Starting phenix.real_space_refine
on Mon Feb 10 21:33:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cu8_7619/02_2025/6cu8_7619.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.002
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: 3
    Type Number    sf(0)   Gaussians
     C    1780      2.51       5
     N     510      2.21       5
     O     590      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 2880
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 288
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 288
          Classifications: {'peptide': 41}
          Link IDs: {'TRANS': 40}
  Restraints were copied for chains:
    C, B, E, D, G, F, I, H, J
  Time building chain proxies: 1.02, per 1000 atoms: 0.35
  Number of scatterers: 2880
  At special positions: 0
  Unit cell: (96.3, 68.48, 44.94, 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     590      8.00
     N     510      7.00
     C    1780      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: 0.63
  Conformation dependent library (CDL) restraints added in 364.3 milliseconds
  

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  720

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 9 sheets defined
      0.0% alpha, 15.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 49
      removed outlier: 6.999A  pdb=" N   LYS A  45 " --> pdb=" O   GLU C  46 " (cutoff:3.500A)
      removed outlier: 8.360A  pdb=" N   VAL C  48 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   GLY A  47 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 7.056A  pdb=" N   GLU E  46 " --> pdb=" O   LYS C  45 " (cutoff:3.500A)
      removed outlier: 7.066A  pdb=" N   LYS E  45 " --> pdb=" O   GLU G  46 " (cutoff:3.500A)
      removed outlier: 8.304A  pdb=" N   VAL G  48 " --> pdb=" O   LYS E  45 " (cutoff:3.500A)
      removed outlier: 5.834A  pdb=" N   GLY E  47 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   LYS G  45 " --> pdb=" O   GLU I  46 " (cutoff:3.500A)
      removed outlier: 8.514A  pdb=" N   VAL I  48 " --> pdb=" O   LYS G  45 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   GLY G  47 " --> pdb=" O   VAL I  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77
      removed outlier: 6.457A  pdb=" N   ALA E  76 " --> pdb=" O   VAL C  77 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 81 through 82
    Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 49
      removed outlier: 6.939A  pdb=" N   LYS B  45 " --> pdb=" O   GLU D  46 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   VAL D  48 " --> pdb=" O   LYS B  45 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   GLY B  47 " --> pdb=" O   VAL D  48 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   LYS D  45 " --> pdb=" O   GLU F  46 " (cutoff:3.500A)
      removed outlier: 8.440A  pdb=" N   VAL F  48 " --> pdb=" O   LYS D  45 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   GLY D  47 " --> pdb=" O   VAL F  48 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   LYS F  45 " --> pdb=" O   GLU H  46 " (cutoff:3.500A)
      removed outlier: 8.362A  pdb=" N   VAL H  48 " --> pdb=" O   LYS F  45 " (cutoff:3.500A)
      removed outlier: 6.089A  pdb=" N   GLY F  47 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   LYS H  45 " --> pdb=" O   GLU J  46 " (cutoff:3.500A)
      removed outlier: 8.425A  pdb=" N   VAL J  48 " --> pdb=" O   LYS H  45 " (cutoff:3.500A)
      removed outlier: 6.040A  pdb=" N   GLY H  47 " --> pdb=" O   VAL J  48 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 77
    Processing sheet with id=AA6, first strand: chain 'B' and resid 81 through 82
      removed outlier: 6.567A  pdb=" N   THR B  81 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'F' and resid 61 through 63
    Processing sheet with id=AA8, first strand: chain 'F' and resid 81 through 82
      removed outlier: 6.601A  pdb=" N   THR F  81 " --> pdb=" O   VAL H  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 81 through 82
      removed outlier: 6.633A  pdb=" N   THR G  81 " --> pdb=" O   VAL I  82 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    13 hydrogen bonds defined for protein.
    39 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: 0.58

