.8197 (ttm110)
REVERT: F   64 HIS cc_start: 0.7756 (m-70) cc_final: 0.7452 (m-70)
REVERT: F  112 ASP cc_start: 0.8912 (p0) cc_final: 0.8608 (p0)
REVERT: F  121 LYS cc_start: 0.9208 (mtpt) cc_final: 0.8890 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1947
  time to fit residues: 46.5737
Evaluate side-chains
  163 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 34 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 21 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 40 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9980
   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 296 ASN
A 322 ASN
B  60 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
C 322 ASN
E 296 ASN
E 322 ASN
D  60 ASN
D  78 GLN
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  53 ASN
F  60 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.130609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.097425 restraints weight = 6988.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.097080 restraints weight = 5514.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.098759 restraints weight = 4939.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.3128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3900  Z= 0.279
  Angle     :  0.681   4.865   5271  Z= 0.370
  Chirality :  0.046   0.153    627
  Planarity :  0.006   0.041    684
  Dihedral  :  5.106  37.124    561
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 9.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 19.77 %
    Favored  : 77.70 %
  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: -0.37 (0.38), residues: 459
  helix:  2.52 (0.26), residues: 261
  sheet: -4.23 (0.47), residues: 30
  loop : -4.33 (0.37), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  92 
 HIS   0.010   0.002   HIS B 106 
 PHE   0.015   0.002   PHE B  70 
 TYR   0.014   0.003   TYR E 308 
 ARG   0.006   0.001   ARG F 123 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 169
  time to evaluate  : 0.368 
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: A  307 LYS cc_start: 0.7570 (mmmt) cc_final: 0.7170 (mtpp)
REVERT: B   51 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8726 (ptpp)
REVERT: B   58 LYS cc_start: 0.8932 (mttp) cc_final: 0.8689 (mmtp)
REVERT: B   64 HIS cc_start: 0.8024 (OUTLIER) cc_final: 0.7296 (t-90)
REVERT: B  110 LEU cc_start: 0.8922 (mt) cc_final: 0.8514 (mt)
REVERT: C  307 LYS cc_start: 0.7415 (mmmt) cc_final: 0.7056 (mtpp)
REVERT: E  320 MET cc_start: 0.6836 (ttm) cc_final: 0.6503 (ttm)
REVERT: D   51 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8611 (ptpp)
REVERT: D   58 LYS cc_start: 0.8927 (mttt) cc_final: 0.8679 (mttm)
REVERT: D  110 LEU cc_start: 0.9093 (mt) cc_final: 0.8884 (mt)
REVERT: F   54 ARG cc_start: 0.8454 (mtp85) cc_final: 0.8175 (ttm110)
REVERT: F   58 LYS cc_start: 0.8965 (mttt) cc_final: 0.8757 (mmtt)
REVERT: F   64 HIS cc_start: 0.8131 (m-70) cc_final: 0.7683 (m-70)
  outliers start: 11
  outliers final: 3
  residues processed: 170
  average time/residue: 0.1936
  time to fit residues: 38.7461
Evaluate side-chains
  158 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain D residue   64 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 29 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0870
   chunk 3 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0370
   chunk 31 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
A 296 ASN
B 105 GLN
C 322 ASN
E 296 ASN
E 322 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.130430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.097738 restraints weight = 6979.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.097458 restraints weight = 7054.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.098673 restraints weight = 5340.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3900  Z= 0.254
  Angle     :  0.749  11.123   5271  Z= 0.404
  Chirality :  0.046   0.147    627
  Planarity :  0.005   0.046    684
  Dihedral  :  4.964  36.419    561
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 21.84 %
    Favored  : 74.02 %
  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:  0.44 (0.40), residues: 459
  helix:  3.23 (0.27), residues: 261
  sheet: -4.23 (0.47), residues: 30
  loop : -4.00 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.011   0.003   HIS B 106 
 PHE   0.010   0.001   PHE B  70 
 TYR   0.012   0.003   TYR C 302 
 ARG   0.005   0.001   ARG F 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.483 
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: A  307 LYS cc_start: 0.7532 (mmmt) cc_final: 0.7172 (mtpp)
