Starting phenix.real_space_refine
on Fri Aug 22 12:38:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6zrf_11380/08_2025/6zrf_11380.map"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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: 3
    Type Number    sf(0)   Gaussians
     C    1368      2.51       5
     N     396      2.21       5
     O     456      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2220
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "C"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "E"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "G"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "I"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "K"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "B"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "D"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "F"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "H"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "J"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
    Chain: "L"
      Number of atoms: 185
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 185
          Classifications: {'peptide': 25}
          Link IDs: {'TRANS': 24}
  Time building chain proxies: 0.73, per 1000 atoms: 0.33
  Number of scatterers: 2220
  At special positions: 0
  Unit cell: (64.965, 47.925, 47.925, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O     456      8.00
     N     396      7.00
     C    1368      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 89.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  552

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...

    No hydrogen bonds 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: 0.00

  Time building geometry restraints manager: 0.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.28: 360
        1.28 -     1.34: 384
        1.34 -     1.41: 276
        1.41 -     1.47: 373
        1.47 -     1.54: 863
  Bond restraints: 2256
  Sorted by residual:
  bond pdb=" CA  TYC F  37 "
       pdb=" C   TYC F  37 "
    ideal  model  delta    sigma   weight residual
    1.525  1.486  0.039 2.10e-02 2.27e+03 3.38e+00
  bond pdb=" CA  TYC B  37 "
       pdb=" C   TYC B  37 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 2.10e-02 2.27e+03 3.32e+00
  bond pdb=" CA  TYC I  37 "
       pdb=" C   TYC I  37 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 2.10e-02 2.27e+03 3.26e+00
  bond pdb=" CA  TYC C  37 "
       pdb=" C   TYC C  37 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 2.10e-02 2.27e+03 3.25e+00
  bond pdb=" CA  TYC G  37 "
       pdb=" C   TYC G  37 "
    ideal  model  delta    sigma   weight residual
    1.525  1.487  0.038 2.10e-02 2.27e+03 3.21e+00
  ... (remaining 2251 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 2723
        1.54 -     3.07: 277
        3.07 -     4.61: 60
        4.61 -     6.14: 1
        6.14 -     7.68: 11
  Bond angle restraints: 3072
  Sorted by residual:
  angle pdb=" C   PHE J  23 "
        pdb=" CA  PHE J  23 "
        pdb=" CB  PHE J  23 "
      ideal   model   delta    sigma   weight residual
     110.65  102.97    7.68 1.95e+00 2.63e-01 1.55e+01
  angle pdb=" C   PHE B  23 "
        pdb=" CA  PHE B  23 "
        pdb=" CB  PHE B  23 "
      ideal   model   delta    sigma   weight residual
     110.65  103.84    6.81 1.95e+00 2.63e-01 1.22e+01
  angle pdb=" C   PHE I  23 "
        pdb=" CA  PHE I  23 "
        pdb=" CB  PHE I  23 "
      ideal   model   delta    sigma   weight residual
     110.65  103.84    6.81 1.95e+00 2.63e-01 1.22e+01
  angle pdb=" C   PHE A  23 "
        pdb=" CA  PHE A  23 "
        pdb=" CB  PHE A  23 "
      ideal   model   delta    sigma   weight residual
     110.65  103.86    6.79 1.95e+00 2.63e-01 1.21e+01
  angle pdb=" C   PHE K  23 "
        pdb=" CA  PHE K  23 "
        pdb=" CB  PHE K  23 "
      ideal   model   delta    sigma   weight residual
     110.65  103.86    6.79 1.95e+00 2.63e-01 1.21e+01
  ... (remaining 3067 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.60: 876
        6.60 -    13.20: 170
       13.20 -    19.80: 143
       19.80 -    26.40: 35
       26.40 -    33.00: 72
  Dihedral angle restraints: 1296
    sinusoidal: 456
      harmonic: 840
  Sorted by residual:
  dihedral pdb=" CA  ALA F  25 "
           pdb=" C   ALA F  25 "
           pdb=" N   ILE F  26 "
           pdb=" CA  ILE F  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.97   18.03     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ALA A  25 "
           pdb=" C   ALA A  25 "
           pdb=" N   ILE A  26 "
           pdb=" CA  ILE A  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.98   18.02     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  ALA D  25 "
           pdb=" C   ALA D  25 "
           pdb=" N   ILE D  26 "
           pdb=" CA  ILE D  26 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.99   18.01     0      5.00e+00 4.00e-02 1.30e+01
  ... (remaining 1293 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 149
       0.026 -    0.051: 172
       0.051 -    0.077: 15
       0.077 -    0.102: 12
       0.102 -    0.128: 12
  Chirality restraints: 360
  Sorted by residual:
  chirality pdb=" CA  ILE F  26 "
            pdb=" N   ILE F  26 "
            pdb=" C   ILE F  26 "
            pdb=" CB  ILE F  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE G  26 "
            pdb=" N   ILE G  26 "
            pdb=" C   ILE G  26 "
            pdb=" CB  ILE G  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  ILE E  26 "
            pdb=" N   ILE E  26 "
            pdb=" C   ILE E  26 "
            pdb=" CB  ILE E  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.04e-01
  ... (remaining 357 not shown)

