Starting phenix.real_space_refine
on Wed Nov 13 22:53:46 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8olg_16957/11_2024/8olg_16957.cif"
  }
  resolution = 4.2
  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=   1.001
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       5      5.16       5
     C     945      2.51       5
     N     270      2.21       5
     O     270      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 1490
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 298
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 298
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
  Restraints were copied for chains:
    C, B, E, D
  Time building chain proxies: 1.00, per 1000 atoms: 0.67
  Number of scatterers: 1490
  At special positions: 0
  Unit cell: (53.328, 57.368, 45.248, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S       5     16.00
     O     270      8.00
     N     270      7.00
     C     945      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 193.3 milliseconds
  

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  330

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 5 sheets defined
      0.0% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 6.132A  pdb=" N   ALA A   2 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA B   2 " --> pdb=" O   GLU C   3 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ALA C   2 " --> pdb=" O   GLU D   3 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 13
    Processing sheet with id=AA3, first strand: chain 'A' and resid 23 through 27
      removed outlier: 6.841A  pdb=" N   VAL B  24 " --> pdb=" O   ASN A  23 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   GLY A  25 " --> pdb=" O   VAL B  24 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   SER B  26 " --> pdb=" O   GLY C  25 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   ASN C  27 " --> pdb=" O   SER B  26 " (cutoff:3.500A)
      removed outlier: 8.589A  pdb=" N   VAL C  24 " --> pdb=" O   GLY D  25 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   ASN D  27 " --> pdb=" O   VAL C  24 " (cutoff:3.500A)
      removed outlier: 9.220A  pdb=" N   SER C  26 " --> pdb=" O   ASN D  27 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   PHE D  20 " --> pdb=" O   ALA E  21 " (cutoff:3.500A)
      removed outlier: 8.113A  pdb=" N   ASN E  23 " --> pdb=" O   PHE D  20 " (cutoff:3.500A)
      removed outlier: 6.265A  pdb=" N   GLN D  22 " --> pdb=" O   ASN E  23 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   GLY E  25 " --> pdb=" O   GLN D  22 " (cutoff:3.500A)
      removed outlier: 8.836A  pdb=" N   VAL D  24 " --> pdb=" O   GLY E  25 " (cutoff:3.500A)
      removed outlier: 7.416A  pdb=" N   ASN E  27 " --> pdb=" O   VAL D  24 " (cutoff:3.500A)
      removed outlier: 9.365A  pdb=" N   SER D  26 " --> pdb=" O   ASN E  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 31
    Processing sheet with id=AA5, first strand: chain 'A' and resid 34 through 35
      removed outlier: 5.916A  pdb=" N   LEU A  34 " --> pdb=" O   MET B  35 " (cutoff:3.500A)
      removed outlier: 5.853A  pdb=" N   LEU B  34 " --> pdb=" O   MET C  35 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   LEU C  34 " --> pdb=" O   MET D  35 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    11 hydrogen bonds defined for protein.
    33 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.52

