Starting phenix.real_space_refine
on Fri Feb 14 04:45:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zxq_15014/02_2025/7zxq_15014.cif"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      90      5.16       5
     C    6558      2.51       5
     N    1656      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9930
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 1655
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 206, 1655
          Classifications: {'peptide': 206}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 198}
          Chain breaks: 1
  Restraints were copied for chains:
    C, B, E, D, F
  Time building chain proxies: 4.79, per 1000 atoms: 0.48
  Number of scatterers: 9930
  At special positions: 0
  Unit cell: (100.062, 100.062, 92.214, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      90     16.00
     O    1626      8.00
     N    1656      7.00
     C    6558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A 179 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS A 173 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  64 " - pdb=" SG  CYS A 168 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.72
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2364

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      73.8% alpha, 2.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR A   7 " --> pdb=" O   TRP A   3 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 42
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 72 through 107
      Proline residue:  A  87  - end of helix
    Processing helix  chain 'A' and resid 123 through 157
    Processing helix  chain 'A' and resid 183 through 220
    Processing helix  chain 'B' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR B   7 " --> pdb=" O   TRP B   3 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 42
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 72 through 107
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 123 through 157
    Processing helix  chain 'B' and resid 183 through 220
    Processing helix  chain 'C' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR C   7 " --> pdb=" O   TRP C   3 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 42
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 72 through 107
      Proline residue:  C  87  - end of helix
    Processing helix  chain 'C' and resid 123 through 157
    Processing helix  chain 'C' and resid 183 through 220
    Processing helix  chain 'D' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR D   7 " --> pdb=" O   TRP D   3 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 21 through 42
    Processing helix  chain 'D' and resid 59 through 69
    Processing helix  chain 'D' and resid 72 through 107
      Proline residue:  D  87  - end of helix
    Processing helix  chain 'D' and resid 123 through 157
    Processing helix  chain 'D' and resid 183 through 220
    Processing helix  chain 'E' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR E   7 " --> pdb=" O   TRP E   3 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 21 through 42
    Processing helix  chain 'E' and resid 59 through 69
    Processing helix  chain 'E' and resid 72 through 107
      Proline residue:  E  87  - end of helix
    Processing helix  chain 'E' and resid 123 through 157
    Processing helix  chain 'E' and resid 183 through 220
    Processing helix  chain 'F' and resid 2 through 11
      removed outlier: 3.687A  pdb=" N   TYR F   7 " --> pdb=" O   TRP F   3 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 21 through 42
    Processing helix  chain 'F' and resid 59 through 69
    Processing helix  chain 'F' and resid 72 through 107
      Proline residue:  F  87  - end of helix
    Processing helix  chain 'F' and resid 123 through 157
    Processing helix  chain 'F' and resid 183 through 220
    Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53
      removed outlier: 4.123A  pdb=" N   ILE A  52 " --> pdb=" O   PHE A 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE A 180 " --> pdb=" O   ILE A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE B  52 " --> pdb=" O   PHE B 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE B 180 " --> pdb=" O   ILE B  52 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE C  52 " --> pdb=" O   PHE C 180 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   PHE C 180 " --> pdb=" O   ILE C  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE D  52 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE D 180 " --> pdb=" O   ILE D  52 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE E  52 " --> pdb=" O   PHE E 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE E 180 " --> pdb=" O   ILE E  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53
      removed outlier: 4.124A  pdb=" N   ILE F  52 " --> pdb=" O   PHE F 180 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   PHE F 180 " --> pdb=" O   ILE F  52 " (cutoff:3.500A)

    756 hydrogen bonds defined for protein.
    2268 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: 2.83