  Planarity restraints: 408
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  23 "    0.012 2.00e-02 2.50e+03   1.04e-02 1.90e+00
        pdb=" CG  PHE C  23 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  23 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  23 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  23 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  23 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  23 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B  23 "    0.012 2.00e-02 2.50e+03   1.04e-02 1.89e+00
        pdb=" CG  PHE B  23 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE B  23 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE B  23 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 PHE B  23 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B  23 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B  23 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE I  23 "    0.012 2.00e-02 2.50e+03   1.04e-02 1.88e+00
        pdb=" CG  PHE I  23 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE I  23 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 PHE I  23 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE I  23 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE I  23 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE I  23 "    0.002 2.00e-02 2.50e+03
  ... (remaining 405 not shown)

  Histogram of nonbonded interaction distances:
        1.99 -     2.57: 78
        2.57 -     3.16: 2248
        3.16 -     3.74: 3211
        3.74 -     4.32: 4612
        4.32 -     4.90: 8142
  Nonbonded interactions: 18291
  Sorted by model distance:
  nonbonded pdb=" O   SER H  20 "
            pdb=" OG  SER J  20 "
     model   vdw
     1.993 3.040
  nonbonded pdb=" ND2 ASN C  31 "
            pdb=" OD1 ASN C  35 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" ND2 ASN B  31 "
            pdb=" OD1 ASN B  35 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" ND2 ASN E  31 "
            pdb=" OD1 ASN E  35 "
     model   vdw
     2.148 3.120
  nonbonded pdb=" ND2 ASN G  31 "
            pdb=" OD1 ASN G  35 "
     model   vdw
     2.148 3.120
  ... (remaining 18286 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'E'
  selection = chain 'G'
  selection = chain 'I'
  selection = chain 'K'
  selection = chain 'B'
  selection = chain 'D'
  selection = chain 'F'
  selection = chain 'H'
  selection = chain 'J'
  selection = chain 'L'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.520
  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:             0.000
  Extract box with map and model:          0.030
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     4.170
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
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      :  0.010   0.039   2256  Z= 0.494
  Angle     :  1.065   7.678   3072  Z= 0.555
  Chirality :  0.041   0.128    360
  Planarity :  0.003   0.010    408
  Dihedral  : 13.340  33.000    744
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 41.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -6.22 (0.32), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.73 (0.24), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.024   0.005   PHE C  23 
 HIS   0.002   0.001   HIS G  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.01018 ( 2256)
  covalent geometry    : angle       1.06501 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   35 ASN cc_start: 0.7912 (m110) cc_final: 0.7708 (m110)
REVERT: F   27 LEU cc_start: 0.9119 (tt) cc_final: 0.8909 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0248
  time to fit residues: 1.7569
Evaluate side-chains
  21 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 4 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:
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.135843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.117991 restraints weight = 3825.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.121002 restraints weight = 2091.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.123183 restraints weight = 1444.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.124598 restraints weight = 1113.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.125498 restraints weight = 930.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.2395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   2256  Z= 0.151
  Angle     :  0.674   6.607   3072  Z= 0.342
  Chirality :  0.044   0.129    360
  Planarity :  0.002   0.007    408
  Dihedral  :  6.940  18.697    372
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 12.08 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.93 (0.33), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.52 (0.26), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.012   0.002   PHE I  23 
 HIS   0.004   0.002   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 2256)
  covalent geometry    : angle       0.67444 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.083 
Fit side-chains
REVERT: E   20 SER cc_start: 0.8334 (p) cc_final: 0.8075 (t)
REVERT: E   27 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8362 (tt)
REVERT: I   27 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8020 (tt)
REVERT: D   27 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8327 (tt)
REVERT: H   34 SER cc_start: 0.8296 (p) cc_final: 0.7504 (m)
  outliers start: 9
  outliers final: 2
  residues processed: 56
  average time/residue: 0.0221
  time to fit residues: 1.8712
Evaluate side-chains
  44 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 39
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain D residue   27 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** C  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.130864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.113497 restraints weight = 3980.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.116376 restraints weight = 2253.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.118434 restraints weight = 1565.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.119681 restraints weight = 1210.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.120769 restraints weight = 1021.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.024   2256  Z= 0.261
  Angle     :  0.693   5.792   3072  Z= 0.355
  Chirality :  0.042   0.126    360
  Planarity :  0.002   0.011    408
  Dihedral  :  7.773  21.058    372
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.85 %
    Favored  : 90.15 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.58 %
    Favored  : 71.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.87 (0.34), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.47 (0.26), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE E  23 
 HIS   0.003   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00562 ( 2256)
  covalent geometry    : angle       0.69316 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.081 
Fit side-chains
REVERT: L   30 THR cc_start: 0.8370 (t) cc_final: 0.8159 (m)
  outliers start: 10
  outliers final: 4
  residues processed: 40
  average time/residue: 0.0198
  time to fit residues: 1.2696
Evaluate side-chains
  39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 35
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain I residue   34 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 1 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0000
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 22 optimal weight:    0.0870
   chunk 15 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    3.9990
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.4962