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 510
        1.34 -     1.46: 350
        1.46 -     1.57: 650
        1.57 -     1.69: 0
        1.69 -     1.80: 10
  Bond restraints: 1520
  Sorted by residual:
  bond pdb=" N   ASP C   1 "
       pdb=" CA  ASP C   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.12e+00
  bond pdb=" N   ASP A   1 "
       pdb=" CA  ASP A   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.10e+00
  bond pdb=" N   ASP D   1 "
       pdb=" CA  ASP D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.04e+00
  bond pdb=" N   ASP B   1 "
       pdb=" CA  ASP B   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.02e+00
  bond pdb=" N   ASP E   1 "
       pdb=" CA  ASP E   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.00e+00
  ... (remaining 1515 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.41: 1620
        0.41 -     0.82: 287
        0.82 -     1.23: 74
        1.23 -     1.64: 39
        1.64 -     2.04: 15
  Bond angle restraints: 2035
  Sorted by residual:
  angle pdb=" N   HIS C  13 "
        pdb=" CA  HIS C  13 "
        pdb=" C   HIS C  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.94   -2.04 1.63e+00 3.76e-01 1.57e+00
  angle pdb=" N   HIS D  13 "
        pdb=" CA  HIS D  13 "
        pdb=" C   HIS D  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.92   -2.02 1.63e+00 3.76e-01 1.53e+00
  angle pdb=" N   HIS B  13 "
        pdb=" CA  HIS B  13 "
        pdb=" C   HIS B  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.91   -2.01 1.63e+00 3.76e-01 1.52e+00
  angle pdb=" N   HIS E  13 "
        pdb=" CA  HIS E  13 "
        pdb=" C   HIS E  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.91   -2.01 1.63e+00 3.76e-01 1.52e+00
  angle pdb=" N   HIS A  13 "
        pdb=" CA  HIS A  13 "
        pdb=" C   HIS A  13 "
      ideal   model   delta    sigma   weight residual
     108.90  110.90   -2.00 1.63e+00 3.76e-01 1.50e+00
  ... (remaining 2030 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.81: 725
        8.81 -    17.61: 95
       17.61 -    26.42: 20
       26.42 -    35.22: 0
       35.22 -    44.03: 10
  Dihedral angle restraints: 850
    sinusoidal: 325
      harmonic: 525
  Sorted by residual:
  dihedral pdb=" N   HIS C   6 "
           pdb=" CA  HIS C   6 "
           pdb=" CB  HIS C   6 "
           pdb=" CG  HIS C   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.14  -38.86     3      1.50e+01 4.44e-03 6.86e+00
  dihedral pdb=" N   HIS A   6 "
           pdb=" CA  HIS A   6 "
           pdb=" CB  HIS A   6 "
           pdb=" CG  HIS A   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.16  -38.84     3      1.50e+01 4.44e-03 6.86e+00
  dihedral pdb=" N   HIS E   6 "
           pdb=" CA  HIS E   6 "
           pdb=" CB  HIS E   6 "
           pdb=" CG  HIS E   6 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -141.16  -38.84     3      1.50e+01 4.44e-03 6.86e+00
  ... (remaining 847 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 89
       0.025 -    0.050: 81
       0.050 -    0.074: 12
       0.074 -    0.099: 8
       0.099 -    0.124: 20
  Chirality restraints: 210
  Sorted by residual:
  chirality pdb=" CA  ILE E  31 "
            pdb=" N   ILE E  31 "
            pdb=" C   ILE E  31 "
            pdb=" CB  ILE E  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  chirality pdb=" CA  ILE A  31 "
            pdb=" N   ILE A  31 "
            pdb=" C   ILE A  31 "
            pdb=" CB  ILE A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.79e-01
  chirality pdb=" CA  ILE D  31 "
            pdb=" N   ILE D  31 "
            pdb=" C   ILE D  31 "
            pdb=" CB  ILE D  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.62e-01
  ... (remaining 207 not shown)

  Planarity restraints: 270
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A  18 "    0.001 2.00e-02 2.50e+03   2.89e-03 8.38e-02
        pdb=" C   VAL A  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL A  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE A  19 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C  18 "    0.001 2.00e-02 2.50e+03   2.88e-03 8.31e-02
        pdb=" C   VAL C  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL C  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE C  19 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  18 "    0.001 2.00e-02 2.50e+03   2.86e-03 8.17e-02
        pdb=" C   VAL B  18 "   -0.005 2.00e-02 2.50e+03
        pdb=" O   VAL B  18 "    0.002 2.00e-02 2.50e+03
        pdb=" N   PHE B  19 "    0.002 2.00e-02 2.50e+03
  ... (remaining 267 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 342
        2.79 -     3.32: 1347
        3.32 -     3.84: 2220
        3.84 -     4.37: 2700
        4.37 -     4.90: 5547
  Nonbonded interactions: 12156
  Sorted by model distance:
  nonbonded pdb=" O   HIS D  14 "
            pdb=" O   GLN E  15 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OD1 ASP D   7 "
            pdb=" N   SER D   8 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OD1 ASP E   7 "
            pdb=" N   SER E   8 "
     model   vdw
     2.395 3.120
  nonbonded pdb=" OD1 ASP A   7 "
            pdb=" N   SER A   8 "
     model   vdw
     2.396 3.120
  nonbonded pdb=" OD1 ASP C   7 "
            pdb=" N   SER C   8 "
     model   vdw
     2.396 3.120
  ... (remaining 12151 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
}

