Starting phenix.real_space_refine
on Wed Mar  5 16:29:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6cu8_7619/03_2025/6cu8_7619.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6cu8_7619/03_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_7619/03_2025/6cu8_7619.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6cu8_7619/03_2025/6cu8_7619.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6cu8_7619/03_2025/6cu8_7619.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6cu8_7619/03_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-5624/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: 1.19, per 1000 atoms: 0.41
  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: 0.59
  Conformation dependent library (CDL) restraints added in 353.0 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: 0.35
  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: 0.57

  Time building geometry restraints manager: 0.73 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:                  0.000
  Normalize map: mean=0, sd=1:             0.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.790
  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:3.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.450
-------------------------------------------------------------------------------
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  : 0.320 
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: 0.1195
  time to fit residues: 16.2879
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  : 0.310 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.102960 restraints weight = 6913.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.105069 restraints weight = 3487.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.106477 restraints weight = 2263.385|
|-----------------------------------------------------------------------------|
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  : 0.303 
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: 0.7589 (pm20) cc_final: 0.7378 (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: 0.0832
  time to fit residues: 8.0198
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  : 0.326 
-------------------------------------------------------------------------------
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:    0.0170
   chunk 28 optimal weight:   40.0000
   chunk 10 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 6 optimal weight:   10.0000
   chunk 7 optimal weight:   30.0000
   chunk 22 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:   30.0000
   overall best weight:    3.4026

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4245 r_free = 0.4245 target = 0.121972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.108528 restraints weight = 6725.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.110933 restraints weight = 3207.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.112561 restraints weight = 1997.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.4144
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.3866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.015   2880  Z= 0.151
  Angle     :  0.587   3.300   3900  Z= 0.349
  Chirality :  0.053   0.119    540
  Planarity :  0.002   0.013    480
  Dihedral  :  6.202  14.001    400
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.19 %
    Favored  : 83.55 %
  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: -2.13 (0.45), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.61 (0.34), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  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
  75 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.460 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7628 (pm20) cc_final: 0.7349 (pm20)
REVERT: A   58 LYS cc_start: 0.8669 (mttp) cc_final: 0.7606 (pttp)
REVERT: A   61 GLU cc_start: 0.7821 (pm20) cc_final: 0.5997 (mm-30)
REVERT: A   75 THR cc_start: 0.7470 (m) cc_final: 0.7017 (p)
REVERT: B   61 GLU cc_start: 0.7774 (pt0) cc_final: 0.5919 (mm-30)
REVERT: G   61 GLU cc_start: 0.7679 (pm20) cc_final: 0.7362 (pm20)
REVERT: H   61 GLU cc_start: 0.7182 (pm20) cc_final: 0.6974 (pm20)
  outliers start: 7
  outliers final: 4
  residues processed: 74
  average time/residue: 0.0875
  time to fit residues: 9.0445
Evaluate side-chains
  62 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain F 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:    0.3980
   chunk 20 optimal weight:    9.9990
   chunk 17 optimal weight:    0.5980
   chunk 32 optimal weight:   20.0000
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:   30.0000
   chunk 29 optimal weight:    0.7980
   chunk 35 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.5584

-------------------------------------------------------------------------------
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 = 0.4248 r_free = 0.4248 target = 0.121786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.108049 restraints weight = 6891.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.110432 restraints weight = 3340.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.112098 restraints weight = 2102.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7161
moved from start:          0.4253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   2880  Z= 0.152
  Angle     :  0.573   3.591   3900  Z= 0.341
  Chirality :  0.053   0.120    540
  Planarity :  0.003   0.013    480
  Dihedral  :  5.940  13.857    400
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.44 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.16 %
    Favored  : 83.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.91 (0.45), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.44 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS C  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
  63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.269 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7517 (pm20) cc_final: 0.7233 (pm20)
REVERT: A   58 LYS cc_start: 0.8472 (mttp) cc_final: 0.7710 (pttp)
REVERT: A   61 GLU cc_start: 0.8038 (pm20) cc_final: 0.6037 (mm-30)
REVERT: B   61 GLU cc_start: 0.7694 (pt0) cc_final: 0.5995 (mm-30)
REVERT: G   61 GLU cc_start: 0.7783 (pm20) cc_final: 0.7337 (pm20)
REVERT: H   61 GLU cc_start: 0.7238 (pm20) cc_final: 0.7000 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.0743
  time to fit residues: 6.4924
Evaluate side-chains
  60 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  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 D residue   81 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:   30.0000
   chunk 12 optimal weight:   30.0000
   chunk 4 optimal weight:    6.9990
   chunk 15 optimal weight:   40.0000
   chunk 3 optimal weight:   10.0000
   chunk 21 optimal weight:   30.0000
   chunk 39 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 19 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   chunk 38 optimal weight:    6.9990
   overall best weight:    7.5992

