Starting phenix.real_space_refine
on Fri Apr  5 12:01:59 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iks_35520/04_2024/8iks_35520_updated.pdb"
  }
  resolution = 3.75
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     I      32     10.91       5
     C     608      2.51       5
     N     176      2.21       5
     O     208      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.00s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib"
  Total number of atoms: 1024
  Number of models: 1
  Model: ""
    Number of chains: 16
    Chain: "F"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "B"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "C"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "D"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "E"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "M"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "G"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "H"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "J"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "K"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "L"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "N"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "O"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "P"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
    Chain: "I"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 64
          Classifications: {'peptide': 9}
          Link IDs: {'TRANS': 8}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'PHI:plan-2': 2}
          Unresolved non-hydrogen planarities: 2
  Time building chain proxies: 0.62, per 1000 atoms: 0.61
  Number of scatterers: 1024
  At special positions: 0
  Unit cell: (122.01, 82.17, 24.9, 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)
     I      32     52.95
     O     208      8.00
     N     176      7.00
     C     608      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  - 3.50
        Amino acid           : False - 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: 0.60
  Conformation dependent library (CDL) restraints added in 83.8 milliseconds
  

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  160

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      0 helices and 0 sheets defined
      0.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...

    No hydrogen bonds defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.00

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.22 -     1.39: 487
        1.39 -     1.57: 521
        1.57 -     1.74: 0
        1.74 -     1.92: 0
        1.92 -     2.09: 32
  Bond restraints: 1040
  Sorted by residual:
  bond pdb=" CZ  PHI E 222 "
       pdb=" I   PHI E 222 "
    ideal  model  delta    sigma   weight residual
    2.106  2.003  0.103 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" CZ  PHI L 216 "
       pdb=" I   PHI L 216 "
    ideal  model  delta    sigma   weight residual
    2.106  2.003  0.103 2.00e-02 2.50e+03 2.67e+01
  bond pdb=" CZ  PHI D 222 "
       pdb=" I   PHI D 222 "
    ideal  model  delta    sigma   weight residual
    2.106  2.003  0.103 2.00e-02 2.50e+03 2.63e+01
  bond pdb=" CZ  PHI N 222 "
       pdb=" I   PHI N 222 "
    ideal  model  delta    sigma   weight residual
    2.106  2.005  0.101 2.00e-02 2.50e+03 2.53e+01
  bond pdb=" CZ  PHI G 216 "
       pdb=" I   PHI G 216 "
    ideal  model  delta    sigma   weight residual
    2.106  2.006  0.100 2.00e-02 2.50e+03 2.50e+01
  ... (remaining 1035 not shown)