REVERT: B   64 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7310 (t-90)
REVERT: B  112 ASP cc_start: 0.8497 (p0) cc_final: 0.8296 (p0)
REVERT: C  307 LYS cc_start: 0.7469 (mmmt) cc_final: 0.7093 (mtpp)
REVERT: E  320 MET cc_start: 0.7024 (ttm) cc_final: 0.6672 (ttm)
REVERT: D   58 LYS cc_start: 0.8860 (mttt) cc_final: 0.8562 (mttm)
REVERT: D  116 ASN cc_start: 0.8719 (m110) cc_final: 0.8030 (t0)
REVERT: F   51 LYS cc_start: 0.9010 (mmtt) cc_final: 0.8750 (ptpp)
REVERT: F   54 ARG cc_start: 0.8075 (mtp85) cc_final: 0.7778 (ttm110)
REVERT: F   58 LYS cc_start: 0.8915 (mttt) cc_final: 0.8631 (mmtp)
REVERT: F   64 HIS cc_start: 0.8117 (m-70) cc_final: 0.7792 (m170)
  outliers start: 18
  outliers final: 12
  residues processed: 171
  average time/residue: 0.1878
  time to fit residues: 38.0349
Evaluate side-chains
  160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain E residue  296 ASN
Chi-restraints excluded: chain D residue   64 HIS
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain F residue   88 LYS
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 18 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0970
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 322 ASN
E 311 GLN
E 322 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.130299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.097341 restraints weight = 6918.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.097629 restraints weight = 6321.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.098591 restraints weight = 5245.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.4325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3900  Z= 0.224
  Angle     :  0.770  11.104   5271  Z= 0.412
  Chirality :  0.045   0.173    627
  Planarity :  0.005   0.048    684
  Dihedral  :  4.891  35.961    561
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.52 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.58 (0.40), residues: 459
  helix:  3.24 (0.28), residues: 261
  sheet: -3.99 (0.50), residues: 30
  loop : -3.79 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  92 
 HIS   0.011   0.003   HIS B 106 
 PHE   0.007   0.001   PHE B  70 
 TYR   0.010   0.002   TYR C 302 
 ARG   0.006   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 0.474 
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: A  307 LYS cc_start: 0.7466 (mmmt) cc_final: 0.6993 (mtpp)
REVERT: B   64 HIS cc_start: 0.7999 (OUTLIER) cc_final: 0.7338 (t-90)
REVERT: C  307 LYS cc_start: 0.7417 (mmmt) cc_final: 0.7045 (mtpp)
REVERT: E  320 MET cc_start: 0.6899 (ttm) cc_final: 0.6547 (ttm)
REVERT: D   47 GLN cc_start: 0.8487 (pp30) cc_final: 0.8263 (pp30)
REVERT: D   58 LYS cc_start: 0.8879 (mttt) cc_final: 0.8585 (mttm)
REVERT: D  112 ASP cc_start: 0.8652 (p0) cc_final: 0.8445 (p0)
REVERT: D  116 ASN cc_start: 0.8627 (m110) cc_final: 0.7653 (t0)
REVERT: D  120 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8161 (mm-30)
REVERT: F   58 LYS cc_start: 0.8852 (mttt) cc_final: 0.8581 (mmtp)
REVERT: F   64 HIS cc_start: 0.8063 (m-70) cc_final: 0.7401 (t-170)
  outliers start: 16
  outliers final: 11
  residues processed: 165
  average time/residue: 0.1952
  time to fit residues: 38.0006
Evaluate side-chains
  159 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   64 HIS
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain D residue   64 HIS
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain F residue   88 LYS
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0870
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0060
   chunk 13 optimal weight:    0.1980
   chunk 16 optimal weight:    0.1980
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.2174

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
C 322 ASN
E 296 ASN
F 106 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.132170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.098964 restraints weight = 6993.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.099185 restraints weight = 5923.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.100218 restraints weight = 5179.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3900  Z= 0.184
  Angle     :  0.796  13.950   5271  Z= 0.419
  Chirality :  0.045   0.243    627
  Planarity :  0.005   0.048    684
  Dihedral  :  4.754  36.090    561
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 27.36 %
    Favored  : 69.43 %
  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:  0.70 (0.40), residues: 459
  helix:  3.24 (0.29), residues: 261
  sheet: -3.68 (0.56), residues: 30