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.188803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.139891 restraints weight = 3650.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.143663 restraints weight = 1892.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.146088 restraints weight = 1234.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4236 r_free = 0.4236 target = 0.147709 restraints weight = 928.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.148632 restraints weight = 744.367|
|-----------------------------------------------------------------------------|
r_work (final): 0.4119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.3108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.013   2256  Z= 0.095
  Angle     :  0.573   6.597   3072  Z= 0.282
  Chirality :  0.043   0.123    360
  Planarity :  0.002   0.006    408
  Dihedral  :  5.779  17.061    372
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 26.67 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.70 (0.35), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.34 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE K  23 
 HIS   0.003   0.002   HIS I  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00199 ( 2256)
  covalent geometry    : angle       0.57279 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.086 
Fit side-chains
REVERT: E   20 SER cc_start: 0.8412 (t) cc_final: 0.8073 (p)
REVERT: E   27 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8170 (tt)
REVERT: I   27 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7766 (tt)
REVERT: D   27 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8164 (tt)
REVERT: J   20 SER cc_start: 0.8732 (t) cc_final: 0.8168 (p)
REVERT: L   30 THR cc_start: 0.8465 (t) cc_final: 0.8232 (m)
  outliers start: 8
  outliers final: 3
  residues processed: 53
  average time/residue: 0.0227
  time to fit residues: 1.8155
Evaluate side-chains
  46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain D residue   27 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 8 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 22 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   chunk 1 optimal weight:    4.9990
   chunk 15 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    1.2382

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.159960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.133572 restraints weight = 3675.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.137143 restraints weight = 1947.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.139496 restraints weight = 1281.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.140980 restraints weight = 956.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.141750 restraints weight = 774.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.022   2256  Z= 0.192
  Angle     :  0.601   5.278   3072  Z= 0.305
  Chirality :  0.042   0.126    360
  Planarity :  0.002   0.008    408
  Dihedral  :  6.646  16.962    372
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 19.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.61 %
    Favored  : 89.39 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 25.83 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.75 (0.35), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.38 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE D  23 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 2256)
  covalent geometry    : angle       0.60131 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.088 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8367 (tt)
REVERT: I   27 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8127 (tt)
REVERT: D   27 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8503 (tt)
REVERT: H   27 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8293 (tt)
REVERT: L   30 THR cc_start: 0.8393 (t) cc_final: 0.8165 (m)
REVERT: L   34 SER cc_start: 0.8737 (p) cc_final: 0.8495 (m)
  outliers start: 11
  outliers final: 6
  residues processed: 47
  average time/residue: 0.0211
  time to fit residues: 1.5553
Evaluate side-chains
  47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain K residue   27 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain H residue   27 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 5 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 3 optimal weight:    0.7980
   chunk 4 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 22 optimal weight:    4.9990
   chunk 9 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    1.8784

