Starting phenix.real_space_refine
on Mon Feb 10 19:27:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tgp_10500/02_2025/6tgp_10500.cif"
  }
  resolution = 4.4
  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=   1.000
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       2      5.16       5
     C     850      2.51       5
     N     230      2.21       5
     O     262      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 1344
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 672
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
    Chain: "B"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 672
          Classifications: {'peptide': 88}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
  Time building chain proxies: 1.25, per 1000 atoms: 0.93
  Number of scatterers: 1344
  At special positions: 0
  Unit cell: (54.054, 62.37, 76.23, 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       2     16.00
     O     262      8.00
     N     230      7.00
     C     850      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 184.9 milliseconds
  

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  328

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 4 sheets defined
      22.7% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 46
      removed outlier: 3.814A  pdb=" N   GLU A  40 " --> pdb=" O   ALA A  36 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   LYS A  41 " --> pdb=" O   GLY A  37 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A  45 " --> pdb=" O   LYS A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 81
      removed outlier: 3.923A  pdb=" N   ASN A  79 " --> pdb=" O   PHE A  75 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   ARG A  81 " --> pdb=" O   VAL A  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 34 through 46
      removed outlier: 3.832A  pdb=" N   GLU B  40 " --> pdb=" O   ALA B  36 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LYS B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ALA B  44 " --> pdb=" O   GLU B  40 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU B  45 " --> pdb=" O   LYS B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 81
      removed outlier: 3.920A  pdb=" N   ASN B  79 " --> pdb=" O   PHE B  75 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ARG B  81 " --> pdb=" O   VAL B  77 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18
      removed outlier: 3.589A  pdb=" N   VAL A  17 " --> pdb=" O   TYR A  14 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A  14 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18
      removed outlier: 3.589A  pdb=" N   VAL A  17 " --> pdb=" O   TYR A  14 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   TYR A  14 " --> pdb=" O   VAL A  17 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   SER A  13 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   VAL A  89 " --> pdb=" O   SER A  13 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.674A  pdb=" N   TYR B  14 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18
      removed outlier: 3.674A  pdb=" N   TYR B  14 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   SER B  13 " --> pdb=" O   ILE B  87 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   VAL B  89 " --> pdb=" O   SER B  13 " (cutoff:3.500A)

    36 hydrogen bonds defined for protein.
    81 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: 0.26