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.116110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.102527 restraints weight = 7144.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.104806 restraints weight = 3591.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.106356 restraints weight = 2279.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.4042
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7239
moved from start:          0.4690

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= 0.299
  Angle     :  0.672   3.688   3900  Z= 0.400
  Chirality :  0.055   0.124    540
  Planarity :  0.003   0.013    480
  Dihedral  :  6.834  15.921    400
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.23 %
    Favored  : 90.77 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.87 %
    Favored  : 83.55 %
  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: -2.43 (0.41), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.84 (0.31), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.001   HIS G  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
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.335 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7626 (pm20) cc_final: 0.7262 (pm20)
REVERT: A   61 GLU cc_start: 0.8243 (pm20) cc_final: 0.6075 (mm-30)
REVERT: B   61 GLU cc_start: 0.7963 (pt0) cc_final: 0.6308 (mm-30)
REVERT: F   62 GLN cc_start: 0.7252 (mt0) cc_final: 0.6732 (mp10)
REVERT: G   61 GLU cc_start: 0.8073 (pm20) cc_final: 0.7819 (pm20)
REVERT: H   61 GLU cc_start: 0.7231 (pm20) cc_final: 0.6970 (pm20)
  outliers start: 8
  outliers final: 5
  residues processed: 57
  average time/residue: 0.0954
  time to fit residues: 7.2739
Evaluate side-chains
  47 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
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   81 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 4 optimal weight:   20.0000
   chunk 38 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 21 optimal weight:   30.0000
   chunk 1 optimal weight:    7.9990
   chunk 10 optimal weight:    2.9990
   chunk 29 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 5 optimal weight:   10.0000
   overall best weight:    8.1990

-------------------------------------------------------------------------------
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**
** G  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 = 0.4169 r_free = 0.4169 target = 0.115152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.101806 restraints weight = 7356.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.104081 restraints weight = 3687.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.105657 restraints weight = 2327.481|
|-----------------------------------------------------------------------------|
r_work (final): 0.4032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7265
moved from start:          0.5068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   2880  Z= 0.324
  Angle     :  0.691   4.411   3900  Z= 0.411
  Chirality :  0.057   0.130    540
  Planarity :  0.003   0.012    480
  Dihedral  :  7.002  16.111    400
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 12.90 %
    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: -2.89 (0.37), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.28), 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
  59 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 46
  time to evaluate  : 0.303 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7763 (pm20) cc_final: 0.7396 (pm20)
REVERT: A   61 GLU cc_start: 0.8252 (pm20) cc_final: 0.6033 (mm-30)
REVERT: A   79 GLN cc_start: 0.8968 (tt0) cc_final: 0.8443 (tt0)
REVERT: B   57 GLU cc_start: 0.3357 (OUTLIER) cc_final: 0.2588 (pt0)
REVERT: B   61 GLU cc_start: 0.8037 (pt0) cc_final: 0.6313 (mm-30)
REVERT: F   62 GLN cc_start: 0.7305 (mt0) cc_final: 0.6805 (mp10)
REVERT: G   61 GLU cc_start: 0.8104 (pm20) cc_final: 0.7690 (pm20)
REVERT: H   61 GLU cc_start: 0.7304 (pm20) cc_final: 0.7045 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 58
  average time/residue: 0.0954
  time to fit residues: 7.3116
Evaluate side-chains
  50 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
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 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:   40.0000
   chunk 36 optimal weight:   30.0000
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:   30.0000
   chunk 32 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 18 optimal weight:    9.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    7.1990

-------------------------------------------------------------------------------
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**
** G  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.115660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.102260 restraints weight = 7314.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.104580 restraints weight = 3690.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.106156 restraints weight = 2329.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7248
moved from start:          0.5268

