Starting phenix.real_space_refine
on Sat Apr 26 15:19:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8spa_40677/04_2025/8spa_40677.cif"
  }
  resolution = 3.0
  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
-------------------------------------------------------------------------------
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=   0.002
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       5      5.16       5
     C    1210      2.51       5
     N     300      2.21       5
     O     355      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 1870
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 374
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 374
          Classifications: {'peptide': 49}
          Link IDs: {'PTRANS': 4, 'TRANS': 44}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 2.86, per 1000 atoms: 1.53
  Number of scatterers: 1870
  At special positions: 0
  Unit cell: (63.64, 61.06, 48.16, 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       5     16.00
     O     355      8.00
     N     300      7.00
     C    1210      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.37
  Conformation dependent library (CDL) restraints added in 573.3 milliseconds
  

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  430

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 1 sheets defined
      0.0% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 37
      removed outlier: 6.782A  pdb=" N   MET A  33 " --> pdb=" O   LEU C  34 " (cutoff:3.500A)
      removed outlier: 8.312A  pdb=" N   GLN C  36 " --> pdb=" O   MET A  33 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   PHE A  35 " --> pdb=" O   GLN C  36 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   MET C  33 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
      removed outlier: 8.267A  pdb=" N   GLN E  36 " --> pdb=" O   MET C  33 " (cutoff:3.500A)
      removed outlier: 6.428A  pdb=" N   PHE C  35 " --> pdb=" O   GLN E  36 " (cutoff:3.500A)

    10 hydrogen bonds defined for protein.
    30 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: 0.30

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 585
        1.34 -     1.46: 441
        1.46 -     1.57: 904
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 1940
  Sorted by residual:
  bond pdb=" CB  VAL A  29 "
       pdb=" CG1 VAL A  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.30e+00
  bond pdb=" CB  VAL D  29 "
       pdb=" CG1 VAL D  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  VAL E  29 "
       pdb=" CG1 VAL E  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.26e+00
  bond pdb=" CB  VAL B  29 "
       pdb=" CG1 VAL B  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.25e+00
  bond pdb=" CB  VAL C  29 "
       pdb=" CG1 VAL C  29 "
    ideal  model  delta    sigma   weight residual
    1.521  1.484  0.037 3.30e-02 9.18e+02 1.24e+00
  ... (remaining 1935 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.10: 2416
        1.10 -     2.19: 169
        2.19 -     3.29: 54
        3.29 -     4.39: 6
        4.39 -     5.48: 10
  Bond angle restraints: 2655
  Sorted by residual:
  angle pdb=" C   PRO D  39 "
        pdb=" N   HIS D  40 "
        pdb=" CA  HIS D  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.87    3.21 1.59e+00 3.96e-01 4.06e+00
  angle pdb=" C   PRO B  39 "
        pdb=" N   HIS B  40 "
        pdb=" CA  HIS B  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.90    3.18 1.59e+00 3.96e-01 4.01e+00
  angle pdb=" C   PRO E  39 "
        pdb=" N   HIS E  40 "
        pdb=" CA  HIS E  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.90    3.18 1.59e+00 3.96e-01 4.00e+00
  angle pdb=" C   PRO A  39 "
        pdb=" N   HIS A  40 "
        pdb=" CA  HIS A  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.94    3.14 1.59e+00 3.96e-01 3.89e+00
  angle pdb=" C   PRO C  39 "
        pdb=" N   HIS C  40 "
        pdb=" CA  HIS C  40 "
      ideal   model   delta    sigma   weight residual
     122.08  118.97    3.11 1.59e+00 3.96e-01 3.83e+00
  ... (remaining 2650 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     6.72: 796
        6.72 -    13.44: 129
       13.44 -    20.17: 75
       20.17 -    26.89: 30
       26.89 -    33.61: 20
  Dihedral angle restraints: 1050
    sinusoidal: 380
      harmonic: 670
  Sorted by residual:
  dihedral pdb=" CA  HIS A  40 "
           pdb=" C   HIS A  40 "
           pdb=" N   HIS A  41 "
           pdb=" CA  HIS A  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  HIS B  40 "
           pdb=" C   HIS B  40 "
           pdb=" N   HIS B  41 "
           pdb=" CA  HIS B  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.82   19.18     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  HIS D  40 "
           pdb=" C   HIS D  40 "
           pdb=" N   HIS D  41 "
           pdb=" CA  HIS D  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.83   19.17     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 1047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 151
       0.030 -    0.060: 94
       0.060 -    0.090: 23
       0.090 -    0.120: 7
       0.120 -    0.150: 10
  Chirality restraints: 285
  Sorted by residual:
  chirality pdb=" CA  HIS C  40 "
            pdb=" N   HIS C  40 "
            pdb=" C   HIS C  40 "
            pdb=" CB  HIS C  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.61e-01
  chirality pdb=" CA  HIS B  40 "
            pdb=" N   HIS B  40 "
            pdb=" C   HIS B  40 "
            pdb=" CB  HIS B  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.49e-01
  chirality pdb=" CA  HIS E  40 "
            pdb=" N   HIS E  40 "
            pdb=" C   HIS E  40 "
            pdb=" CB  HIS E  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.45e-01
  ... (remaining 282 not shown)