  Time building geometry restraints manager: 3.06 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2994
        1.35 -     1.47: 2716
        1.47 -     1.59: 4358
        1.59 -     1.71: 0
        1.71 -     1.83: 132
  Bond restraints: 10200
  Sorted by residual:
  bond pdb=" CG  PRO E  58 "
       pdb=" CD  PRO E  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.77e+00
  bond pdb=" CG  PRO B  58 "
       pdb=" CD  PRO B  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.75e+00
  bond pdb=" CG  PRO A  58 "
       pdb=" CD  PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO D  58 "
       pdb=" CD  PRO D  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  bond pdb=" CG  PRO C  58 "
       pdb=" CD  PRO C  58 "
    ideal  model  delta    sigma   weight residual
    1.503  1.548 -0.045 3.40e-02 8.65e+02 1.74e+00
  ... (remaining 10195 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 13556
        1.88 -     3.75: 286
        3.75 -     5.63: 36
        5.63 -     7.51: 12
        7.51 -     9.38: 6
  Bond angle restraints: 13896
  Sorted by residual:
  angle pdb=" C   ASN B  14 "
        pdb=" CA  ASN B  14 "
        pdb=" CB  ASN B  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN E  14 "
        pdb=" CA  ASN E  14 "
        pdb=" CB  ASN E  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN D  14 "
        pdb=" CA  ASN D  14 "
        pdb=" CB  ASN D  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.74    6.60 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN A  14 "
        pdb=" CA  ASN A  14 "
        pdb=" CB  ASN A  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" C   ASN F  14 "
        pdb=" CA  ASN F  14 "
        pdb=" CB  ASN F  14 "
      ideal   model   delta    sigma   weight residual
     116.34  109.75    6.59 1.40e+00 5.10e-01 2.21e+01
  ... (remaining 13891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.52: 5164
       13.52 -    27.03: 533
       27.03 -    40.55: 171
       40.55 -    54.07: 33
       54.07 -    67.58: 12
  Dihedral angle restraints: 5913
    sinusoidal: 2271
      harmonic: 3642
  Sorted by residual:
  dihedral pdb=" CB  CYS A  64 "
           pdb=" SG  CYS A  64 "
           pdb=" SG  CYS A 168 "
           pdb=" CB  CYS A 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  143.32  -50.32     1      1.00e+01 1.00e-02 3.47e+01
  dihedral pdb=" CB  CYS A  53 "
           pdb=" SG  CYS A  53 "
           pdb=" SG  CYS A 179 "
           pdb=" CB  CYS A 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   42.88   50.12     1      1.00e+01 1.00e-02 3.44e+01
  dihedral pdb=" CA  CYS E 179 "
           pdb=" C   CYS E 179 "
           pdb=" N   PHE E 180 "
           pdb=" CA  PHE E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.48  -22.52     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 5910 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1051
       0.033 -    0.066: 399
       0.066 -    0.099: 127
       0.099 -    0.133: 55
       0.133 -    0.166: 6
  Chirality restraints: 1638
  Sorted by residual:
  chirality pdb=" CA  ILE F  20 "
            pdb=" N   ILE F  20 "
            pdb=" C   ILE F  20 "
            pdb=" CB  ILE F  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE C  20 "
            pdb=" N   ILE C  20 "
            pdb=" C   ILE C  20 "
            pdb=" CB  ILE C  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.86e-01
  chirality pdb=" CA  ILE A  20 "
            pdb=" N   ILE A  20 "
            pdb=" C   ILE A  20 "
            pdb=" CB  ILE A  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.16 2.00e-01 2.50e+01 6.77e-01
  ... (remaining 1635 not shown)

  Planarity restraints: 1662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  57 "   -0.050 5.00e-02 4.00e+02   7.56e-02 9.15e+00
        pdb=" N   PRO B  58 "    0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO B  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO B  58 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A  57 "    0.050 5.00e-02 4.00e+02   7.55e-02 9.12e+00
        pdb=" N   PRO A  58 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A  58 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A  58 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  57 "   -0.050 5.00e-02 4.00e+02   7.54e-02 9.10e+00
        pdb=" N   PRO C  58 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "   -0.041 5.00e-02 4.00e+02
  ... (remaining 1659 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 99
        2.60 -     3.18: 8823
        3.18 -     3.75: 16279
        3.75 -     4.33: 18800
        4.33 -     4.90: 33422
  Nonbonded interactions: 77423
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E  60 "
            pdb=" SG  CYS E 173 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" SG  CYS B  60 "
            pdb=" SG  CYS B 173 "
     model   vdw
     2.027 3.760
  nonbonded pdb=" O   ILE D  71 "
            pdb=" OH  TYR D 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE E  71 "
            pdb=" OH  TYR E 157 "
     model   vdw
     2.027 3.040
  nonbonded pdb=" O   ILE B  71 "
            pdb=" OH  TYR B 157 "
     model   vdw
     2.027 3.040
  ... (remaining 77418 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: 0.08
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             7.100
  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:          0.450
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.390
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  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:             0.010
  Load rotamer database and sin/cos tables:3.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
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      :  0.003   0.045  10200  Z= 0.208
  Angle     :  0.662   9.385  13896  Z= 0.363
  Chirality :  0.041   0.166   1638
  Planarity :  0.006   0.076   1662
  Dihedral  : 12.725  67.582   3540
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.45 (0.24), residues: 1212
  helix:  3.25 (0.16), residues: 852
  sheet: -0.01 (0.73), residues: 60
  loop : -3.28 (0.27), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C  73 
 PHE   0.007   0.001   PHE B 190 
 TYR   0.011   0.001   TYR A 151 
 ARG   0.003   0.000   ARG E 183 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 1.071 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2797
  time to fit residues: 62.1143
Evaluate side-chains
  106 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.4980
   chunk 90 optimal weight:    8.9990
   chunk 50 optimal weight:    9.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 48 optimal weight:    6.9990
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 57 optimal weight:    5.9990
   chunk 70 optimal weight:   20.0000
   chunk 108 optimal weight:    2.9990
   overall best weight:    4.2988