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.29: 520
        1.29 -     1.35: 452
        1.35 -     1.42: 28
        1.42 -     1.48: 480
        1.48 -     1.55: 1400
  Bond restraints: 2880
  Sorted by residual:
  bond pdb=" CB  ASN A  65 "
       pdb=" CG  ASN A  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.18e+00
  bond pdb=" CB  ASN D  65 "
       pdb=" CG  ASN D  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.17e+00
  bond pdb=" CB  ASN I  65 "
       pdb=" CG  ASN I  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.16e+00
  bond pdb=" CB  ASN F  65 "
       pdb=" CG  ASN F  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.15e+00
  bond pdb=" CB  ASN E  65 "
       pdb=" CG  ASN E  65 "
    ideal  model  delta    sigma   weight residual
    1.516  1.489  0.027 2.50e-02 1.60e+03 1.14e+00
  ... (remaining 2875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.69: 2928
        0.69 -     1.39: 760
        1.39 -     2.08: 112
        2.08 -     2.78: 80
        2.78 -     3.47: 20
  Bond angle restraints: 3900
  Sorted by residual:
  angle pdb=" C   GLU G  57 "
        pdb=" N   LYS G  58 "
        pdb=" CA  LYS G  58 "
      ideal   model   delta    sigma   weight residual
     122.19  124.91   -2.72 1.41e+00 5.03e-01 3.72e+00
  angle pdb=" C   GLY E  51 "
        pdb=" N   VAL E  52 "
        pdb=" CA  VAL E  52 "
      ideal   model   delta    sigma   weight residual
     121.97  125.44   -3.47 1.80e+00 3.09e-01 3.72e+00
  angle pdb=" C   GLY C  51 "
        pdb=" N   VAL C  52 "
        pdb=" CA  VAL C  52 "
      ideal   model   delta    sigma   weight residual
     121.97  125.43   -3.46 1.80e+00 3.09e-01 3.70e+00
  angle pdb=" C   GLY I  51 "
        pdb=" N   VAL I  52 "
        pdb=" CA  VAL I  52 "
      ideal   model   delta    sigma   weight residual
     121.97  125.42   -3.45 1.80e+00 3.09e-01 3.68e+00
  angle pdb=" C   GLU B  57 "
        pdb=" N   LYS B  58 "
        pdb=" CA  LYS B  58 "
      ideal   model   delta    sigma   weight residual
     122.19  124.89   -2.70 1.41e+00 5.03e-01 3.67e+00
  ... (remaining 3895 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     4.30: 1190
        4.30 -     8.59: 260
        8.59 -    12.88: 141
       12.88 -    17.18: 99
       17.18 -    21.47: 30
  Dihedral angle restraints: 1720
    sinusoidal: 600
      harmonic: 1120
  Sorted by residual:
  dihedral pdb=" CA  VAL C  74 "
           pdb=" C   VAL C  74 "
           pdb=" N   THR C  75 "
           pdb=" CA  THR C  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.09   18.91     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  VAL E  74 "
           pdb=" C   VAL E  74 "
           pdb=" N   THR E  75 "
           pdb=" CA  THR E  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.12   18.88     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" CA  VAL B  74 "
           pdb=" C   VAL B  74 "
           pdb=" N   THR B  75 "
           pdb=" CA  THR B  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.13   18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 1717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 317
       0.033 -    0.066: 86
       0.066 -    0.099: 44
       0.099 -    0.132: 65
       0.132 -    0.165: 28
  Chirality restraints: 540
  Sorted by residual:
  chirality pdb=" CA  VAL D  52 "
            pdb=" N   VAL D  52 "
            pdb=" C   VAL D  52 "
            pdb=" CB  VAL D  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  VAL H  52 "
            pdb=" N   VAL H  52 "
            pdb=" C   VAL H  52 "
            pdb=" CB  VAL H  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  VAL J  52 "
            pdb=" N   VAL J  52 "
            pdb=" C   VAL J  52 "
            pdb=" CB  VAL J  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.62e-01
  ... (remaining 537 not shown)