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 280
        1.33 -     1.45: 345
        1.45 -     1.58: 724
        1.58 -     1.70: 2
        1.70 -     1.83: 5
  Bond restraints: 1356
  Sorted by residual:
  bond pdb=" CD  ARG A  19 "
       pdb=" NE  ARG A  19 "
    ideal  model  delta    sigma   weight residual
    1.458  1.603 -0.145 1.40e-02 5.10e+03 1.08e+02
  bond pdb=" CG  ARG A  19 "
       pdb=" CD  ARG A  19 "
    ideal  model  delta    sigma   weight residual
    1.520  1.810 -0.290 3.00e-02 1.11e+03 9.36e+01
  bond pdb=" NE  ARG A  19 "
       pdb=" CZ  ARG A  19 "
    ideal  model  delta    sigma   weight residual
    1.326  1.391 -0.065 1.10e-02 8.26e+03 3.48e+01
  bond pdb=" C   VAL A   9 "
       pdb=" O   VAL A   9 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 9.90e-03 1.02e+04 1.30e+01
  bond pdb=" CZ  ARG A  19 "
       pdb=" NH2 ARG A  19 "
    ideal  model  delta    sigma   weight residual
    1.330  1.376 -0.046 1.30e-02 5.92e+03 1.23e+01
  ... (remaining 1351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.03: 1653
        3.03 -     6.06: 167
        6.06 -     9.09: 11
        9.09 -    12.12: 0
       12.12 -    15.15: 1
  Bond angle restraints: 1832
  Sorted by residual:
  angle pdb=" C   ALA B   5 "
        pdb=" CA  ALA B   5 "
        pdb=" CB  ALA B   5 "
      ideal   model   delta    sigma   weight residual
     110.50  125.65  -15.15 1.50e+00 4.44e-01 1.02e+02
  angle pdb=" NE  ARG A  19 "
        pdb=" CZ  ARG A  19 "
        pdb=" NH2 ARG A  19 "
      ideal   model   delta    sigma   weight residual
     119.20  125.66   -6.46 9.00e-01 1.23e+00 5.15e+01
  angle pdb=" NE  ARG A  19 "
        pdb=" CZ  ARG A  19 "
        pdb=" NH1 ARG A  19 "
      ideal   model   delta    sigma   weight residual
     121.50  115.97    5.53 1.00e+00 1.00e+00 3.06e+01
  angle pdb=" C   ASP A  32 "
        pdb=" CA  ASP A  32 "
        pdb=" CB  ASP A  32 "
      ideal   model   delta    sigma   weight residual
     111.14  117.89   -6.75 1.39e+00 5.18e-01 2.36e+01
  angle pdb=" CD  ARG A  19 "
        pdb=" NE  ARG A  19 "
        pdb=" CZ  ARG A  19 "
      ideal   model   delta    sigma   weight residual
     124.40  130.75   -6.35 1.40e+00 5.10e-01 2.06e+01
  ... (remaining 1827 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.01 -    10.57: 659
       10.57 -    21.14: 120
       21.14 -    31.71: 30
       31.71 -    42.27: 10
       42.27 -    52.84: 5
  Dihedral angle restraints: 824
    sinusoidal: 318
      harmonic: 506
  Sorted by residual:
  dihedral pdb=" C   ALA B   5 "
           pdb=" N   ALA B   5 "
           pdb=" CA  ALA B   5 "
           pdb=" CB  ALA B   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.10   14.50     0      2.50e+00 1.60e-01 3.37e+01
  dihedral pdb=" CA  ASP A  62 "
           pdb=" C   ASP A  62 "
           pdb=" N   GLY A  63 "
           pdb=" CA  GLY A  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.90   25.10     0      5.00e+00 4.00e-02 2.52e+01
  dihedral pdb=" CA  ALA B   5 "
           pdb=" C   ALA B   5 "
           pdb=" N   ASN B   6 "
           pdb=" CA  ASN B   6 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.47  -24.53     0      5.00e+00 4.00e-02 2.41e+01
  ... (remaining 821 not shown)

  Histogram of chiral volume deviations from ideal:
       0.002 -    0.097: 123
       0.097 -    0.191: 70
       0.191 -    0.286: 21
       0.286 -    0.381: 5
       0.381 -    0.475: 1
  Chirality restraints: 220
  Sorted by residual:
  chirality pdb=" CB  VAL B   9 "
            pdb=" CA  VAL B   9 "
            pdb=" CG1 VAL B   9 "
            pdb=" CG2 VAL B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CG  LEU B   8 "
            pdb=" CB  LEU B   8 "
            pdb=" CD1 LEU B   8 "
            pdb=" CD2 LEU B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.12e+00
  chirality pdb=" CB  VAL B  77 "
            pdb=" CA  VAL B  77 "
            pdb=" CG1 VAL B  77 "
            pdb=" CG2 VAL B  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.03e+00
  ... (remaining 217 not shown)