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.066756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.051184 restraints weight = 48585.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.052555 restraints weight = 26625.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.053258 restraints weight = 19135.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.2879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10200  Z= 0.289
  Angle     :  0.595   7.997  13896  Z= 0.304
  Chirality :  0.042   0.171   1638
  Planarity :  0.005   0.043   1662
  Dihedral  :  3.944  23.756   1344
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.18 %
    Allowed  :  7.79 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 (0.24), residues: 1212
  helix:  3.26 (0.16), residues: 864
  sheet:  0.05 (0.70), residues: 60
  loop : -2.61 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  77 
 HIS   0.003   0.001   HIS B 100 
 PHE   0.011   0.002   PHE A 180 
 TYR   0.013   0.002   TYR A 151 
 ARG   0.004   0.001   ARG A  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 1.166 
Fit side-chains
REVERT: A   93 MET cc_start: 0.8931 (mtm) cc_final: 0.8710 (mtm)
REVERT: D   93 MET cc_start: 0.8937 (mtm) cc_final: 0.8716 (mtm)
  outliers start: 13
  outliers final: 3
  residues processed: 130
  average time/residue: 0.2328
  time to fit residues: 42.1728
Evaluate side-chains
  104 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue   41 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 82 optimal weight:    5.9990
   chunk 24 optimal weight:    8.9990
   chunk 14 optimal weight:    9.9990
   chunk 73 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 55 optimal weight:    4.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.066027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.050614 restraints weight = 49114.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.052024 restraints weight = 26493.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.052952 restraints weight = 18854.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.3439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10200  Z= 0.259
  Angle     :  0.553   5.906  13896  Z= 0.288
  Chirality :  0.041   0.172   1638
  Planarity :  0.004   0.033   1662
  Dihedral  :  3.871  23.544   1344
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  :  9.96 %
    Favored  : 87.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.70 (0.24), residues: 1212
  helix:  3.22 (0.16), residues: 858
  sheet:  0.21 (0.69), residues: 60
  loop : -2.63 (0.31), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  77 
 HIS   0.003   0.001   HIS E  73 
 PHE   0.011   0.001   PHE A  68 
 TYR   0.013   0.001   TYR A 151 
 ARG   0.003   0.000   ARG B  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.131 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8871 (OUTLIER) cc_final: 0.8398 (ttm)
REVERT: E  162 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8436 (ttm)
  outliers start: 29
  outliers final: 23
  residues processed: 122
  average time/residue: 0.2489
  time to fit residues: 42.0988
Evaluate side-chains
  119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 115 optimal weight:    0.3980
   chunk 13 optimal weight:    0.9990
   chunk 82 optimal weight:    3.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 49 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   overall best weight:    2.2788

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
B  80 GLN
C  80 GLN
D  80 GLN
E  80 GLN
F  80 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.066775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.051722 restraints weight = 48068.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.053156 restraints weight = 26133.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.054016 restraints weight = 18567.645|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8438
moved from start:          0.3702