  Histogram of bond angle deviations from ideal:
       71.68 -    86.11: 7
       86.11 -   100.53: 19
      100.53 -   114.96: 326
      114.96 -   129.39: 1019
      129.39 -   143.82: 5
  Bond angle restraints: 1376
  Sorted by residual:
  angle pdb=" C   PHI M 216 "
        pdb=" CA  PHI M 216 "
        pdb=" CB  PHI M 216 "
      ideal   model   delta    sigma   weight residual
     110.10   74.92   35.18 1.90e+00 2.77e-01 3.43e+02
  angle pdb=" N   ASP P 220 "
        pdb=" CA  ASP P 220 "
        pdb=" C   ASP P 220 "
      ideal   model   delta    sigma   weight residual
     108.34   82.51   25.83 1.64e+00 3.72e-01 2.48e+02
  angle pdb=" N   ASP H 220 "
        pdb=" CA  ASP H 220 "
        pdb=" C   ASP H 220 "
      ideal   model   delta    sigma   weight residual
     109.96   85.83   24.13 1.68e+00 3.54e-01 2.06e+02
  angle pdb=" N   GLY M 217 "
        pdb=" CA  GLY M 217 "
        pdb=" C   GLY M 217 "
      ideal   model   delta    sigma   weight residual
     113.30   72.51   40.79 2.90e+00 1.19e-01 1.98e+02
  angle pdb=" N   ASN P 221 "
        pdb=" CA  ASN P 221 "
        pdb=" C   ASN P 221 "
      ideal   model   delta    sigma   weight residual
     111.00   71.68   39.32 2.80e+00 1.28e-01 1.97e+02
  ... (remaining 1371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.03 -    15.47: 361
       15.47 -    30.92: 34
       30.92 -    46.36: 9
       46.36 -    61.81: 6
       61.81 -    77.25: 6
  Dihedral angle restraints: 416
    sinusoidal: 128
      harmonic: 288
  Sorted by residual:
  dihedral pdb=" C   PHI M 222 "
           pdb=" N   PHI M 222 "
           pdb=" CA  PHI M 222 "
           pdb=" CB  PHI M 222 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.95   29.35     0      2.50e+00 1.60e-01 1.38e+02
  dihedral pdb=" C   PHI M 216 "
           pdb=" N   PHI M 216 "
           pdb=" CA  PHI M 216 "
           pdb=" CB  PHI M 216 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60  -95.34  -27.26     0      2.50e+00 1.60e-01 1.19e+02
  dihedral pdb=" N   PHI M 222 "
           pdb=" C   PHI M 222 "
           pdb=" CA  PHI M 222 "
           pdb=" CB  PHI M 222 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  149.14  -26.34     0      2.50e+00 1.60e-01 1.11e+02
  ... (remaining 413 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.250: 72
       0.250 -    0.500: 2
       0.500 -    0.749: 4
       0.749 -    0.999: 1
       0.999 -    1.249: 1
  Chirality restraints: 80
  Sorted by residual:
  chirality pdb=" CA  PHI M 222 "
            pdb=" N   PHI M 222 "
            pdb=" C   PHI M 222 "
            pdb=" CB  PHI M 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.26    1.25 2.00e-01 2.50e+01 3.90e+01
  chirality pdb=" CA  ASN F 219 "
            pdb=" N   ASN F 219 "
            pdb=" C   ASN F 219 "
            pdb=" CB  ASN F 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.62    0.89 2.00e-01 2.50e+01 2.00e+01
  chirality pdb=" CA  PHI M 216 "
            pdb=" N   PHI M 216 "
            pdb=" C   PHI M 216 "
            pdb=" CB  PHI M 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.05e+01
  ... (remaining 77 not shown)

  Planarity restraints: 208
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F 217 "   -0.010 2.00e-02 2.50e+03   1.92e-02 3.70e+00
        pdb=" C   GLY F 217 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLY F 217 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   GLY F 218 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN M 221 "   -0.007 2.00e-02 2.50e+03   1.42e-02 2.01e+00
        pdb=" CG  ASN M 221 "    0.025 2.00e-02 2.50e+03
        pdb=" OD1 ASN M 221 "   -0.009 2.00e-02 2.50e+03
        pdb=" ND2 ASN M 221 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP D 220 "    0.005 2.00e-02 2.50e+03   1.01e-02 1.01e+00
        pdb=" CG  ASP D 220 "   -0.017 2.00e-02 2.50e+03
        pdb=" OD1 ASP D 220 "    0.006 2.00e-02 2.50e+03
        pdb=" OD2 ASP D 220 "    0.006 2.00e-02 2.50e+03
  ... (remaining 205 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.50: 33
        2.50 -     3.11: 856
        3.11 -     3.73: 1131
        3.73 -     4.34: 1642
        4.34 -     4.96: 2074
  Nonbonded interactions: 5736
  Sorted by model distance:
  nonbonded pdb=" O   PHI M 216 "
            pdb=" CB  PHI M 216 "
     model   vdw
     1.885 2.752
  nonbonded pdb=" N   GLY M 217 "
            pdb=" O   GLY M 217 "
     model   vdw
     1.952 2.496
  nonbonded pdb=" N   ASN P 221 "
            pdb=" O   ASN P 221 "
     model   vdw
     1.982 2.496
  nonbonded pdb=" O   ASN H 221 "
            pdb=" OD1 ASN H 221 "
     model   vdw
     2.002 3.040
  nonbonded pdb=" O   GLY M 223 "
            pdb=" N   GLY H 215 "
     model   vdw
     2.226 2.520
  ... (remaining 5731 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
  selection = chain 'K'
  selection = chain 'L'
  selection = chain 'M'
  selection = chain 'N'
  selection = chain 'O'
  selection = chain 'P'
}