  Planarity restraints: 240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  14 "    0.052 2.00e-02 2.50e+03   3.29e-02 2.16e+01
        pdb=" CG  TYR B  14 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  14 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  14 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  14 "    0.027 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  14 "   -0.026 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  14 "    0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR B  14 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  14 "   -0.051 2.00e-02 2.50e+03   2.82e-02 1.59e+01
        pdb=" CG  TYR A  14 "    0.015 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  14 "    0.043 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  14 "    0.023 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  14 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  14 "    0.016 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  14 "   -0.021 2.00e-02 2.50e+03
        pdb=" OH  TYR A  14 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A  19 "    0.016 2.00e-02 2.50e+03   3.11e-02 9.67e+00
        pdb=" C   ARG A  19 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ARG A  19 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ARG A  20 "    0.018 2.00e-02 2.50e+03
  ... (remaining 237 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 181
        2.76 -     3.30: 1165
        3.30 -     3.83: 1865
        3.83 -     4.37: 2293
        4.37 -     4.90: 3751
  Nonbonded interactions: 9255
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  60 "
            pdb=" N   GLU A  61 "
     model   vdw
     2.228 3.120
  nonbonded pdb=" OD1 ASP B  60 "
            pdb=" N   GLU B  61 "
     model   vdw
     2.236 3.120
  nonbonded pdb=" O   PHE A  46 "
            pdb=" OD1 ASN B  28 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" N   ASP A  60 "
            pdb=" O   ASP A  60 "
     model   vdw
     2.579 2.496
  nonbonded pdb=" N   ASP B  60 "
            pdb=" O   ASP B  60 "
     model   vdw
     2.582 2.496
  ... (remaining 9250 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.860
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
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      :  0.013   0.290   1356  Z= 0.737
  Angle     :  1.899  15.148   1832  Z= 1.215
  Chirality :  0.126   0.475    220
  Planarity :  0.010   0.067    240
  Dihedral  : 12.884  52.842    496
  Min Nonbonded Distance : 2.228

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  :  4.86 %
    Favored  : 93.06 %
  Cbeta Deviations :  0.61 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.36 (0.53), residues: 172
  helix: -4.65 (0.23), residues: 36
  sheet: -1.04 (0.72), residues: 56
  loop : -1.79 (0.50), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.042   0.010   PHE B  46 
 TYR   0.059   0.020   TYR B  14 
 ARG   0.029   0.005   ARG A  19 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 42
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9449 (mmm) cc_final: 0.9185 (mmm)
REVERT: B   72 ASN cc_start: 0.9548 (m-40) cc_final: 0.9120 (t0)
REVERT: B   82 LEU cc_start: 0.9166 (tp) cc_final: 0.8930 (mt)
REVERT: B   83 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9002 (tptt)
  outliers start: 3
  outliers final: 0
  residues processed: 44
  average time/residue: 0.2701
  time to fit residues: 12.6352
Evaluate side-chains
  21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 20
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 13 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 6 optimal weight:   30.0000
   chunk 4 optimal weight:    7.9990
   chunk 8 optimal weight:   50.0000
   chunk 7 optimal weight:   30.0000
   chunk 9 optimal weight:   20.0000
   chunk 14 optimal weight:   50.0000
   chunk 15 optimal weight:   10.0000
   chunk 11 optimal weight:   20.0000
   chunk 10 optimal weight:   40.0000
   overall best weight:   15.5998

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN
A  80 GLN
B  80 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.059040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.050381 restraints weight = 12594.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.051353 restraints weight = 9346.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.051941 restraints weight = 7601.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.3733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   1356  Z= 0.253
  Angle     :  0.631   5.668   1832  Z= 0.341
  Chirality :  0.040   0.120    220
  Planarity :  0.003   0.016    240
  Dihedral  :  5.193  16.301    186
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.22 (0.58), residues: 172
  helix: -2.48 (0.61), residues: 48
  sheet: -0.44 (0.71), residues: 60
  loop : -1.44 (0.59), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.007   0.001   PHE B  75 
 TYR   0.008   0.002   TYR B  58 
 ARG   0.002   0.000   ARG B  20 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  23 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 ASP cc_start: 0.9184 (p0) cc_final: 0.8956 (p0)
REVERT: A   72 ASN cc_start: 0.9332 (m-40) cc_final: 0.9120 (m110)
REVERT: B   35 MET cc_start: 0.9374 (tpp) cc_final: 0.7794 (tpp)
REVERT: B   39 LYS cc_start: 0.9443 (ptpp) cc_final: 0.8449 (ptpp)
  outliers start: 0
  outliers final: 0
  residues processed: 23
  average time/residue: 0.2231
  time to fit residues: 5.6346
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 14 optimal weight:   50.0000
   chunk 15 optimal weight:    4.9990
   chunk 5 optimal weight:   50.0000
   chunk 8 optimal weight:   80.0000
   chunk 13 optimal weight:    9.9990
   chunk 10 optimal weight:    4.9990
   chunk 2 optimal weight:   30.0000
   chunk 0 optimal weight:   50.0000
   chunk 9 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:   50.0000
   overall best weight:    9.3992