  Planarity restraints: 350
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN E  43 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO E  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO E  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO E  44 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A  43 "    0.022 5.00e-02 4.00e+02   3.39e-02 1.84e+00
        pdb=" N   PRO A  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A  44 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  43 "    0.022 5.00e-02 4.00e+02   3.38e-02 1.83e+00
        pdb=" N   PRO B  44 "   -0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO B  44 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO B  44 "    0.019 5.00e-02 4.00e+02
  ... (remaining 347 not shown)

  Histogram of nonbonded interaction distances:
        2.61 -     3.07: 1221
        3.07 -     3.53: 1837
        3.53 -     3.99: 2653
        3.99 -     4.44: 3041
        4.44 -     4.90: 5102
  Nonbonded interactions: 13854
  Sorted by model distance:
  nonbonded pdb=" O   HIS D  40 "
            pdb=" ND1 HIS D  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS B  40 "
            pdb=" ND1 HIS B  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS E  40 "
            pdb=" ND1 HIS E  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS A  40 "
            pdb=" ND1 HIS A  41 "
     model   vdw
     2.614 3.120
  nonbonded pdb=" O   HIS C  40 "
            pdb=" ND1 HIS C  41 "
     model   vdw
     2.614 3.120
  ... (remaining 13849 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 'B'
  selection = chain 'E'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     16.760
  Find NCS groups from input model:        0.040
  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:17.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
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      :  0.006   0.038   1940  Z= 0.239
  Angle     :  0.753   5.482   2655  Z= 0.403
  Chirality :  0.045   0.150    285
  Planarity :  0.005   0.034    350
  Dihedral  : 10.816  33.609    620
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.42), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.38 (0.32), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP D  10 
 HIS   0.005   0.002   HIS D  40 
 PHE   0.012   0.002   PHE A  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.21596 (   10)
  hydrogen bonds       : angle       7.11050 (   30)
  covalent geometry    : bond        0.00577 ( 1940)
  covalent geometry    : angle       0.75278 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.219 
Fit side-chains
REVERT: C   10 TRP cc_start: 0.7650 (t-100) cc_final: 0.6809 (t-100)
REVERT: D   19 GLU cc_start: 0.7977 (tt0) cc_final: 0.7568 (tm-30)
REVERT: E   33 MET cc_start: 0.8984 (mtp) cc_final: 0.8663 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.8101
  time to fit residues: 36.6396
Evaluate side-chains
  18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 8 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    1.7584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.091563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.076746 restraints weight = 4662.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 3.76
r_work: 0.3726 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8295
moved from start:          0.1660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   1940  Z= 0.169
  Angle     :  0.692   5.177   2655  Z= 0.352
  Chirality :  0.043   0.149    285
  Planarity :  0.003   0.018    350
  Dihedral  :  6.383  20.358    240
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.29 %
    Favored  : 82.38 %
  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: -2.77 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.10 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  10 
 HIS   0.006   0.002   HIS C  40 
 PHE   0.011   0.002   PHE A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04299 (   10)
  hydrogen bonds       : angle       5.66240 (   30)
  covalent geometry    : bond        0.00422 ( 1940)
  covalent geometry    : angle       0.69171 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 25
  time to evaluate  : 0.203 
Fit side-chains
REVERT: C   10 TRP cc_start: 0.7926 (t-100) cc_final: 0.7171 (t-100)
REVERT: E   33 MET cc_start: 0.9112 (mtp) cc_final: 0.8877 (mtt)
  outliers start: 7
  outliers final: 4
  residues processed: 30
  average time/residue: 0.6762
  time to fit residues: 21.0771
Evaluate side-chains
  25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 21
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain D residue   21 SER
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 4 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0870
   chunk 0 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.094818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.079376 restraints weight = 4533.390|
|-----------------------------------------------------------------------------|
r_work (start): 0.3911 rms_B_bonded: 3.79