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:             1.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     10.200
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
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      :  0.002   0.034   1520  Z= 0.157
  Angle     :  0.408   2.045   2035  Z= 0.240
  Chirality :  0.048   0.124    210
  Planarity :  0.001   0.005    270
  Dihedral  :  9.550  44.027    520
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 9.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.51 %
    Favored  : 86.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.82 (0.39), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.67 (0.30), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.001   0.000   HIS A  13 
 PHE   0.004   0.001   PHE B   4 
 TYR   0.003   0.001   TYR C  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A    7 ASP cc_start: 0.6200 (t0) cc_final: 0.5912 (p0)
REVERT: A   10 TYR cc_start: 0.7200 (t80) cc_final: 0.6833 (p90)
REVERT: A   20 PHE cc_start: 0.7185 (m-80) cc_final: 0.6908 (m-80)
REVERT: B   20 PHE cc_start: 0.6862 (m-80) cc_final: 0.6650 (m-80)
REVERT: C   10 TYR cc_start: 0.8033 (t80) cc_final: 0.7808 (t80)
REVERT: C   23 ASN cc_start: 0.8467 (m-40) cc_final: 0.8188 (p0)
REVERT: C   34 LEU cc_start: 0.7478 (tt) cc_final: 0.7191 (tt)
REVERT: D    7 ASP cc_start: 0.5072 (t0) cc_final: 0.4091 (m-30)
REVERT: D   23 ASN cc_start: 0.8371 (m-40) cc_final: 0.8017 (p0)
REVERT: E   13 HIS cc_start: 0.7125 (t-90) cc_final: 0.6919 (p90)
REVERT: E   23 ASN cc_start: 0.7074 (m-40) cc_final: 0.5713 (p0)
REVERT: E   35 MET cc_start: 0.4910 (ttp) cc_final: 0.4470 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.0754
  time to fit residues: 7.3023
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:   20.0000
   chunk 11 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 3 optimal weight:    7.9990
   chunk 7 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:    6.9990
   chunk 13 optimal weight:    7.9990
   chunk 9 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6563
moved from start:          0.4168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   1520  Z= 0.278
  Angle     :  0.724   4.807   2035  Z= 0.397
  Chirality :  0.051   0.159    210
  Planarity :  0.003   0.014    270
  Dihedral  :  5.643  17.974    200
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.68 %
    Favored  : 84.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.29 (0.46), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.27 (0.35), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS C  14 
 PHE   0.013   0.002   PHE A   4 
 TYR   0.012   0.003   TYR D  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.178 
Fit side-chains
REVERT: A    7 ASP cc_start: 0.5509 (t0) cc_final: 0.4811 (m-30)
REVERT: B    7 ASP cc_start: 0.6167 (t0) cc_final: 0.5731 (t0)
REVERT: D    7 ASP cc_start: 0.5543 (t0) cc_final: 0.4761 (m-30)
REVERT: D   27 ASN cc_start: 0.8393 (t0) cc_final: 0.7862 (t0)
REVERT: D   34 LEU cc_start: 0.8186 (tp) cc_final: 0.7811 (tp)
REVERT: E   10 TYR cc_start: 0.7529 (t80) cc_final: 0.7327 (t80)
REVERT: E   12 VAL cc_start: 0.8884 (t) cc_final: 0.8557 (m)
REVERT: E   13 HIS cc_start: 0.6602 (t-90) cc_final: 0.6320 (p90)
REVERT: E   35 MET cc_start: 0.5843 (ttp) cc_final: 0.4875 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 65
  average time/residue: 0.0673
  time to fit residues: 5.4323
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:   10.0000
   chunk 6 optimal weight:   20.0000
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 12 optimal weight:   10.0000
   chunk 3 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6537
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   1520  Z= 0.283
  Angle     :  0.691   5.199   2035  Z= 0.377
  Chirality :  0.051   0.163    210
  Planarity :  0.003   0.015    270
  Dihedral  :  5.456  18.535    200
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.14 %
    Favored  : 84.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.46 (0.44), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.40 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS C  14 
 PHE   0.014   0.002   PHE B   4 
 TYR   0.015   0.004   TYR D  10 
 ARG   0.001   0.000   ARG C   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.184 
Fit side-chains
REVERT: B    7 ASP cc_start: 0.5990 (t0) cc_final: 0.5768 (t0)
REVERT: C   22 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8816 (mm-40)
REVERT: D    7 ASP cc_start: 0.5879 (t0) cc_final: 0.5127 (m-30)
REVERT: D   27 ASN cc_start: 0.8280 (t0) cc_final: 0.7855 (t0)
REVERT: E   10 TYR cc_start: 0.7884 (t80) cc_final: 0.7524 (t80)
REVERT: E   13 HIS cc_start: 0.6700 (t-90) cc_final: 0.6284 (p90)
REVERT: E   35 MET cc_start: 0.6007 (ttp) cc_final: 0.5242 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0968
  time to fit residues: 6.7510
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 12 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 7 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 4 optimal weight:    6.9990
   chunk 2 optimal weight:    0.5980
   chunk 8 optimal weight:    5.9990
   chunk 14 optimal weight:    9.9990
   overall best weight:    4.5188