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= 0.284
  Angle     :  0.657   4.042   3900  Z= 0.390
  Chirality :  0.057   0.136    540
  Planarity :  0.003   0.014    480
  Dihedral  :  6.812  15.466    400
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.74 %
    Favored  : 90.26 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 13.23 %
    Favored  : 82.26 %
  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 (0.37), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.20 (0.28), 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
  54 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 40
  time to evaluate  : 0.326 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7729 (pm20) cc_final: 0.7408 (pm20)
REVERT: A   61 GLU cc_start: 0.8267 (pm20) cc_final: 0.6111 (mm-30)
REVERT: B   57 GLU cc_start: 0.3273 (OUTLIER) cc_final: 0.2498 (pt0)
REVERT: B   61 GLU cc_start: 0.8112 (pt0) cc_final: 0.6318 (mm-30)
REVERT: F   62 GLN cc_start: 0.7345 (mt0) cc_final: 0.6828 (mp10)
REVERT: G   57 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.7875 (tm-30)
REVERT: G   61 GLU cc_start: 0.8085 (pm20) cc_final: 0.7764 (pm20)
REVERT: H   61 GLU cc_start: 0.7337 (pm20) cc_final: 0.7071 (pm20)
  outliers start: 14
  outliers final: 8
  residues processed: 53
  average time/residue: 0.0825
  time to fit residues: 6.0736
Evaluate side-chains
  49 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 39
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 VAL
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 D residue   81 THR
Chi-restraints excluded: chain F residue   57 GLU
Chi-restraints excluded: chain F residue   75 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   57 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 21 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 13 optimal weight:   10.0000
   chunk 1 optimal weight:   10.0000
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** C  79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  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 = 0.4184 r_free = 0.4184 target = 0.116393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.103091 restraints weight = 7136.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.105444 restraints weight = 3613.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.106982 restraints weight = 2273.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.5411

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= 0.262
  Angle     :  0.642   3.876   3900  Z= 0.379
  Chirality :  0.056   0.135    540
  Planarity :  0.002   0.012    480
  Dihedral  :  6.663  15.456    400
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.26 %
    Favored  : 89.74 %
  Rotamer:
    Outliers :  4.84 %
    Allowed  : 14.19 %
    Favored  : 80.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.36), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.23 (0.28), 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
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 42
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8269 (pm20) cc_final: 0.6088 (mm-30)
REVERT: B   57 GLU cc_start: 0.3300 (OUTLIER) cc_final: 0.2472 (pt0)
REVERT: B   61 GLU cc_start: 0.7996 (pt0) cc_final: 0.6228 (mm-30)
REVERT: D   58 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8883 (mtpt)
REVERT: F   62 GLN cc_start: 0.7353 (mt0) cc_final: 0.6856 (mp10)
REVERT: G   57 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7907 (tm-30)
REVERT: G   61 GLU cc_start: 0.8097 (pm20) cc_final: 0.7474 (pm20)
REVERT: H   61 GLU cc_start: 0.7339 (pm20) cc_final: 0.7080 (pm20)
  outliers start: 15
  outliers final: 9
  residues processed: 54
  average time/residue: 0.0789
  time to fit residues: 5.7674
Evaluate side-chains
  52 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 40
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
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   66 VAL
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 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
Chi-restraints excluded: chain G residue   57 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    3.9990
   chunk 3 optimal weight:   40.0000
   chunk 28 optimal weight:    0.4980
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:   20.0000
   chunk 30 optimal weight:    7.9990
   chunk 25 optimal weight:   30.0000
   chunk 37 optimal weight:    0.0470
   chunk 35 optimal weight:   30.0000
   chunk 39 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   overall best weight:    3.1084