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.123752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.105174 restraints weight = 3937.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.108251 restraints weight = 2160.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.110498 restraints weight = 1480.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.112000 restraints weight = 1132.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.112713 restraints weight = 933.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.025   2256  Z= 0.278
  Angle     :  0.651   4.374   3072  Z= 0.334
  Chirality :  0.042   0.129    360
  Planarity :  0.002   0.009    408
  Dihedral  :  7.668  22.011    372
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 21.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.83 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.80 (0.35), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.41 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.013   0.003   PHE A  23 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00600 ( 2256)
  covalent geometry    : angle       0.65074 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.089 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: I   27 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8262 (tt)
REVERT: D   27 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8598 (tt)
REVERT: H   27 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8387 (tt)
REVERT: L   30 THR cc_start: 0.8409 (t) cc_final: 0.8145 (m)
REVERT: L   34 SER cc_start: 0.8757 (p) cc_final: 0.8461 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 37
  average time/residue: 0.0151
  time to fit residues: 0.8851
Evaluate side-chains
  40 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain H residue   27 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 23 optimal weight:    0.5980
   chunk 7 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.160303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.134732 restraints weight = 3649.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.138384 restraints weight = 1932.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.140751 restraints weight = 1258.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.142343 restraints weight = 940.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.143441 restraints weight = 750.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   2256  Z= 0.147
  Angle     :  0.573   5.475   3072  Z= 0.284
  Chirality :  0.042   0.126    360
  Planarity :  0.001   0.006    408
  Dihedral  :  6.332  17.635    372
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.09 %
    Favored  : 90.91 %
  Rotamer:
    Outliers :  5.42 %
    Allowed  : 25.42 %
    Favored  : 69.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.82 (0.35), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.43 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.002   PHE D  23 
 HIS   0.002   0.001   HIS E  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 2256)
  covalent geometry    : angle       0.57331 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.086 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8326 (tt)
REVERT: I   27 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8059 (tt)
REVERT: D   27 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8385 (tt)
REVERT: H   27 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8151 (tt)
REVERT: L   27 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8386 (tt)
REVERT: L   30 THR cc_start: 0.8441 (t) cc_final: 0.8226 (m)
REVERT: L   34 SER cc_start: 0.8695 (p) cc_final: 0.8495 (m)
  outliers start: 13
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0224
  time to fit residues: 1.6592
Evaluate side-chains
  46 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 34
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   27 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain H residue   27 LEU
Chi-restraints excluded: chain L residue   27 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 17 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 11 optimal weight:    0.6980
   overall best weight:    1.3782

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

Flipped N/Q/H residues before XYZ refinement:
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.158771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.131347 restraints weight = 3687.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.134942 restraints weight = 1961.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.136964 restraints weight = 1293.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.138630 restraints weight = 1002.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.139558 restraints weight = 803.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.018   2256  Z= 0.207
  Angle     :  0.602   5.259   3072  Z= 0.302
  Chirality :  0.042   0.126    360
  Planarity :  0.002   0.008    408
  Dihedral  :  6.765  18.330    372
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.74 %
    Favored  : 88.26 %
  Rotamer:
    Outliers :  5.83 %
    Allowed  : 25.42 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.83 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.43 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE K  23 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 2256)
  covalent geometry    : angle       0.60230 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 34
  time to evaluate  : 0.086 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8387 (tt)
REVERT: I   27 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8192 (tt)
REVERT: D   27 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8510 (tt)
REVERT: H   27 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8286 (tt)
REVERT: L   30 THR cc_start: 0.8465 (t) cc_final: 0.8235 (m)
REVERT: L   34 SER cc_start: 0.8777 (p) cc_final: 0.8515 (m)
  outliers start: 14
  outliers final: 8
  residues processed: 44
  average time/residue: 0.0224
  time to fit residues: 1.5401
Evaluate side-chains
  43 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 0.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   27 LEU
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain G residue   34 SER
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain H residue   27 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    2.3786