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.057969 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.049817 restraints weight = 12680.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.050704 restraints weight = 9400.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.051316 restraints weight = 7593.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.4929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1356  Z= 0.165
  Angle     :  0.520   5.098   1832  Z= 0.276
  Chirality :  0.039   0.104    220
  Planarity :  0.003   0.021    240
  Dihedral  :  4.699  11.547    186
  Min Nonbonded Distance : 2.640

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  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: -0.96 (0.61), residues: 172
  helix: -1.51 (0.67), residues: 40
  sheet:  0.27 (0.72), residues: 60
  loop : -0.75 (0.65), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE A  75 
 TYR   0.009   0.002   TYR B  58 
 ARG   0.002   0.000   ARG B  20 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.9421 (m-40) cc_final: 0.9216 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2311
  time to fit residues: 5.6500
Evaluate side-chains
  11 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 11
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 15 optimal weight:    0.0030
   chunk 13 optimal weight:   30.0000
   chunk 9 optimal weight:   40.0000
   chunk 7 optimal weight:   50.0000
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 14 optimal weight:   30.0000
   chunk 10 optimal weight:    0.6980
   chunk 2 optimal weight:    8.9990
   chunk 0 optimal weight:   50.0000
   chunk 1 optimal weight:   40.0000
   overall best weight:    7.7398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.057357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.049385 restraints weight = 12602.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.050335 restraints weight = 8928.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.050997 restraints weight = 7059.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.5432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   1356  Z= 0.144
  Angle     :  0.495   5.621   1832  Z= 0.269
  Chirality :  0.040   0.124    220
  Planarity :  0.002   0.012    240
  Dihedral  :  4.316  10.494    186
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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: -0.35 (0.64), residues: 172
  helix: -1.10 (0.73), residues: 40
  sheet:  0.63 (0.73), residues: 60
  loop : -0.29 (0.71), residues: 72

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE B  21 
 TYR   0.007   0.001   TYR B  58 
 ARG   0.002   0.000   ARG A  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
REVERT: A   53 GLU cc_start: 0.6655 (mt-10) cc_final: 0.6417 (tm-30)
REVERT: A   72 ASN cc_start: 0.9466 (m-40) cc_final: 0.9223 (m110)
REVERT: B   35 MET cc_start: 0.9110 (mtt) cc_final: 0.8219 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.2905
  time to fit residues: 6.8694
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 9 optimal weight:   50.0000
   chunk 13 optimal weight:   50.0000
   chunk 8 optimal weight:   50.0000
   chunk 14 optimal weight:   20.0000
   chunk 12 optimal weight:   10.0000
   chunk 2 optimal weight:   50.0000
   chunk 0 optimal weight:   50.0000
   chunk 6 optimal weight:   50.0000
   chunk 5 optimal weight:   10.0000
   chunk 15 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   overall best weight:   16.0000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.055474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.047779 restraints weight = 12194.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.048682 restraints weight = 8662.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.049326 restraints weight = 6826.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.6033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.023   1356  Z= 0.228
  Angle     :  0.605   5.779   1832  Z= 0.312
  Chirality :  0.039   0.121    220
  Planarity :  0.003   0.015    240
  Dihedral  :  4.355  10.947    186
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  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: -0.08 (0.64), residues: 172
  helix: -0.57 (0.74), residues: 42
  sheet:  0.69 (0.69), residues: 60
  loop : -0.22 (0.75), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.011   0.001   PHE A  75 
 TYR   0.005   0.002   TYR B  14 
 ARG   0.002   0.000   ARG B  20 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.172 
Fit side-chains
REVERT: B   35 MET cc_start: 0.8964 (mtt) cc_final: 0.8474 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.2138
  time to fit residues: 4.3086
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 15 optimal weight:   40.0000
   chunk 4 optimal weight:   50.0000
   chunk 2 optimal weight:   30.0000
   chunk 11 optimal weight:   50.0000
   chunk 0 optimal weight:   50.0000
   chunk 3 optimal weight:    7.9990
   chunk 7 optimal weight:   20.0000
   chunk 5 optimal weight:   40.0000
   chunk 8 optimal weight:   90.0000
   chunk 13 optimal weight:   10.0000
   chunk 14 optimal weight:    8.9990
   overall best weight:   15.3996