r_work: 0.3795 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.017   1940  Z= 0.099
  Angle     :  0.628   6.364   2655  Z= 0.305
  Chirality :  0.040   0.136    285
  Planarity :  0.003   0.018    350
  Dihedral  :  5.728  21.143    240
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 16.19 %
    Favored  : 80.95 %
  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: -2.68 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.03 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP D  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.009   0.001   PHE B  38 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02373 (   10)
  hydrogen bonds       : angle       4.82393 (   30)
  covalent geometry    : bond        0.00253 ( 1940)
  covalent geometry    : angle       0.62803 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 27
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: C   10 TRP cc_start: 0.7862 (t-100) cc_final: 0.6666 (t-100)
REVERT: E   10 TRP cc_start: 0.7344 (t-100) cc_final: 0.5588 (p-90)
REVERT: E   33 MET cc_start: 0.8959 (mtp) cc_final: 0.8050 (pmt)
  outliers start: 6
  outliers final: 1
  residues processed: 30
  average time/residue: 0.5995
  time to fit residues: 18.7540
Evaluate side-chains
  23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 22
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 14 optimal weight:    4.9990
   chunk 16 optimal weight:    4.9990
   chunk 19 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   chunk 18 optimal weight:    5.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    7.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 GLN ** 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 = 0.3848 r_free = 0.3848 target = 0.086402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 20)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.070911 restraints weight = 4731.002|
|-----------------------------------------------------------------------------|
r_work (start): 0.3677 rms_B_bonded: 3.68
r_work: 0.3574 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044   1940  Z= 0.276
  Angle     :  0.743   7.460   2655  Z= 0.379
  Chirality :  0.045   0.159    285
  Planarity :  0.004   0.024    350
  Dihedral  :  6.586  19.959    240
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 19.52 %
    Favored  : 78.57 %
  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: -2.73 (0.43), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.07 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E  10 
 HIS   0.005   0.002   HIS C  40 
 PHE   0.014   0.002   PHE A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03959 (   10)
  hydrogen bonds       : angle       4.67022 (   30)
  covalent geometry    : bond        0.00660 ( 1940)
  covalent geometry    : angle       0.74263 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 23
  time to evaluate  : 0.183 
Fit side-chains
REVERT: C   10 TRP cc_start: 0.8142 (t-100) cc_final: 0.7410 (t-100)
REVERT: E   33 MET cc_start: 0.9327 (mtp) cc_final: 0.9011 (mtt)
  outliers start: 4
  outliers final: 3
  residues processed: 26
  average time/residue: 1.0063
  time to fit residues: 26.9865
Evaluate side-chains
  20 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 17
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   49 THR
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   49 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 5 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 GLN ** 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 = 0.3894 r_free = 0.3894 target = 0.087127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.071946 restraints weight = 4811.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.3721 rms_B_bonded: 3.80
r_work: 0.3624 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   1940  Z= 0.193
  Angle     :  0.710   8.606   2655  Z= 0.352
  Chirality :  0.042   0.151    285
  Planarity :  0.003   0.023    350
  Dihedral  :  6.350  20.348    240
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 19.05 %
    Favored  : 76.19 %
  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: -2.84 (0.43), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E  10 
 HIS   0.005   0.002   HIS C  40 
 PHE   0.018   0.002   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03025 (   10)
  hydrogen bonds       : angle       4.50379 (   30)
  covalent geometry    : bond        0.00474 ( 1940)
  covalent geometry    : angle       0.71031 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 20
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 MET cc_start: 0.9295 (mtp) cc_final: 0.8953 (mtt)
  outliers start: 10
  outliers final: 6
  residues processed: 27
  average time/residue: 0.5582
  time to fit residues: 15.7529
Evaluate side-chains
  23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 17
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 THR
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   42 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.6166