  Planarity restraints: 480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN G  79 "   -0.004 2.00e-02 2.50e+03   7.48e-03 5.59e-01
        pdb=" CD  GLN G  79 "    0.013 2.00e-02 2.50e+03
        pdb=" OE1 GLN G  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 GLN G  79 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A  79 "   -0.004 2.00e-02 2.50e+03   7.43e-03 5.53e-01
        pdb=" CD  GLN A  79 "    0.013 2.00e-02 2.50e+03
        pdb=" OE1 GLN A  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 GLN A  79 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN E  79 "   -0.004 2.00e-02 2.50e+03   7.41e-03 5.49e-01
        pdb=" CD  GLN E  79 "    0.013 2.00e-02 2.50e+03
        pdb=" OE1 GLN E  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE2 GLN E  79 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 477 not shown)

  Histogram of nonbonded interaction distances:
        2.41 -     2.91: 1138
        2.91 -     3.41: 2277
        3.41 -     3.90: 4694
        3.90 -     4.40: 4410
        4.40 -     4.90: 9453
  Nonbonded interactions: 21972
  Sorted by model distance:
  nonbonded pdb=" N   ASN B  65 "
            pdb=" OD1 ASN B  65 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" N   ASN J  65 "
            pdb=" OD1 ASN J  65 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" N   ASN H  65 "
            pdb=" OD1 ASN H  65 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" N   ASN C  65 "
            pdb=" OD1 ASN C  65 "
     model   vdw
     2.412 3.120
  nonbonded pdb=" N   ASN F  65 "
            pdb=" OD1 ASN F  65 "
     model   vdw
     2.412 3.120
  ... (remaining 21967 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
  selection = chain 'I'
  selection = chain 'H'
  selection = chain 'J'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             0.310
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.040
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2880  Z= 0.252
  Angle     :  0.726   3.470   3900  Z= 0.430
  Chirality :  0.062   0.165    540
  Planarity :  0.002   0.007    480
  Dihedral  :  7.746  21.472   1000
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.86 (0.47), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.17 (0.36), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8501 (mttp) cc_final: 0.7794 (pttm)
REVERT: I   75 THR cc_start: 0.7029 (m) cc_final: 0.6813 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1165
  time to fit residues: 15.9780
Evaluate side-chains
  69 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    6.9990
   chunk 30 optimal weight:    7.9990
   chunk 16 optimal weight:   40.0000
   chunk 10 optimal weight:    0.0980
   chunk 20 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 12 optimal weight:   40.0000
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    5.9990
   chunk 36 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   overall best weight:    5.2188

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

Flipped N/Q/H residues before XYZ refinement:
** E  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  79 GLN
D  79 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.116589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.102960 restraints weight = 6913.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.105067 restraints weight = 3488.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.106485 restraints weight = 2267.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7144
moved from start:          0.3160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2880  Z= 0.214
  Angle     :  0.685   3.481   3900  Z= 0.409
  Chirality :  0.053   0.122    540
  Planarity :  0.003   0.011    480
  Dihedral  :  6.877  15.655    400
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 12.58 %
    Favored  : 85.81 %
  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: -2.69 (0.44), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.04 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS I  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A   58 LYS cc_start: 0.8664 (mttp) cc_final: 0.7769 (pttm)
REVERT: A   61 GLU cc_start: 0.7685 (pm20) cc_final: 0.6162 (mm-30)
REVERT: B   61 GLU cc_start: 0.7986 (pt0) cc_final: 0.6134 (mm-30)
REVERT: D   61 GLU cc_start: 0.7588 (pm20) cc_final: 0.7377 (pm20)
REVERT: H   61 GLU cc_start: 0.7288 (pm20) cc_final: 0.7067 (pm20)
  outliers start: 5
  outliers final: 3
  residues processed: 71
  average time/residue: 0.0871
  time to fit residues: 8.4210
Evaluate side-chains
  59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 28 optimal weight:   40.0000
   chunk 10 optimal weight:   10.0000
   chunk 37 optimal weight:    8.9990
   chunk 32 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:   30.0000
   chunk 22 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 16 optimal weight:   30.0000
   overall best weight:    6.6788