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.056340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.048394 restraints weight = 12648.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.049224 restraints weight = 9459.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.049806 restraints weight = 7733.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.6495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   1356  Z= 0.212
  Angle     :  0.561   6.676   1832  Z= 0.290
  Chirality :  0.038   0.105    220
  Planarity :  0.003   0.016    240
  Dihedral  :  4.215  11.375    186
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  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:  0.31 (0.66), residues: 172
  helix: -0.59 (0.70), residues: 44
  sheet:  0.80 (0.69), residues: 60
  loop :  0.44 (0.86), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.006   0.001   PHE A  46 
 TYR   0.005   0.002   TYR A  58 
 ARG   0.004   0.001   ARG A  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.9121 (mtt) cc_final: 0.8647 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.2234
  time to fit residues: 4.9486
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 1 optimal weight:   40.0000
   chunk 2 optimal weight:    0.7980
   chunk 4 optimal weight:    9.9990
   chunk 12 optimal weight:   50.0000
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:   20.0000
   chunk 8 optimal weight:   50.0000
   chunk 7 optimal weight:   50.0000
   chunk 13 optimal weight:   50.0000
   chunk 5 optimal weight:   20.0000
   overall best weight:    9.3590

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.056616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.048375 restraints weight = 12942.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.049242 restraints weight = 9648.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.049863 restraints weight = 7907.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.6957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   1356  Z= 0.166
  Angle     :  0.593   7.381   1832  Z= 0.308
  Chirality :  0.041   0.129    220
  Planarity :  0.002   0.019    240
  Dihedral  :  4.075  12.194    186
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  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:  0.48 (0.68), residues: 172
  helix: -1.07 (0.70), residues: 44
  sheet:  1.06 (0.68), residues: 60
  loop :  0.86 (0.91), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.003   0.001   PHE A  75 
 TYR   0.005   0.001   TYR B  58 
 ARG   0.002   0.000   ARG B  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.8966 (mtt) cc_final: 0.8448 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.2103
  time to fit residues: 4.4685
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 3 optimal weight:    7.9990
   chunk 0 optimal weight:   50.0000
   chunk 10 optimal weight:    8.9990
   chunk 12 optimal weight:   50.0000
   chunk 14 optimal weight:   50.0000
   chunk 9 optimal weight:   20.0000
   chunk 15 optimal weight:   10.0000
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:   20.0000
   chunk 7 optimal weight:   40.0000
   chunk 2 optimal weight:   20.0000
   overall best weight:   13.3996