  loop : -3.60 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  92 
 HIS   0.010   0.003   HIS D 106 
 PHE   0.005   0.001   PHE B  63 
 TYR   0.007   0.002   TYR C 302 
 ARG   0.007   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.493 
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: A  307 LYS cc_start: 0.7457 (mmmt) cc_final: 0.7006 (mtpp)
REVERT: B   64 HIS cc_start: 0.7964 (m-70) cc_final: 0.7326 (t-90)
REVERT: C  307 LYS cc_start: 0.7373 (mmmt) cc_final: 0.7017 (mtpp)
REVERT: C  315 LYS cc_start: 0.7899 (mmtm) cc_final: 0.7546 (mmtm)
REVERT: E  320 MET cc_start: 0.6966 (ttm) cc_final: 0.6661 (ttm)
REVERT: D   58 LYS cc_start: 0.8894 (mttt) cc_final: 0.8635 (mttm)
REVERT: D   64 HIS cc_start: 0.7968 (m-70) cc_final: 0.7274 (t-90)
REVERT: F   54 ARG cc_start: 0.8133 (ttm110) cc_final: 0.7926 (ttm110)
REVERT: F   58 LYS cc_start: 0.8865 (mttt) cc_final: 0.8546 (mttm)
REVERT: F   64 HIS cc_start: 0.7958 (m-70) cc_final: 0.7430 (t-170)
REVERT: F  114 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8260 (mt-10)
  outliers start: 14
  outliers final: 10
  residues processed: 161
  average time/residue: 0.1954
  time to fit residues: 36.9676
Evaluate side-chains
  153 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain C residue  296 ASN
Chi-restraints excluded: chain E residue  281 CYS
Chi-restraints excluded: chain E residue  290 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 39 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 21 optimal weight:    0.0670
   overall best weight:    0.3318

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

Flipped N/Q/H residues before XYZ refinement:
** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 296 ASN
C 322 ASN
E 296 ASN
** D  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.131657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.090098 restraints weight = 6836.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.092413 restraints weight = 4717.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.093655 restraints weight = 3838.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3533
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3900  Z= 0.224
  Angle     :  0.896  16.474   5271  Z= 0.463
  Chirality :  0.047   0.177    627
  Planarity :  0.005   0.049    684
  Dihedral  :  4.802  36.371    561
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 13.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 26.21 %
    Favored  : 68.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.39), residues: 459
  helix:  2.92 (0.29), residues: 261
  sheet: -3.35 (0.62), residues: 30
  loop : -3.49 (0.39), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.010   0.003   HIS D 106 
 PHE   0.005   0.001   PHE F  70 
 TYR   0.010   0.002   TYR A 302 
 ARG   0.008   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.433 
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: A   41 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7130 (tm-30)
REVERT: A  307 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7252 (mtpp)
REVERT: A  322 ASN cc_start: 0.7469 (t0) cc_final: 0.6715 (t0)
REVERT: B   58 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8749 (mmtp)
REVERT: B   64 HIS cc_start: 0.8327 (m-70) cc_final: 0.7653 (t-90)
REVERT: C  307 LYS cc_start: 0.7523 (mmmt) cc_final: 0.7147 (mtpp)
REVERT: C  320 MET cc_start: 0.6486 (ttm) cc_final: 0.6222 (ttm)
REVERT: E  320 MET cc_start: 0.6815 (ttm) cc_final: 0.6504 (ttm)
REVERT: D   58 LYS cc_start: 0.9172 (mttt) cc_final: 0.8799 (mttm)
REVERT: D   64 HIS cc_start: 0.8304 (m-70) cc_final: 0.7601 (t-90)
REVERT: F   54 ARG cc_start: 0.8740 (ttm110) cc_final: 0.8353 (ttm110)
REVERT: F   58 LYS cc_start: 0.9165 (mttt) cc_final: 0.8944 (mttt)
REVERT: F   64 HIS cc_start: 0.8159 (m-70) cc_final: 0.7560 (t-170)
REVERT: F   67 GLU cc_start: 0.7721 (pp20) cc_final: 0.7463 (pp20)
  outliers start: 21
  outliers final: 14
  residues processed: 160
  average time/residue: 0.1895
  time to fit residues: 35.6909
Evaluate side-chains
  154 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 140
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 MET
Chi-restraints excluded: chain F residue   41 THR
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 39 optimal weight:    0.7980
   chunk 43 optimal weight:    0.1980
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN
C 322 ASN