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.120950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.102084 restraints weight = 4058.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.105007 restraints weight = 2252.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.107037 restraints weight = 1569.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.108353 restraints weight = 1226.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.109219 restraints weight = 1039.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.027   2256  Z= 0.340
  Angle     :  0.707   5.991   3072  Z= 0.358
  Chirality :  0.043   0.132    360
  Planarity :  0.002   0.011    408
  Dihedral  :  7.901  23.737    372
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 24.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.26 %
    Favored  : 86.74 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 26.67 %
    Favored  : 68.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.83 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.44 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.015   0.003   PHE K  23 
 HIS   0.002   0.001   HIS A  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00731 ( 2256)
  covalent geometry    : angle       0.70721 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 29
  time to evaluate  : 0.108 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8572 (tt)
REVERT: I   27 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8261 (tt)
REVERT: D   27 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8614 (tt)
REVERT: L   27 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8406 (tt)
REVERT: L   30 THR cc_start: 0.8434 (t) cc_final: 0.8174 (m)
REVERT: L   34 SER cc_start: 0.8809 (p) cc_final: 0.8490 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 40
  average time/residue: 0.0227
  time to fit residues: 1.4337
Evaluate side-chains
  39 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain G residue   36 THR
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain L residue   27 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 20 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.4980
   chunk 0 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  35 ASN
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.131248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.112487 restraints weight = 3833.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.115426 restraints weight = 2224.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.117636 restraints weight = 1567.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.119109 restraints weight = 1225.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.119867 restraints weight = 1026.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.015   2256  Z= 0.138
  Angle     :  0.592   7.633   3072  Z= 0.288
  Chirality :  0.043   0.127    360
  Planarity :  0.001   0.006    408
  Dihedral  :  6.297  17.428    372
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 25.00 %
    Favored  : 70.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.86 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.46 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.009   0.002   PHE K  23 
 HIS   0.003   0.001   HIS E  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 2256)
  covalent geometry    : angle       0.59201 ( 3072)

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

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

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  528 Ramachandran restraints generated.
    264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.085 
Fit side-chains
REVERT: E   27 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8355 (tt)
REVERT: I   27 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8085 (tt)
REVERT: D   27 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8343 (tt)
REVERT: L   27 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8380 (tt)
REVERT: L   30 THR cc_start: 0.8497 (t) cc_final: 0.8276 (m)
REVERT: L   34 SER cc_start: 0.8772 (p) cc_final: 0.8542 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 51
  average time/residue: 0.0229
  time to fit residues: 1.7711
Evaluate side-chains
  47 residues out of total 240 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   27 LEU
Chi-restraints excluded: chain C residue   28 SER
Chi-restraints excluded: chain E residue   27 LEU
Chi-restraints excluded: chain G residue   28 SER
Chi-restraints excluded: chain I residue   27 LEU
Chi-restraints excluded: chain I residue   34 SER
Chi-restraints excluded: chain K residue   27 LEU
Chi-restraints excluded: chain K residue   34 SER
Chi-restraints excluded: chain K residue   36 THR
Chi-restraints excluded: chain D residue   27 LEU
Chi-restraints excluded: chain L residue   27 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 24
   random chunks:
   chunk 22 optimal weight:    0.0980
   chunk 1 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
** A  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.127583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.108333 restraints weight = 3917.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.111561 restraints weight = 2210.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.113765 restraints weight = 1523.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.115157 restraints weight = 1182.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.116243 restraints weight = 997.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.016   2256  Z= 0.183
  Angle     :  0.615   6.767   3072  Z= 0.302
  Chirality :  0.042   0.127    360
  Planarity :  0.001   0.007    408
  Dihedral  :  6.499  17.361    372
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 16.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.50 %
    Favored  : 87.50 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 25.83 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.85 (0.36), residues: 264
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.45 (0.27), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.002   PHE K  23 
 HIS   0.002   0.001   HIS E  18 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 2256)
  covalent geometry    : angle       0.61498 ( 3072)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 642.25 seconds
wall clock time: 12 minutes 7.83 seconds (727.83 seconds total)