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

Flipped N/Q/H residues before XYZ refinement:
E  79 GLN
B  79 GLN
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  79 GLN
G  79 GLN
H  79 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.116029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.102250 restraints weight = 7146.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.104547 restraints weight = 3564.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.106132 restraints weight = 2287.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.4035
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2880  Z= 0.260
  Angle     :  0.689   3.433   3900  Z= 0.412
  Chirality :  0.055   0.120    540
  Planarity :  0.003   0.014    480
  Dihedral  :  6.997  15.347    400
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.16 %
    Favored  : 82.90 %
  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: -2.79 (0.40), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.12 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS D  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.375 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7528 (pm20) cc_final: 0.7261 (pm20)
REVERT: A   61 GLU cc_start: 0.8010 (pm20) cc_final: 0.6102 (mm-30)
REVERT: A   79 GLN cc_start: 0.8926 (tt0) cc_final: 0.8359 (tt0)
REVERT: B   61 GLU cc_start: 0.7856 (pt0) cc_final: 0.6071 (mm-30)
REVERT: B   81 THR cc_start: 0.8303 (p) cc_final: 0.8053 (p)
REVERT: D   46 GLU cc_start: 0.6761 (tt0) cc_final: 0.6379 (tt0)
REVERT: G   61 GLU cc_start: 0.7839 (pm20) cc_final: 0.7634 (pm20)
  outliers start: 6
  outliers final: 3
  residues processed: 67
  average time/residue: 0.0915
  time to fit residues: 8.2615
Evaluate side-chains
  54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain D residue   81 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 8 optimal weight:   20.0000
   chunk 28 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 17 optimal weight:    7.9990
   chunk 32 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 24 optimal weight:    6.9990
   chunk 29 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** H  79 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 = 0.4180 r_free = 0.4180 target = 0.116828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.103163 restraints weight = 7206.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.105535 restraints weight = 3580.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.107162 restraints weight = 2263.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.4584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2880  Z= 0.263
  Angle     :  0.673   3.676   3900  Z= 0.400
  Chirality :  0.055   0.124    540
  Planarity :  0.003   0.013    480
  Dihedral  :  6.794  14.685    400
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.95 %
    Favored  : 92.05 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.84 %
    Favored  : 81.94 %
  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: -2.83 (0.40), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 47
  time to evaluate  : 0.341 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7625 (pm20) cc_final: 0.7204 (pm20)
REVERT: E   79 GLN cc_start: 0.9005 (tt0) cc_final: 0.8567 (tt0)
REVERT: A   61 GLU cc_start: 0.8167 (pm20) cc_final: 0.6118 (mm-30)
REVERT: B   61 GLU cc_start: 0.7904 (pt0) cc_final: 0.6179 (mm-30)
REVERT: D   61 GLU cc_start: 0.7583 (pm20) cc_final: 0.7351 (pm20)
REVERT: G   61 GLU cc_start: 0.8071 (pm20) cc_final: 0.7504 (pm20)
REVERT: I   61 GLU cc_start: 0.7200 (pm20) cc_final: 0.6914 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 57
  average time/residue: 0.0829
  time to fit residues: 6.6787
Evaluate side-chains
  47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:   40.0000
   chunk 12 optimal weight:   30.0000
   chunk 4 optimal weight:    5.9990
   chunk 15 optimal weight:   20.0000
   chunk 3 optimal weight:    9.9990
   chunk 21 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:   30.0000
   chunk 8 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  79 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 = 0.4166 r_free = 0.4166 target = 0.115259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.101923 restraints weight = 7334.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.104180 restraints weight = 3771.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.105734 restraints weight = 2403.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7276
moved from start:          0.4924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   2880  Z= 0.307
  Angle     :  0.688   4.125   3900  Z= 0.410
  Chirality :  0.056   0.127    540
  Planarity :  0.003   0.013    480
  Dihedral  :  6.995  16.134    400
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 13.87 %
    Favored  : 81.29 %
  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: -2.99 (0.38), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.27 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.307 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7735 (pm20) cc_final: 0.7352 (pm20)
REVERT: E   79 GLN cc_start: 0.9016 (tt0) cc_final: 0.8592 (tt0)
REVERT: A   61 GLU cc_start: 0.8251 (pm20) cc_final: 0.6050 (mm-30)
REVERT: B   57 GLU cc_start: 0.3390 (OUTLIER) cc_final: 0.2587 (pt0)
REVERT: B   61 GLU cc_start: 0.8016 (pt0) cc_final: 0.6243 (mm-30)
REVERT: D   61 GLU cc_start: 0.7487 (pm20) cc_final: 0.7210 (pm20)
REVERT: G   61 GLU cc_start: 0.8031 (pm20) cc_final: 0.7729 (pm20)
  outliers start: 15
  outliers final: 10
  residues processed: 59
  average time/residue: 0.1119
  time to fit residues: 8.9402
Evaluate side-chains
  50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 38 optimal weight:   20.0000
   chunk 22 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   chunk 1 optimal weight:   20.0000
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    6.9990
   chunk 14 optimal weight:    5.9990
   chunk 36 optimal weight:    4.9990
   chunk 5 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
H  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.117211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.103323 restraints weight = 7259.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.105723 restraints weight = 3643.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.107360 restraints weight = 2299.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.5157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   2880  Z= 0.241
  Angle     :  0.626   3.517   3900  Z= 0.372
  Chirality :  0.056   0.127    540
  Planarity :  0.002   0.013    480
  Dihedral  :  6.617  14.889    400
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 13.87 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.38), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.366 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7613 (pm20) cc_final: 0.7267 (pm20)
REVERT: A   57 GLU cc_start: 0.3350 (OUTLIER) cc_final: 0.1723 (pm20)
REVERT: A   61 GLU cc_start: 0.8180 (pm20) cc_final: 0.6010 (mm-30)
REVERT: B   57 GLU cc_start: 0.3211 (OUTLIER) cc_final: 0.2590 (pt0)
REVERT: B   61 GLU cc_start: 0.8036 (pt0) cc_final: 0.6245 (mm-30)
REVERT: D   58 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8511 (mtpt)
REVERT: D   61 GLU cc_start: 0.7397 (pm20) cc_final: 0.6953 (pm20)
REVERT: F   62 GLN cc_start: 0.7315 (mt0) cc_final: 0.6764 (mp10)
REVERT: G   61 GLU cc_start: 0.8089 (pm20) cc_final: 0.7778 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0964
  time to fit residues: 7.5412
Evaluate side-chains
  54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 31 optimal weight:   20.0000
   chunk 36 optimal weight:   30.0000
   chunk 29 optimal weight:   20.0000
   chunk 24 optimal weight:   30.0000
   chunk 32 optimal weight:    8.9990
   chunk 23 optimal weight:    1.9990
   chunk 39 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 1 optimal weight:    4.9990
   chunk 18 optimal weight:   10.0000
   chunk 6 optimal weight:    2.9990
   overall best weight:    5.7992