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

Flipped N/Q/H residues before XYZ refinement:
** D  27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6562
moved from start:          0.5735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   1520  Z= 0.276
  Angle     :  0.707   6.942   2035  Z= 0.375
  Chirality :  0.049   0.143    210
  Planarity :  0.003   0.012    270
  Dihedral  :  5.360  17.546    200
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.76 %
    Favored  : 83.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.50 (0.43), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.42 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.007   0.002   HIS D  13 
 PHE   0.015   0.002   PHE A   4 
 TYR   0.012   0.002   TYR D  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.178 
Fit side-chains
REVERT: B    7 ASP cc_start: 0.6009 (t0) cc_final: 0.5715 (t0)
REVERT: E   13 HIS cc_start: 0.6757 (t-90) cc_final: 0.6255 (p-80)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0621
  time to fit residues: 4.4115
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 12 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   chunk 13 optimal weight:   10.0000
   chunk 8 optimal weight:    5.9990
   chunk 10 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 9 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6554
moved from start:          0.6327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   1520  Z= 0.336
  Angle     :  0.778   8.069   2035  Z= 0.415
  Chirality :  0.050   0.157    210
  Planarity :  0.003   0.015    270
  Dihedral  :  5.922  19.205    200
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 17.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.60 (0.41), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.50 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.003   HIS D  13 
 PHE   0.015   0.002   PHE A   4 
 TYR   0.023   0.004   TYR C  10 
 ARG   0.001   0.000   ARG E   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.158 
Fit side-chains
REVERT: D   23 ASN cc_start: 0.8537 (m-40) cc_final: 0.6800 (p0)
REVERT: E   13 HIS cc_start: 0.6713 (t-90) cc_final: 0.6295 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0789
  time to fit residues: 5.3283
Evaluate side-chains
  51 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   chunk 1 optimal weight:    6.9990
   chunk 11 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 12 optimal weight:    6.9990
   chunk 5 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    4.7388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6538
moved from start:          0.6590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   1520  Z= 0.307
  Angle     :  0.748   6.452   2035  Z= 0.397
  Chirality :  0.050   0.145    210
  Planarity :  0.003   0.012    270
  Dihedral  :  5.798  17.803    200
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 17.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 16.76 %
    Favored  : 83.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.55 (0.41), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.46 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.008   0.002   HIS D  13 
 PHE   0.014   0.002   PHE A   4 
 TYR   0.022   0.004   TYR C  10 
 ARG   0.001   0.000   ARG C   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.145 
Fit side-chains
REVERT: C   22 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8677 (mm-40)
REVERT: C   27 ASN cc_start: 0.8483 (t0) cc_final: 0.8256 (t0)
REVERT: C   31 ILE cc_start: 0.9352 (mm) cc_final: 0.9034 (mm)
REVERT: D   23 ASN cc_start: 0.8375 (m-40) cc_final: 0.6711 (p0)
REVERT: E    7 ASP cc_start: 0.6142 (t0) cc_final: 0.5861 (t70)
REVERT: E   13 HIS cc_start: 0.6514 (t-90) cc_final: 0.6193 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0588
  time to fit residues: 4.1600
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 4 optimal weight:    8.9990
   chunk 12 optimal weight:    8.9990
   chunk 13 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 6 optimal weight:   20.0000
   chunk 9 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 1 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   overall best weight:    6.5990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6571
moved from start:          0.6874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   1520  Z= 0.386
  Angle     :  0.849   8.206   2035  Z= 0.446
  Chirality :  0.054   0.162    210
  Planarity :  0.004   0.015    270
  Dihedral  :  6.365  20.726    200
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 17.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.59 (0.40), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS D  13 
 PHE   0.017   0.003   PHE D   4 
 TYR   0.025   0.005   TYR C  10 
 ARG   0.001   0.000   ARG D   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.177 
Fit side-chains
REVERT: E   10 TYR cc_start: 0.7357 (t80) cc_final: 0.7058 (t80)
REVERT: E   13 HIS cc_start: 0.6640 (t-90) cc_final: 0.6258 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0634
  time to fit residues: 4.3696
Evaluate side-chains
  51 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 10 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 12 optimal weight:    5.9990
   chunk 2 optimal weight:    9.9990
   chunk 0 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 9 optimal weight:    7.9990
   overall best weight:    6.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6535
moved from start:          0.7267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   1520  Z= 0.379
  Angle     :  0.865   7.435   2035  Z= 0.461
  Chirality :  0.055   0.164    210
  Planarity :  0.004   0.015    270
  Dihedral  :  6.545  21.306    200
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 19.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.58 (0.40), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.49 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.011   0.003   HIS D  13 
 PHE   0.016   0.002   PHE D   4 
 TYR   0.034   0.005   TYR C  10 
 ARG   0.001   0.000   ARG B   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.179 
Fit side-chains
REVERT: B   10 TYR cc_start: 0.7209 (t80) cc_final: 0.6454 (t80)
REVERT: E   10 TYR cc_start: 0.7728 (t80) cc_final: 0.7324 (t80)
REVERT: E   13 HIS cc_start: 0.6567 (t-90) cc_final: 0.6166 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0614
  time to fit residues: 4.3250
Evaluate side-chains
  53 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 8 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0170
   chunk 0 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 3 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 6 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6820