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10200  Z= 0.177
  Angle     :  0.513   7.445  13896  Z= 0.262
  Chirality :  0.038   0.163   1638
  Planarity :  0.003   0.028   1662
  Dihedral  :  3.634  20.581   1344
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 12.23 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.24), residues: 1212
  helix:  3.34 (0.16), residues: 864
  sheet:  0.28 (0.74), residues: 60
  loop : -2.63 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP D   3 
 HIS   0.002   0.001   HIS B  97 
 PHE   0.008   0.001   PHE A  68 
 TYR   0.014   0.001   TYR F 171 
 ARG   0.003   0.000   ARG A  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 1.143 
Fit side-chains
REVERT: B  162 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8339 (ttm)
REVERT: B  171 TYR cc_start: 0.8977 (t80) cc_final: 0.8775 (t80)
REVERT: E  162 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8371 (ttm)
REVERT: E  171 TYR cc_start: 0.8972 (t80) cc_final: 0.8771 (t80)
  outliers start: 34
  outliers final: 23
  residues processed: 128
  average time/residue: 0.2287
  time to fit residues: 40.8547
Evaluate side-chains
  124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 99
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 72 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 104 optimal weight:    4.9990
   chunk 76 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 36 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
** A  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 205 ASN
** D  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 205 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.065881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.050974 restraints weight = 48417.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.052354 restraints weight = 27093.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.053186 restraints weight = 19567.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10200  Z= 0.201
  Angle     :  0.509   7.272  13896  Z= 0.263
  Chirality :  0.039   0.161   1638
  Planarity :  0.003   0.025   1662
  Dihedral  :  3.540  19.237   1344
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 13.13 %
    Favored  : 83.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.92 (0.24), residues: 1212
  helix:  3.42 (0.16), residues: 864
  sheet: -0.27 (0.69), residues: 60
  loop : -2.66 (0.31), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  44 
 HIS   0.003   0.001   HIS A  73 
 PHE   0.009   0.001   PHE A  68 
 TYR   0.010   0.001   TYR A 151 
 ARG   0.002   0.000   ARG D  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 104
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  162 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8337 (ttm)
REVERT: B  171 TYR cc_start: 0.9049 (t80) cc_final: 0.8603 (t80)
REVERT: E  162 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8340 (ttm)
REVERT: E  171 TYR cc_start: 0.9041 (t80) cc_final: 0.8599 (t80)
  outliers start: 37
  outliers final: 24
  residues processed: 131
  average time/residue: 0.2159
  time to fit residues: 40.3429
Evaluate side-chains
  122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 96
  time to evaluate  : 1.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain B residue  178 ASP
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain D residue  178 ASP
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 103 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 64 optimal weight:    0.1980
   chunk 41 optimal weight:    3.9990
   chunk 19 optimal weight:    5.9990
   chunk 74 optimal weight:    3.9990
   chunk 16 optimal weight:    7.9990
   chunk 8 optimal weight:    0.9980
   chunk 87 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.066878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.051883 restraints weight = 48418.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.053342 restraints weight = 25846.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.054256 restraints weight = 18227.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10200  Z= 0.153
  Angle     :  0.489   7.939  13896  Z= 0.247
  Chirality :  0.038   0.156   1638
  Planarity :  0.003   0.023   1662
  Dihedral  :  3.394  17.095   1344
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 14.49 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.05 (0.24), residues: 1212
  helix:  3.49 (0.16), residues: 876
  sheet: -0.24 (0.67), residues: 60
  loop : -2.78 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.000   TRP E   3 
 HIS   0.002   0.001   HIS B  94 
 PHE   0.007   0.001   PHE A  68 
 TYR   0.006   0.001   TYR E 151 
 ARG   0.003   0.000   ARG B  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  162 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8323 (ttm)
REVERT: B  171 TYR cc_start: 0.9049 (t80) cc_final: 0.8614 (t80)
REVERT: D  171 TYR cc_start: 0.9041 (t80) cc_final: 0.8672 (t80)
REVERT: E  162 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8348 (ttm)
REVERT: E  171 TYR cc_start: 0.9037 (t80) cc_final: 0.8603 (t80)
REVERT: E  178 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (p0)
REVERT: F  171 TYR cc_start: 0.8983 (t80) cc_final: 0.8724 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 136
  average time/residue: 0.2040
  time to fit residues: 40.9356
Evaluate side-chains
  122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    6.9990
   chunk 111 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 45 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 75 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.065036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.050041 restraints weight = 49430.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.051328 restraints weight = 27475.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.052154 restraints weight = 19933.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8499
moved from start:          0.4283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10200  Z= 0.250
  Angle     :  0.539   7.423  13896  Z= 0.276
  Chirality :  0.039   0.164   1638
  Planarity :  0.003   0.025   1662
  Dihedral  :  3.585  20.934   1344
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.94 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  2.92 (0.24), residues: 1212
  helix:  3.36 (0.16), residues: 876
  sheet: -0.18 (0.71), residues: 60
  loop : -2.74 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  44 
 HIS   0.003   0.001   HIS D  73 
 PHE   0.011   0.001   PHE A  68 
 TYR   0.027   0.001   TYR A 171 
 ARG   0.002   0.000   ARG B 107 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  162 MET cc_start: 0.8858 (OUTLIER) cc_final: 0.8386 (ttm)
REVERT: B  171 TYR cc_start: 0.9100 (t80) cc_final: 0.8701 (t80)
REVERT: C  171 TYR cc_start: 0.9079 (t80) cc_final: 0.8684 (t80)
REVERT: D  171 TYR cc_start: 0.9132 (t80) cc_final: 0.8811 (t80)
REVERT: E  162 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8388 (ttm)
REVERT: E  171 TYR cc_start: 0.9106 (t80) cc_final: 0.8710 (t80)
REVERT: F  171 TYR cc_start: 0.9081 (t80) cc_final: 0.8711 (t80)
  outliers start: 35
  outliers final: 25
  residues processed: 128
  average time/residue: 0.1912
  time to fit residues: 36.1433
Evaluate side-chains
  121 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain B residue  162 MET
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  162 MET
Chi-restraints excluded: chain E residue  178 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Chi-restraints excluded: chain F residue   43 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0970
   chunk 85 optimal weight:    0.0070
   chunk 94 optimal weight:    0.0270
   chunk 96 optimal weight:    0.1980
   chunk 115 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.2654