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  36 GLN ** 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 = 0.4046 r_free = 0.4046 target = 0.103960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.087836 restraints weight = 4825.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.42
r_work: 0.3710 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8016
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.024   1940  Z= 0.157
  Angle     :  0.691   8.789   2655  Z= 0.338
  Chirality :  0.041   0.147    285
  Planarity :  0.003   0.025    350
  Dihedral  :  6.153  20.258    240
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 20.48 %
    Favored  : 74.76 %
  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: -2.90 (0.43), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.015   0.002   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02572 (   10)
  hydrogen bonds       : angle       4.18862 (   30)
  covalent geometry    : bond        0.00393 ( 1940)
  covalent geometry    : angle       0.69053 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 19
  time to evaluate  : 0.209 
Fit side-chains
REVERT: E   33 MET cc_start: 0.9298 (mtp) cc_final: 0.8953 (mtt)
  outliers start: 10
  outliers final: 10
  residues processed: 28
  average time/residue: 0.4216
  time to fit residues: 12.5370
Evaluate side-chains
  26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 16
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   20 ASP
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   14 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
B  36 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.108655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.092895 restraints weight = 4685.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3950 rms_B_bonded: 3.40
r_work: 0.3851 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8472
moved from start:          0.2985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.020   1940  Z= 0.106
  Angle     :  0.653   9.350   2655  Z= 0.306
  Chirality :  0.039   0.134    285
  Planarity :  0.003   0.025    350
  Dihedral  :  5.682  20.594    240
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.86 %
    Favored  : 73.81 %
  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: -2.85 (0.43), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.16 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.015   0.001   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01713 (   10)
  hydrogen bonds       : angle       3.73335 (   30)
  covalent geometry    : bond        0.00281 ( 1940)
  covalent geometry    : angle       0.65320 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 MET cc_start: 0.9100 (mtp) cc_final: 0.8226 (pmt)
  outliers start: 7
  outliers final: 6
  residues processed: 28
  average time/residue: 0.6241
  time to fit residues: 18.2545
Evaluate side-chains
  24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 18
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   32 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   chunk 13 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0270
   chunk 3 optimal weight:    2.9990
   chunk 19 optimal weight:    0.2980
   chunk 0 optimal weight:    5.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.4242