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6469
moved from start:          0.7379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   1520  Z= 0.158
  Angle     :  0.678   7.251   2035  Z= 0.339
  Chirality :  0.048   0.164    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.625  17.114    200
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 15.14 %
    Favored  : 84.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.27 (0.44), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.25 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS A  14 
 PHE   0.005   0.001   PHE B  19 
 TYR   0.009   0.001   TYR D  10 
 ARG   0.000   0.000   ARG C   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.6684 (mm-40) cc_final: 0.6285 (mm-40)
REVERT: B    7 ASP cc_start: 0.5925 (t0) cc_final: 0.4648 (m-30)
REVERT: B   10 TYR cc_start: 0.7460 (t80) cc_final: 0.6611 (t80)
REVERT: C   27 ASN cc_start: 0.8767 (t0) cc_final: 0.8502 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0629
  time to fit residues: 4.7239
Evaluate side-chains
  55 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    9.9990
   chunk 14 optimal weight:    0.0170
   chunk 2 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:   20.0000
   chunk 13 optimal weight:    7.9990
   chunk 3 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   overall best weight:    3.8022

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6483
moved from start:          0.7569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   1520  Z= 0.250
  Angle     :  0.727   6.753   2035  Z= 0.378
  Chirality :  0.051   0.175    210
  Planarity :  0.002   0.011    270
  Dihedral  :  5.936  17.616    200
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 16.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.30 %
    Favored  : 82.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.42 (0.44), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.36 (0.33), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.002   HIS D  13 
 PHE   0.011   0.002   PHE D   4 
 TYR   0.007   0.002   TYR E  10 
 ARG   0.001   0.000   ARG D   5 

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

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

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  370 Ramachandran restraints generated.
    185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   22 GLN cc_start: 0.7046 (mm-40) cc_final: 0.6475 (mm-40)
REVERT: E   10 TYR cc_start: 0.7761 (t80) cc_final: 0.7326 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0652
  time to fit residues: 4.4717
Evaluate side-chains
  54 residues out of total 150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 15
   random chunks:
   chunk 2 optimal weight:    6.9990
   chunk 7 optimal weight:    9.9990
   chunk 6 optimal weight:   20.0000
   chunk 8 optimal weight:    2.9990
   chunk 4 optimal weight:    7.9990
   chunk 5 optimal weight:    6.9990
   chunk 12 optimal weight:   20.0000
   chunk 3 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** C  27 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 = 0.4371 r_free = 0.4371 target = 0.154560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.134608 restraints weight = 2881.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.138166 restraints weight = 1408.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.140484 restraints weight = 883.087|
|-----------------------------------------------------------------------------|
r_work (final): 0.4198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6842
moved from start:          0.7754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   1520  Z= 0.374
  Angle     :  0.853   6.487   2035  Z= 0.447
  Chirality :  0.054   0.161    210
  Planarity :  0.003   0.012    270
  Dihedral  :  6.648  22.179    200
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 19.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 17.84 %
    Favored  : 82.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.69 (0.41), residues: 185
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.57 (0.31), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.009   0.003   HIS D  13 
 PHE   0.017   0.002   PHE D   4 
 TYR   0.011   0.003   TYR E  10 
 ARG   0.002   0.000   ARG B   5 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 852.37 seconds
wall clock time: 16 minutes 1.10 seconds (961.10 seconds total)