-------------------------------------------------------------------------------
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 = 0.4189 r_free = 0.4189 target = 0.116632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.102613 restraints weight = 7334.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.105024 restraints weight = 3693.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.106665 restraints weight = 2335.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7253
moved from start:          0.5312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2880  Z= 0.237
  Angle     :  0.632   5.823   3900  Z= 0.373
  Chirality :  0.056   0.127    540
  Planarity :  0.002   0.014    480
  Dihedral  :  6.524  14.945    400
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.49 %
    Favored  : 90.51 %
  Rotamer:
    Outliers :  6.13 %
    Allowed  : 14.84 %
    Favored  : 79.03 %
  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 (0.38), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.15 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.276 
Fit side-chains
REVERT: A   57 GLU cc_start: 0.3344 (OUTLIER) cc_final: 0.1690 (pm20)
REVERT: A   61 GLU cc_start: 0.8246 (pm20) cc_final: 0.6082 (mm-30)
REVERT: B   57 GLU cc_start: 0.3176 (OUTLIER) cc_final: 0.2519 (pt0)
REVERT: B   61 GLU cc_start: 0.8021 (pt0) cc_final: 0.6266 (mm-30)
REVERT: D   58 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8760 (mtpt)
REVERT: D   61 GLU cc_start: 0.7401 (pm20) cc_final: 0.6950 (pm20)
REVERT: F   62 GLN cc_start: 0.7328 (mt0) cc_final: 0.6763 (mp10)
REVERT: G   61 GLU cc_start: 0.8018 (pm20) cc_final: 0.7377 (pm20)
  outliers start: 19
  outliers final: 11
  residues processed: 56
  average time/residue: 0.0952
  time to fit residues: 7.0642
Evaluate side-chains
  53 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:   40.0000
   chunk 33 optimal weight:    9.9990
   chunk 23 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:   30.0000
   chunk 28 optimal weight:    6.9990
   chunk 21 optimal weight:    9.9990
   chunk 4 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   overall best weight:    8.9990