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:             3.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          12.330
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.510
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4762
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      :  0.018   0.103   1040  Z= 0.906
  Angle     :  4.073  40.794   1376  Z= 1.888
  Chirality :  0.239   1.249     80
  Planarity :  0.004   0.019    208
  Dihedral  : 18.129  77.253    256
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 50.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations : 10.00 %
  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: -5.59 (0.43), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.25 (0.33), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  9 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 9
  time to evaluate  : 0.071 
Fit side-chains
REVERT: F  220 ASP cc_start: 0.7737 (m-30) cc_final: 0.6743 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0648
  time to fit residues: 0.7494
Evaluate side-chains
  1 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 1
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** M 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5387
moved from start:          0.6188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.034   0.143   1040  Z= 1.733
  Angle     :  2.964  27.151   1376  Z= 1.309
  Chirality :  0.156   0.421     80
  Planarity :  0.011   0.042    208
  Dihedral  : 25.796  88.968    160
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 108.30
  Ramachandran Plot:
    Outliers :  4.17 %
    Allowed  : 31.25 %
    Favored  : 64.58 %
  Rotamer:
    Outliers : 27.08 %
    Allowed  : 18.75 %
    Favored  : 54.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.12 %

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: -6.43 (0.32), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -4.89 (0.25), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  13 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 0
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 13
  outliers final: 9
  residues processed: 13
  average time/residue: 0.0594
  time to fit residues: 0.9794
Evaluate side-chains
  9 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 0
  time to evaluate  : 0.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  221 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
M 221 ASN
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O 219 ASN
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5361
moved from start:          0.7684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.033   0.145   1040  Z= 1.669
  Angle     :  2.958  23.488   1376  Z= 1.277
  Chirality :  0.152   0.398     80
  Planarity :  0.011   0.037    208
  Dihedral  : 25.124  86.837    160
  Min Nonbonded Distance : 1.894

Molprobity Statistics.
  All-atom Clashscore : 101.82
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 52.08 %
    Favored  : 45.83 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.34 %

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: -6.70 (0.37), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.10 (0.28), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.084 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 16
  average time/residue: 0.0604
  time to fit residues: 1.2086
Evaluate side-chains
  13 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 0
  time to evaluate  : 0.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** D 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5379
moved from start:          0.8255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.033   0.143   1040  Z= 1.661
  Angle     :  2.871  18.445   1376  Z= 1.254
  Chirality :  0.150   0.381     80
  Planarity :  0.011   0.035    208
  Dihedral  : 24.992  86.527    160
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 101.70
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 50.00 %
    Favored  : 47.92 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.12 %

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: -6.76 (0.30), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.15 (0.23), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 16
  average time/residue: 0.0590
  time to fit residues: 1.1838
Evaluate side-chains
  13 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 0
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
D 219 ASN
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5367
moved from start:          0.8536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.144   1040  Z= 1.657
  Angle     :  2.870  18.488   1376  Z= 1.252
  Chirality :  0.150   0.378     80
  Planarity :  0.011   0.034    208
  Dihedral  : 25.018  86.871    160
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 102.94
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 50.00 %
    Favored  : 47.92 %
  Rotamer:
    Outliers : 39.58 %
    Allowed  : 20.83 %
    Favored  : 39.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.12 %

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: -6.83 (0.27), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.20 (0.20), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 0
  time to evaluate  : 0.083 
Fit side-chains
  outliers start: 19
  outliers final: 15
  residues processed: 19
  average time/residue: 0.0600
  time to fit residues: 1.3994
Evaluate side-chains
  15 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 0
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5353
moved from start:          0.8663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.145   1040  Z= 1.651
  Angle     :  2.878  18.600   1376  Z= 1.256
  Chirality :  0.151   0.380     80
  Planarity :  0.011   0.040    208
  Dihedral  : 24.973  86.843    160
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 104.06
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 45.83 %
    Favored  : 52.08 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 25.00 %
    Favored  : 41.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 3.12 %

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: -6.79 (0.28), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.17 (0.21), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.083 
Fit side-chains
REVERT: K  219 ASN cc_start: 0.7998 (OUTLIER) cc_final: 0.7790 (p0)
  outliers start: 16
  outliers final: 14
  residues processed: 16
  average time/residue: 0.0527
  time to fit residues: 1.0575
Evaluate side-chains
  15 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 0
  time to evaluate  : 0.063 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain K residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    1.9990
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
F 221 ASN
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5308
moved from start:          0.8805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.146   1040  Z= 1.651
  Angle     :  2.888  18.507   1376  Z= 1.262
  Chirality :  0.150   0.372     80
  Planarity :  0.011   0.038    208
  Dihedral  : 24.852  86.855    160
  Min Nonbonded Distance : 1.943

Molprobity Statistics.
  All-atom Clashscore : 103.53
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 45.83 %
    Favored  : 52.08 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 22.92 %
    Favored  : 43.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 1.56 %