E 296 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.130147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.094890 restraints weight = 6886.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.095418 restraints weight = 5398.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096386 restraints weight = 5212.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.5225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3900  Z= 0.261
  Angle     :  0.905  13.219   5271  Z= 0.481
  Chirality :  0.050   0.204    627
  Planarity :  0.006   0.046    684
  Dihedral  :  4.938  36.226    561
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 30.57 %
    Favored  : 65.52 %
  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:  0.37 (0.39), residues: 459
  helix:  2.70 (0.29), residues: 261
  sheet: -3.18 (0.68), residues: 30
  loop : -3.38 (0.41), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.014   0.004   HIS B 106 
 PHE   0.006   0.001   PHE F  70 
 TYR   0.011   0.002   TYR C 302 
 ARG   0.009   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 151
  time to evaluate  : 0.469 
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: A   41 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: A  307 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7175 (mtpp)
REVERT: B   58 LYS cc_start: 0.8942 (mmtp) cc_final: 0.8655 (mmtp)
REVERT: B   64 HIS cc_start: 0.8003 (m-70) cc_final: 0.7416 (t-90)
REVERT: C  307 LYS cc_start: 0.7427 (mmmt) cc_final: 0.7044 (mtpp)
REVERT: C  320 MET cc_start: 0.6541 (ttm) cc_final: 0.6300 (ttm)
REVERT: D   58 LYS cc_start: 0.8976 (mttt) cc_final: 0.8676 (mttm)
REVERT: D   64 HIS cc_start: 0.8056 (m-70) cc_final: 0.7407 (t-90)
REVERT: F   54 ARG cc_start: 0.8325 (ttm110) cc_final: 0.8036 (ttm110)
REVERT: F   58 LYS cc_start: 0.8988 (mttt) cc_final: 0.8623 (mttm)
REVERT: F   64 HIS cc_start: 0.7946 (m-70) cc_final: 0.7338 (t-170)
REVERT: F  120 GLU cc_start: 0.8717 (mm-30) cc_final: 0.8490 (mm-30)
  outliers start: 17
  outliers final: 13
  residues processed: 159
  average time/residue: 0.1879
  time to fit residues: 35.1667
Evaluate side-chains
  160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 147
  time to evaluate  : 0.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain E residue  296 ASN
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  115 MET
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 7 optimal weight:    0.0170
   chunk 22 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   chunk 43 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9980
   chunk 42 optimal weight:    0.2980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
A 322 ASN
C 296 ASN
C 322 ASN
E 296 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.134047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.094340 restraints weight = 6895.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.096926 restraints weight = 4619.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.098294 restraints weight = 3683.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.5415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   3900  Z= 0.258
  Angle     :  0.937  14.011   5271  Z= 0.501
  Chirality :  0.050   0.181    627
  Planarity :  0.006   0.043    684
  Dihedral  :  5.027  36.366    561
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 31.49 %
    Favored  : 63.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.27 (0.39), residues: 459
  helix:  2.53 (0.29), residues: 261
  sheet: -3.48 (0.62), residues: 36
  loop : -3.14 (0.42), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.015   0.004   HIS B 106 
 PHE   0.005   0.001   PHE B  70 
 TYR   0.011   0.002   TYR C 302 
 ARG   0.009   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 0.483 
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: A  307 LYS cc_start: 0.7815 (mmmt) cc_final: 0.7336 (mtpp)
REVERT: B   64 HIS cc_start: 0.8115 (m-70) cc_final: 0.7566 (t-90)
REVERT: B  112 ASP cc_start: 0.8955 (p0) cc_final: 0.8688 (p0)
REVERT: C  307 LYS cc_start: 0.7688 (mmmt) cc_final: 0.7277 (mtpp)
REVERT: D   47 GLN cc_start: 0.9043 (pp30) cc_final: 0.8612 (pp30)
REVERT: D   51 LYS cc_start: 0.9221 (mmtp) cc_final: 0.9006 (mmtt)
REVERT: D   58 LYS cc_start: 0.9078 (mttt) cc_final: 0.8771 (mttm)
REVERT: D   64 HIS cc_start: 0.8107 (m-70) cc_final: 0.7492 (t-90)
REVERT: F   37 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.7714 (t70)
REVERT: F   54 ARG cc_start: 0.8644 (ttm110) cc_final: 0.8322 (ttm110)
REVERT: F   58 LYS cc_start: 0.9106 (mttt) cc_final: 0.8708 (mttm)
REVERT: F   64 HIS cc_start: 0.8025 (m-70) cc_final: 0.7543 (t-170)
REVERT: F  121 LYS cc_start: 0.8747 (tptp) cc_final: 0.8534 (tptp)
  outliers start: 22
  outliers final: 12
  residues processed: 165