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 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 = 0.4153 r_free = 0.4153 target = 0.113524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.099936 restraints weight = 7438.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.102228 restraints weight = 3828.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.103750 restraints weight = 2431.429|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   2880  Z= 0.352
  Angle     :  0.720   4.877   3900  Z= 0.426
  Chirality :  0.058   0.130    540
  Planarity :  0.003   0.013    480
  Dihedral  :  7.134  16.176    400
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.36 %
    Favored  : 85.64 %
  Rotamer:
    Outliers :  5.81 %
    Allowed  : 13.87 %
    Favored  : 80.32 %
  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: -3.34 (0.35), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.54 (0.27), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 47
  time to evaluate  : 0.323 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7883 (pm20) cc_final: 0.7559 (pm20)
REVERT: E   79 GLN cc_start: 0.8991 (tt0) cc_final: 0.8548 (tt0)
REVERT: A   57 GLU cc_start: 0.3471 (OUTLIER) cc_final: 0.1796 (pm20)
REVERT: A   61 GLU cc_start: 0.8269 (pm20) cc_final: 0.6050 (mm-30)
REVERT: A   79 GLN cc_start: 0.8959 (tt0) cc_final: 0.8419 (tt0)
REVERT: B   57 GLU cc_start: 0.3481 (OUTLIER) cc_final: 0.2628 (pt0)
REVERT: B   61 GLU cc_start: 0.8100 (pt0) cc_final: 0.6370 (mm-30)
REVERT: D   58 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8712 (mtpt)
REVERT: D   61 GLU cc_start: 0.7432 (pm20) cc_final: 0.6959 (pm20)
REVERT: F   62 GLN cc_start: 0.7387 (mt0) cc_final: 0.6820 (mp10)
  outliers start: 18
  outliers final: 12
  residues processed: 60
  average time/residue: 0.0841
  time to fit residues: 7.0245
Evaluate side-chains
  61 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   81 THR
Chi-restraints excluded: chain A residue   44 THR
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   52 VAL
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    0.6980
   chunk 3 optimal weight:    5.9990
   chunk 28 optimal weight:   40.0000
   chunk 26 optimal weight:    7.9990
   chunk 8 optimal weight:   20.0000
   chunk 30 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 37 optimal weight:    0.0870
   chunk 35 optimal weight:    8.9990
   chunk 39 optimal weight:    9.9990
   chunk 11 optimal weight:   20.0000
   overall best weight:    3.5564