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.105547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.089303 restraints weight = 4866.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3891 rms_B_bonded: 3.48
r_work: 0.3791 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.3023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1940  Z= 0.144
  Angle     :  0.673   9.727   2655  Z= 0.324
  Chirality :  0.041   0.143    285
  Planarity :  0.003   0.022    350
  Dihedral  :  5.776  19.918    240
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 21.90 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.88 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.18 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.012   0.001   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02369 (   10)
  hydrogen bonds       : angle       4.00422 (   30)
  covalent geometry    : bond        0.00367 ( 1940)
  covalent geometry    : angle       0.67347 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 18
  time to evaluate  : 0.197 
Fit side-chains
REVERT: E   33 MET cc_start: 0.9268 (mtp) cc_final: 0.8252 (pmt)
REVERT: E   49 THR cc_start: 0.8832 (p) cc_final: 0.8516 (t)
  outliers start: 10
  outliers final: 9
  residues processed: 28
  average time/residue: 0.3433
  time to fit residues: 10.3336
Evaluate side-chains
  26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 17
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   21 SER
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   20 ASP
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   14 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0010
   chunk 19 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 4 optimal weight:    0.8980
   chunk 0 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    5.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.6386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.178145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4624 r_free = 0.4624 target = 0.147361 restraints weight = 4928.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3939 rms_B_bonded: 2.29
r_work: 0.3861 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3792 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1940  Z= 0.097
  Angle     :  0.640   9.686   2655  Z= 0.297
  Chirality :  0.039   0.130    285
  Planarity :  0.003   0.023    350
  Dihedral  :  5.480  20.535    240
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 23.81 %
    Favored  : 72.86 %
  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: -2.89 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.33), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.013   0.001   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01527 (   10)
  hydrogen bonds       : angle       3.76817 (   30)
  covalent geometry    : bond        0.00266 ( 1940)
  covalent geometry    : angle       0.63959 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 28
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: E   10 TRP cc_start: 0.7390 (t-100) cc_final: 0.5558 (p-90)
REVERT: E   22 PHE cc_start: 0.8470 (m-10) cc_final: 0.8251 (m-10)
REVERT: E   33 MET cc_start: 0.9002 (mtp) cc_final: 0.8112 (pmt)
REVERT: E   49 THR cc_start: 0.8422 (p) cc_final: 0.8098 (t)
  outliers start: 7
  outliers final: 7
  residues processed: 35
  average time/residue: 0.4841
  time to fit residues: 17.7931
Evaluate side-chains
  29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 22
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain E residue   14 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 4 optimal weight:    5.9990
   chunk 1 optimal weight:   10.0000
   chunk 18 optimal weight:    0.0470
   chunk 15 optimal weight:    1.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 13 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    1.1282

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

Flipped N/Q/H residues before XYZ refinement:
D  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.095722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.079921 restraints weight = 4822.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3941 rms_B_bonded: 3.75
r_work: 0.3821 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8327
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1940  Z= 0.124
  Angle     :  0.692  10.010   2655  Z= 0.319
  Chirality :  0.041   0.137    285
  Planarity :  0.003   0.021    350
  Dihedral  :  5.507  19.150    240
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.29 %
    Favored  : 71.43 %
  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: -2.89 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.19 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.012   0.001   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02153 (   10)
  hydrogen bonds       : angle       3.95309 (   30)
  covalent geometry    : bond        0.00324 ( 1940)
  covalent geometry    : angle       0.69186 ( 2655)

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

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

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  470 Ramachandran restraints generated.
    235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 21
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: E   33 MET cc_start: 0.9342 (mtp) cc_final: 0.8209 (pmt)
REVERT: E   49 THR cc_start: 0.8438 (p) cc_final: 0.8111 (t)
  outliers start: 9
  outliers final: 8
  residues processed: 30
  average time/residue: 0.3461
  time to fit residues: 11.1869
Evaluate side-chains
  27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 19
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain B residue   21 SER
Chi-restraints excluded: chain B residue   29 VAL
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   32 THR
Chi-restraints excluded: chain D residue   40 HIS
Chi-restraints excluded: chain E residue   14 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 20
   random chunks:
   chunk 14 optimal weight:    0.0030
   chunk 6 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    5.9990
   chunk 15 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    1.1194

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

Flipped N/Q/H residues before XYZ refinement:
D  40 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.095815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.080060 restraints weight = 4852.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 3.82
r_work: 0.3822 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   1940  Z= 0.123
  Angle     :  0.696  10.004   2655  Z= 0.317
  Chirality :  0.040   0.136    285
  Planarity :  0.003   0.019    350
  Dihedral  :  5.552  19.637    240
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 24.29 %
    Favored  : 71.43 %
  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: -2.89 (0.44), residues: 235
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.34), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A  10 
 HIS   0.005   0.001   HIS C  40 
 PHE   0.012   0.001   PHE B  50 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.01989 (   10)
  hydrogen bonds       : angle       3.89193 (   30)
  covalent geometry    : bond        0.00321 ( 1940)
  covalent geometry    : angle       0.69568 ( 2655)

===============================================================================
Job complete
usr+sys time: 1792.61 seconds
wall clock time: 31 minutes 41.34 seconds (1901.34 seconds total)