  average time/residue: 0.1881
  time to fit residues: 36.7012
Evaluate side-chains
  158 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.488 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain F residue   37 ASP
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    0.0670
   chunk 36 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0980
   chunk 27 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN
C 322 ASN
E 296 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.133582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.093644 restraints weight = 6757.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.096243 restraints weight = 4531.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.097858 restraints weight = 3606.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
moved from start:          0.5608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3900  Z= 0.273
  Angle     :  1.060  15.822   5271  Z= 0.557
  Chirality :  0.054   0.267    627
  Planarity :  0.006   0.040    684
  Dihedral  :  5.312  36.603    561
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 18.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 32.18 %
    Favored  : 63.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.13 (0.40), residues: 459
  helix:  2.30 (0.30), residues: 261
  sheet: -3.35 (0.66), residues: 36
  loop : -3.02 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.016   0.004   HIS B 106 
 PHE   0.006   0.001   PHE B  70 
 TYR   0.012   0.002   TYR A 302 
 ARG   0.011   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 149
  time to evaluate  : 0.539 
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: A  307 LYS cc_start: 0.7930 (mmmt) cc_final: 0.7439 (mtpp)
REVERT: B   58 LYS cc_start: 0.9085 (mttt) cc_final: 0.8627 (mmtp)
REVERT: B  112 ASP cc_start: 0.8967 (p0) cc_final: 0.8719 (p0)
REVERT: C  307 LYS cc_start: 0.7714 (mmmt) cc_final: 0.7260 (mtpp)
REVERT: C  320 MET cc_start: 0.6660 (ttm) cc_final: 0.6138 (ttp)
REVERT: C  322 ASN cc_start: 0.7271 (t0) cc_final: 0.6553 (t0)
REVERT: E  302 TYR cc_start: 0.4116 (t80) cc_final: 0.2690 (m-80)
REVERT: E  315 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7877 (tppt)
REVERT: D   58 LYS cc_start: 0.9093 (mttt) cc_final: 0.8770 (mttm)
REVERT: D   64 HIS cc_start: 0.8119 (m-70) cc_final: 0.7510 (t-90)
REVERT: F   37 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.7792 (t70)
REVERT: F   58 LYS cc_start: 0.9098 (mttt) cc_final: 0.8720 (mttm)
REVERT: F   64 HIS cc_start: 0.8057 (m-70) cc_final: 0.7606 (t-170)
REVERT: F  110 LEU cc_start: 0.9041 (mm) cc_final: 0.8837 (mt)
REVERT: F  121 LYS cc_start: 0.8700 (tptp) cc_final: 0.8475 (tptp)
  outliers start: 20
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1913
  time to fit residues: 35.8309
Evaluate side-chains
  155 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain E residue  296 ASN
Chi-restraints excluded: chain D residue   66 ILE
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain F residue   37 ASP
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 31 optimal weight:    0.9980
   chunk 13 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0170
   chunk 42 optimal weight:    0.9990
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.2396

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN
E 296 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.135799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.094229 restraints weight = 6846.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.097196 restraints weight = 4415.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.098650 restraints weight = 3455.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.5837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3900  Z= 0.247
  Angle     :  1.081  16.389   5271  Z= 0.570
  Chirality :  0.053   0.339    627
  Planarity :  0.006   0.040    684
  Dihedral  :  5.460  36.705    561
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 33.79 %
    Favored  : 62.53 %
  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:  0.13 (0.40), residues: 459
  helix:  2.23 (0.31), residues: 261
  sheet: -3.40 (0.65), residues: 36
  loop : -2.86 (0.43), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  92 
 HIS   0.016   0.004   HIS B 106 
 PHE   0.004   0.001   PHE B  70 
 TYR   0.008   0.002   TYR A 302 
 ARG   0.011   0.001   ARG B 124 

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

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

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  918 Ramachandran restraints generated.