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.068145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.053286 restraints weight = 49150.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.054754 restraints weight = 25699.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.055684 restraints weight = 17929.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10200  Z= 0.140
  Angle     :  0.499   8.219  13896  Z= 0.248
  Chirality :  0.037   0.149   1638
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.337  18.180   1344
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.76 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.07 (0.24), residues: 1212
  helix:  3.55 (0.15), residues: 876
  sheet:  None (None), residues: 0
  loop : -2.53 (0.29), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP E   3 
 HIS   0.002   0.000   HIS A  73 
 PHE   0.005   0.001   PHE B 149 
 TYR   0.006   0.001   TYR A 171 
 ARG   0.003   0.000   ARG B  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 97
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  171 TYR cc_start: 0.8897 (t80) cc_final: 0.8663 (t80)
REVERT: B  171 TYR cc_start: 0.9069 (t80) cc_final: 0.8688 (t80)
REVERT: C  171 TYR cc_start: 0.9013 (t80) cc_final: 0.8747 (t80)
REVERT: D  171 TYR cc_start: 0.9078 (t80) cc_final: 0.8787 (t80)
REVERT: E  171 TYR cc_start: 0.9067 (t80) cc_final: 0.8652 (t80)
REVERT: F  171 TYR cc_start: 0.9031 (t80) cc_final: 0.8793 (t80)
REVERT: F  178 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8137 (p0)
  outliers start: 26
  outliers final: 22
  residues processed: 120
  average time/residue: 0.1879
  time to fit residues: 33.5448
Evaluate side-chains
  113 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   43 VAL
Chi-restraints excluded: chain C residue  169 ASP
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   43 VAL
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  169 ASP
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   43 VAL
Chi-restraints excluded: chain F residue  169 ASP
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 116 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9990
   chunk 118 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 95 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.065055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.050099 restraints weight = 48896.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.051420 restraints weight = 27258.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.052118 restraints weight = 19720.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10200  Z= 0.255
  Angle     :  0.532   7.628  13896  Z= 0.273
  Chirality :  0.039   0.163   1638
  Planarity :  0.003   0.028   1662
  Dihedral  :  3.495  20.664   1344
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 17.39 %
    Favored  : 80.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.09 (0.24), residues: 1212
  helix:  3.49 (0.16), residues: 876
  sheet: -0.26 (0.71), residues: 60
  loop : -2.63 (0.31), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 132 
 HIS   0.003   0.001   HIS F  94 
 PHE   0.010   0.001   PHE A  68 
 TYR   0.013   0.001   TYR B 151 
 ARG   0.002   0.000   ARG B 107 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.1947 (mtt) cc_final: 0.1638 (mtp)
REVERT: A  171 TYR cc_start: 0.9033 (t80) cc_final: 0.8831 (t80)
REVERT: B  171 TYR cc_start: 0.9096 (t80) cc_final: 0.8726 (t80)
REVERT: C  171 TYR cc_start: 0.9091 (t80) cc_final: 0.8689 (t80)
REVERT: D  171 TYR cc_start: 0.9144 (t80) cc_final: 0.8853 (t80)
REVERT: E  171 TYR cc_start: 0.9113 (t80) cc_final: 0.8735 (t80)
REVERT: F  171 TYR cc_start: 0.9107 (t80) cc_final: 0.8724 (t80)
  outliers start: 25
  outliers final: 22
  residues processed: 115
  average time/residue: 0.1877
  time to fit residues: 32.5837
Evaluate side-chains
  109 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   41 GLU
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue   41 GLU
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   41 GLU
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   41 GLU
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue   41 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 2 optimal weight:    0.0670
   chunk 75 optimal weight:    0.0770
   chunk 52 optimal weight:    9.9990
   chunk 40 optimal weight:    5.9990
   chunk 106 optimal weight:    1.9990
   chunk 24 optimal weight:    6.9990
   chunk 72 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   overall best weight:    1.0080