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: -6.86 (0.26), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.23 (0.20), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.083 
Fit side-chains
  outliers start: 16
  outliers final: 15
  residues processed: 16
  average time/residue: 0.0605
  time to fit residues: 1.2065
Evaluate side-chains
  15 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 0
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5304
moved from start:          0.8907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.145   1040  Z= 1.649
  Angle     :  2.928  18.566   1376  Z= 1.274
  Chirality :  0.150   0.358     80
  Planarity :  0.011   0.037    208
  Dihedral  : 24.888  86.792    160
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 101.70
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 43.75 %
    Favored  : 54.17 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.34 %

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: -6.86 (0.27), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.22 (0.20), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.082 
Fit side-chains
  outliers start: 16
  outliers final: 15
  residues processed: 16
  average time/residue: 0.0607
  time to fit residues: 1.2113
Evaluate side-chains
  15 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 0
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5288
moved from start:          0.8931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.145   1040  Z= 1.648
  Angle     :  2.930  18.507   1376  Z= 1.276
  Chirality :  0.148   0.357     80
  Planarity :  0.011   0.037    208
  Dihedral  : 24.877  86.834    160
  Min Nonbonded Distance : 1.974

Molprobity Statistics.
  All-atom Clashscore : 102.88
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 45.83 %
    Favored  : 52.08 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.34 %

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: -6.89 (0.25), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.24 (0.19), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.064 
Fit side-chains
  outliers start: 16
  outliers final: 15
  residues processed: 16
  average time/residue: 0.0520
  time to fit residues: 1.0426
Evaluate side-chains
  15 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 0
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.9980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5292
moved from start:          0.8937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.146   1040  Z= 1.646
  Angle     :  2.930  18.528   1376  Z= 1.275
  Chirality :  0.148   0.358     80
  Planarity :  0.011   0.037    208
  Dihedral  : 24.877  86.869    160
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 103.47
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 45.83 %
    Favored  : 52.08 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.34 %

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: -6.91 (0.25), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.26 (0.19), residues: 48


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

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

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  96 Ramachandran restraints generated.
    48 Oldfield, 0 Emsley, 48 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.074 
Fit side-chains
  outliers start: 16
  outliers final: 16
  residues processed: 16
  average time/residue: 0.0566
  time to fit residues: 1.1323
Evaluate side-chains
  16 residues out of total 48 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 0
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 ASN
Chi-restraints excluded: chain C residue  219 ASN
Chi-restraints excluded: chain D residue  220 ASP
Chi-restraints excluded: chain E residue  220 ASP
Chi-restraints excluded: chain M residue  220 ASP
Chi-restraints excluded: chain G residue  220 ASP
Chi-restraints excluded: chain G residue  221 ASN
Chi-restraints excluded: chain H residue  221 ASN
Chi-restraints excluded: chain J residue  220 ASP
Chi-restraints excluded: chain L residue  219 ASN
Chi-restraints excluded: chain L residue  220 ASP
Chi-restraints excluded: chain N residue  220 ASP
Chi-restraints excluded: chain O residue  221 ASN
Chi-restraints excluded: chain P residue  221 ASN
Chi-restraints excluded: chain I residue  220 ASP
Chi-restraints excluded: chain I residue  221 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 1
   random chunks:
   chunk 0 optimal weight:    0.8980
   overall best weight:   50.0000

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

Flipped N/Q/H residues before XYZ refinement:
** E 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** P 219 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 = 0.4449 r_free = 0.4449 target = 0.119498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.110776 restraints weight = 1960.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.114134 restraints weight = 792.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.115656 restraints weight = 344.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.4131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5247
moved from start:          0.8940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.032   0.145   1040  Z= 1.647
  Angle     :  2.930  18.534   1376  Z= 1.275
  Chirality :  0.148   0.359     80
  Planarity :  0.011   0.037    208
  Dihedral  : 24.874  86.913    160
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 104.06
  Ramachandran Plot:
    Outliers :  2.08 %
    Allowed  : 45.83 %
    Favored  : 52.08 %
  Rotamer:
    Outliers : 33.33 %
    Allowed  : 20.83 %
    Favored  : 45.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.34 %

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: -6.90 (0.25), residues: 48
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -5.25 (0.19), residues: 48

Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 331.25 seconds
wall clock time: 6 minutes 33.32 seconds (393.32 seconds total)