    459 Oldfield, 0 Emsley, 459 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 154
  time to evaluate  : 0.461 
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: A  307 LYS cc_start: 0.7864 (mmmt) cc_final: 0.7394 (mtpp)
REVERT: B   58 LYS cc_start: 0.9115 (mttt) cc_final: 0.8612 (mmtp)
REVERT: B  112 ASP cc_start: 0.9023 (p0) cc_final: 0.8795 (p0)
REVERT: B  115 MET cc_start: 0.7035 (tpt) cc_final: 0.6804 (ttm)
REVERT: C  307 LYS cc_start: 0.7646 (mmmt) cc_final: 0.7204 (mtpp)
REVERT: C  320 MET cc_start: 0.6704 (ttm) cc_final: 0.6247 (ttt)
REVERT: E  302 TYR cc_start: 0.4001 (t80) cc_final: 0.2528 (m-80)
REVERT: E  315 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7763 (tppt)
REVERT: D   51 LYS cc_start: 0.9360 (mmtp) cc_final: 0.9086 (mmtt)
REVERT: D   58 LYS cc_start: 0.9160 (mttt) cc_final: 0.8824 (mttm)
REVERT: D  121 LYS cc_start: 0.9009 (tptp) cc_final: 0.8727 (tptp)
REVERT: F   37 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7877 (t70)
REVERT: F   58 LYS cc_start: 0.9133 (mttt) cc_final: 0.8922 (mttt)
REVERT: F   64 HIS cc_start: 0.8149 (m-70) cc_final: 0.7687 (t-170)
REVERT: F   67 GLU cc_start: 0.7831 (pp20) cc_final: 0.7566 (pp20)
  outliers start: 16
  outliers final: 10
  residues processed: 163
  average time/residue: 0.1936
  time to fit residues: 37.1314
Evaluate side-chains
  160 residues out of total 435 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 149
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  290 ASN
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain B residue   91 LEU
Chi-restraints excluded: chain C residue   20 VAL
Chi-restraints excluded: chain C residue  281 CYS
Chi-restraints excluded: chain C residue  290 ASN
Chi-restraints excluded: chain E residue  290 ASN
Chi-restraints excluded: chain E residue  296 ASN
Chi-restraints excluded: chain F residue   37 ASP
Chi-restraints excluded: chain F residue   91 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 20 optimal weight:    0.0030
   chunk 39 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 16 optimal weight:    0.9990
   chunk 9 optimal weight:    0.6980
   chunk 17 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.2980
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.4190

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

Flipped N/Q/H residues before XYZ refinement:
C 296 ASN
E 296 ASN
** D  47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.134381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.093603 restraints weight = 6715.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.096109 restraints weight = 4597.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.097588 restraints weight = 3712.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.5884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3900  Z= 0.287
  Angle     :  1.085  16.339   5271  Z= 0.578
  Chirality :  0.053   0.193    627
  Planarity :  0.006   0.039    684
  Dihedral  :  5.768  37.021    561
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 18.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 34.94 %
    Favored  : 62.30 %
  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:  0.18 (0.40), residues: 459
  helix:  2.27 (0.30), residues: 261
  sheet: -3.45 (0.66), residues: 36
  loop : -2.83 (0.44), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B  92 
 HIS   0.016   0.005   HIS B 106 
 PHE   0.005   0.001   PHE D  63 
 TYR   0.011   0.002   TYR C 302 
 ARG   0.010   0.001   ARG B 124 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2042.92 seconds
wall clock time: 37 minutes 12.27 seconds (2232.27 seconds total)