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.066776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.052193 restraints weight = 48646.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.053570 restraints weight = 26450.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.054324 restraints weight = 18845.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.4566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10200  Z= 0.143
  Angle     :  0.499   8.845  13896  Z= 0.250
  Chirality :  0.037   0.153   1638
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.332  19.323   1344
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 6.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.21 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.22 (0.24), residues: 1212
  helix:  3.55 (0.16), residues: 882
  sheet: -0.56 (0.71), residues: 60
  loop : -2.53 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP E   3 
 HIS   0.002   0.000   HIS F  94 
 PHE   0.006   0.001   PHE E 149 
 TYR   0.004   0.001   TYR D   7 
 ARG   0.002   0.000   ARG B  75 

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

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

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2424 Ramachandran restraints generated.
    1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.2219 (mtt) cc_final: 0.1901 (mtp)
REVERT: A  171 TYR cc_start: 0.8964 (t80) cc_final: 0.8758 (t80)
REVERT: B  171 TYR cc_start: 0.9067 (t80) cc_final: 0.8716 (t80)
REVERT: C  171 TYR cc_start: 0.9078 (t80) cc_final: 0.8728 (t80)
REVERT: D  105 MET cc_start: 0.2114 (mtt) cc_final: 0.1794 (mtp)
REVERT: D  171 TYR cc_start: 0.9098 (t80) cc_final: 0.8780 (t80)
REVERT: E  171 TYR cc_start: 0.9068 (t80) cc_final: 0.8707 (t80)
REVERT: F  171 TYR cc_start: 0.9081 (t80) cc_final: 0.8797 (t80)
  outliers start: 20
  outliers final: 20
  residues processed: 110
  average time/residue: 0.1880
  time to fit residues: 31.2021
Evaluate side-chains
  110 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 90
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    3 TRP
Chi-restraints excluded: chain A residue   23 VAL
Chi-restraints excluded: chain A residue   41 GLU
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   93 MET
Chi-restraints excluded: chain B residue    3 TRP
Chi-restraints excluded: chain B residue   23 VAL
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain C residue    3 TRP
Chi-restraints excluded: chain C residue   23 VAL
Chi-restraints excluded: chain C residue  178 ASP
Chi-restraints excluded: chain D residue    3 TRP
Chi-restraints excluded: chain D residue   23 VAL
Chi-restraints excluded: chain D residue   93 MET
Chi-restraints excluded: chain E residue    3 TRP
Chi-restraints excluded: chain E residue   23 VAL
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain F residue    3 TRP
Chi-restraints excluded: chain F residue   23 VAL
Chi-restraints excluded: chain F residue  178 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 74 optimal weight:    0.9980
   chunk 51 optimal weight:    0.2980
   chunk 83 optimal weight:    3.9990
   chunk 53 optimal weight:    8.9990
   chunk 61 optimal weight:   20.0000
   chunk 76 optimal weight:    2.9990
   chunk 21 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   chunk 1 optimal weight:    5.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
** B  14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.066175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.051079 restraints weight = 49430.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.052463 restraints weight = 26579.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.053340 restraints weight = 18895.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10200  Z= 0.165
  Angle     :  0.502   8.525  13896  Z= 0.252
  Chirality :  0.038   0.156   1638
  Planarity :  0.003   0.029   1662
  Dihedral  :  3.309  19.080   1344
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.93 %
    Favored  : 79.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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:  3.21 (0.24), residues: 1212
  helix:  3.54 (0.16), residues: 882
  sheet: -0.70 (0.71), residues: 60
  loop : -2.48 (0.32), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 132 
 HIS   0.002   0.001   HIS A  73 
 PHE   0.007   0.001   PHE A  68 
 TYR   0.007   0.001   TYR B 151 
 ARG   0.002   0.000   ARG B  75 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2621.56 seconds
wall clock time: 48 minutes 44.47 seconds (2924.47 seconds total)