-------------------------------------------------------------------------------
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 = 0.4239 r_free = 0.4239 target = 0.120540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.107165 restraints weight = 6993.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.109670 restraints weight = 3378.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4132 r_free = 0.4132 target = 0.111368 restraints weight = 2071.348|
|-----------------------------------------------------------------------------|
r_work (final): 0.4127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.5501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2880  Z= 0.170
  Angle     :  0.599   4.297   3900  Z= 0.351
  Chirality :  0.055   0.126    540
  Planarity :  0.002   0.015    480
  Dihedral  :  6.239  14.609    400
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.42 %
    Favored  : 80.32 %
  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: -2.78 (0.39), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.11 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.360 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7803 (pm20) cc_final: 0.7400 (pm20)
REVERT: A   61 GLU cc_start: 0.8204 (pm20) cc_final: 0.5965 (mm-30)
REVERT: B   61 GLU cc_start: 0.7912 (pt0) cc_final: 0.6247 (mm-30)
REVERT: D   61 GLU cc_start: 0.7428 (pm20) cc_final: 0.7035 (pm20)
REVERT: F   62 GLN cc_start: 0.7340 (mt0) cc_final: 0.6827 (mp10)
REVERT: G   61 GLU cc_start: 0.7777 (pm20) cc_final: 0.7566 (pm20)
  outliers start: 7
  outliers final: 5
  residues processed: 54
  average time/residue: 0.0811
  time to fit residues: 6.2352
Evaluate side-chains
  51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:   50.0000
   chunk 21 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:   10.0000
   chunk 36 optimal weight:    7.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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 = 0.4205 r_free = 0.4205 target = 0.118097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.104487 restraints weight = 7183.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.106885 restraints weight = 3545.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.108498 restraints weight = 2221.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2880  Z= 0.255
  Angle     :  0.641   4.971   3900  Z= 0.377
  Chirality :  0.055   0.124    540
  Planarity :  0.003   0.014    480
  Dihedral  :  6.457  14.864    400
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 18.06 %
    Favored  : 79.03 %
  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: -2.95 (0.38), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.24 (0.29), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS B  50 

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

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

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  780 Ramachandran restraints generated.
    390 Oldfield, 0 Emsley, 390 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.321 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7706 (pm20) cc_final: 0.7435 (pm20)
REVERT: A   57 GLU cc_start: 0.3462 (OUTLIER) cc_final: 0.1839 (pm20)
REVERT: A   61 GLU cc_start: 0.8242 (pm20) cc_final: 0.5983 (mm-30)
REVERT: B   57 GLU cc_start: 0.3412 (OUTLIER) cc_final: 0.2587 (pt0)
REVERT: B   61 GLU cc_start: 0.7910 (pt0) cc_final: 0.6203 (mm-30)
REVERT: D   61 GLU cc_start: 0.7427 (pm20) cc_final: 0.7024 (pm20)
REVERT: F   62 GLN cc_start: 0.7371 (mt0) cc_final: 0.6867 (mp10)
  outliers start: 9
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0722
  time to fit residues: 5.0414
Evaluate side-chains
  48 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   57 GLU
Chi-restraints excluded: chain B residue   44 THR
Chi-restraints excluded: chain B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   75 THR
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain C residue   75 THR
Chi-restraints excluded: chain D residue   81 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 20 optimal weight:   30.0000
   chunk 1 optimal weight:    7.9990
   chunk 4 optimal weight:   20.0000
   chunk 37 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 38 optimal weight:   20.0000
   chunk 28 optimal weight:    8.9990
   chunk 12 optimal weight:    5.9990
   chunk 27 optimal weight:   40.0000
   chunk 11 optimal weight:   30.0000
   chunk 24 optimal weight:   30.0000
   overall best weight:    6.7992

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 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 = 0.4195 r_free = 0.4195 target = 0.117304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.103763 restraints weight = 7093.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.106115 restraints weight = 3566.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.107663 restraints weight = 2257.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7299
moved from start:          0.5670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2880  Z= 0.274
  Angle     :  0.645   4.221   3900  Z= 0.381
  Chirality :  0.056   0.125    540
  Planarity :  0.003   0.017    480
  Dihedral  :  6.639  15.199    400
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.05 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 17.74 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.11 (0.37), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.37 (0.28), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS D  50 

===============================================================================
Job complete
usr+sys time: 1011.35 seconds
wall clock time: 19 minutes 13.35 seconds (1153.35 seconds total)