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.122453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.108777 restraints weight = 6893.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.111432 restraints weight = 3349.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.113227 restraints weight = 2055.421|
|-----------------------------------------------------------------------------|
r_work (final): 0.4154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7185
moved from start:          0.5445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   2880  Z= 0.154
  Angle     :  0.574   5.093   3900  Z= 0.335
  Chirality :  0.055   0.131    540
  Planarity :  0.002   0.015    480
  Dihedral  :  5.968  14.255    400
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 16.13 %
    Favored  : 80.65 %
  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: -2.36 (0.40), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -1.79 (0.31), 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
  63 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.341 
Fit side-chains
REVERT: E   61 GLU cc_start: 0.7958 (pm20) cc_final: 0.7625 (pm20)
REVERT: A   61 GLU cc_start: 0.8174 (pm20) cc_final: 0.5944 (mm-30)
REVERT: B   57 GLU cc_start: 0.3241 (OUTLIER) cc_final: 0.2587 (pt0)
REVERT: B   61 GLU cc_start: 0.7942 (pt0) cc_final: 0.6309 (mm-30)
REVERT: D   58 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8846 (mtpt)
REVERT: F   62 GLN cc_start: 0.7362 (mt0) cc_final: 0.6924 (mp10)
REVERT: G   57 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7813 (tm-30)
REVERT: G   61 GLU cc_start: 0.8000 (pm20) cc_final: 0.7732 (pm20)
REVERT: H   61 GLU cc_start: 0.7319 (pm20) cc_final: 0.7034 (pm20)
  outliers start: 10
  outliers final: 6
  residues processed: 59
  average time/residue: 0.0763
  time to fit residues: 6.3312
Evaluate side-chains
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
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 B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   57 GLU
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:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 28 optimal weight:    8.9990
   chunk 17 optimal weight:    7.9990
   chunk 8 optimal weight:    9.9990
   chunk 36 optimal weight:    6.9990
   overall best weight:    7.3990

-------------------------------------------------------------------------------
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**
** G  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 = 0.4200 r_free = 0.4200 target = 0.117221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.103540 restraints weight = 7254.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.105944 restraints weight = 3656.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.107533 restraints weight = 2288.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.5565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   2880  Z= 0.298
  Angle     :  0.662   4.994   3900  Z= 0.390
  Chirality :  0.056   0.131    540
  Planarity :  0.003   0.013    480
  Dihedral  :  6.607  15.421    400
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.03 %
    Favored  : 88.97 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 16.45 %
    Favored  : 79.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.81 (0.38), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.14 (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
  57 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 44
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A   61 GLU cc_start: 0.8223 (pm20) cc_final: 0.5969 (mm-30)
REVERT: B   57 GLU cc_start: 0.3471 (OUTLIER) cc_final: 0.2621 (pt0)
REVERT: B   61 GLU cc_start: 0.8064 (pt0) cc_final: 0.6356 (mm-30)
REVERT: D   58 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8860 (mtpt)
REVERT: F   62 GLN cc_start: 0.7418 (mt0) cc_final: 0.6818 (mp10)
REVERT: G   57 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7963 (tm-30)
REVERT: G   61 GLU cc_start: 0.8162 (pm20) cc_final: 0.7942 (pm20)
REVERT: H   61 GLU cc_start: 0.7318 (pm20) cc_final: 0.7035 (pm20)
  outliers start: 13
  outliers final: 7
  residues processed: 55
  average time/residue: 0.0856
  time to fit residues: 6.4015
Evaluate side-chains
  51 residues out of total 310 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
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 B residue   54 THR
Chi-restraints excluded: chain B residue   57 GLU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain D residue   58 LYS
Chi-restraints excluded: chain D residue   81 THR
Chi-restraints excluded: chain F residue   81 THR
Chi-restraints excluded: chain G residue   57 GLU
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:    6.9990
   chunk 4 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    9.9990
   chunk 38 optimal weight:    9.9990
   chunk 28 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 27 optimal weight:   20.0000
   chunk 11 optimal weight:    0.5980
   chunk 24 optimal weight:   40.0000
   overall best weight:    5.0586

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

Flipped N/Q/H residues before XYZ refinement:
** G  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 = 0.4228 r_free = 0.4228 target = 0.120102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.106644 restraints weight = 6907.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.109072 restraints weight = 3430.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.110695 restraints weight = 2152.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.4106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.5577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   2880  Z= 0.209
  Angle     :  0.594   4.517   3900  Z= 0.350
  Chirality :  0.055   0.129    540
  Planarity :  0.002   0.016    480
  Dihedral  :  6.315  14.454    400
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 17.10 %
    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: -2.67 (0.39), residues: 390
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.02 (0.30), residues: 390

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

===============================================================================
Job complete
usr+sys time: 1025.04 seconds
wall clock time: 19 minutes 5.71 seconds (1145.71 seconds total)