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.056382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.048273 restraints weight = 12873.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.049099 restraints weight = 9638.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.049722 restraints weight = 7887.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.7168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   1356  Z= 0.197
  Angle     :  0.574   7.954   1832  Z= 0.297
  Chirality :  0.038   0.105    220
  Planarity :  0.002   0.019    240
  Dihedral  :  4.145  10.314    186
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.69 %
    Favored  : 99.31 %
  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:  0.47 (0.67), residues: 172
  helix: -1.17 (0.68), residues: 44
  sheet:  1.17 (0.67), residues: 60
  loop :  0.79 (0.89), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE A  46 
 TYR   0.004   0.001   TYR B  14 
 ARG   0.003   0.000   ARG B  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.9074 (mtt) cc_final: 0.8612 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.2043
  time to fit residues: 4.3177
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 10 optimal weight:   50.0000
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 0 optimal weight:   80.0000
   chunk 9 optimal weight:   40.0000
   chunk 12 optimal weight:   40.0000
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 11 optimal weight:    8.9990
   overall best weight:    4.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.057238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.049170 restraints weight = 11839.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.050080 restraints weight = 8466.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.050721 restraints weight = 6727.342|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.7183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   1356  Z= 0.130
  Angle     :  0.513   9.165   1832  Z= 0.272
  Chirality :  0.039   0.115    220
  Planarity :  0.002   0.019    240
  Dihedral  :  3.855  10.260    186
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  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:  0.80 (0.69), residues: 172
  helix: -1.20 (0.72), residues: 44
  sheet:  1.58 (0.67), residues: 60
  loop :  1.01 (0.91), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE B  21 
 TYR   0.007   0.001   TYR B  58 
 ARG   0.001   0.000   ARG B  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  19 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8662 (m-80) cc_final: 0.8322 (m-80)
REVERT: B   35 MET cc_start: 0.9028 (mtt) cc_final: 0.8516 (mtt)
REVERT: B   55 SER cc_start: 0.9002 (m) cc_final: 0.8575 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 19
  average time/residue: 0.1899
  time to fit residues: 4.0402
Evaluate side-chains
  14 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 14
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 4 optimal weight:   30.0000
   chunk 10 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 14 optimal weight:   10.0000
   chunk 13 optimal weight:   30.0000
   chunk 7 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    7.9992

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.057403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.049270 restraints weight = 12442.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.050083 restraints weight = 9293.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.050703 restraints weight = 7596.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.7365

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   1356  Z= 0.156
  Angle     :  0.575   9.275   1832  Z= 0.299
  Chirality :  0.038   0.107    220
  Planarity :  0.002   0.020    240
  Dihedral  :  3.780   9.267    186
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  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:  0.92 (0.70), residues: 172
  helix: -1.22 (0.73), residues: 44
  sheet:  1.49 (0.62), residues: 72
  loop :  1.28 (1.02), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.004   0.001   PHE A  46 
 TYR   0.005   0.001   TYR B  58 
 ARG   0.001   0.000   ARG B  81 

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

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

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  344 Ramachandran restraints generated.
    172 Oldfield, 0 Emsley, 172 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  18 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 18
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   75 PHE cc_start: 0.8711 (m-80) cc_final: 0.8318 (m-80)
REVERT: B   35 MET cc_start: 0.9119 (mtt) cc_final: 0.8563 (mtt)
REVERT: B   55 SER cc_start: 0.9104 (m) cc_final: 0.8665 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.2030
  time to fit residues: 4.1469
Evaluate side-chains
  15 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 15
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 15 optimal weight:    0.0030
   chunk 9 optimal weight:   40.0000
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 8 optimal weight:   40.0000
   chunk 11 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 10 optimal weight:    0.0270
   chunk 3 optimal weight:   10.0000
   chunk 5 optimal weight:   50.0000
   chunk 14 optimal weight:   20.0000
   overall best weight:    2.8054

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

Flipped N/Q/H residues before XYZ refinement:
A  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.058940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.050579 restraints weight = 12459.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.051435 restraints weight = 9318.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.052049 restraints weight = 7641.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.7368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   1356  Z= 0.122
  Angle     :  0.505   9.324   1832  Z= 0.266
  Chirality :  0.038   0.112    220
  Planarity :  0.002   0.019    240
  Dihedral  :  3.624   9.421    186
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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:  1.26 (0.71), residues: 172
  helix: -1.17 (0.75), residues: 44
  sheet:  1.79 (0.64), residues: 72
  loop :  1.51 (1.04), residues: 56

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 PHE   0.005   0.001   PHE B  21 
 TYR   0.007   0.001   TYR B  58 
 ARG   0.001   0.000   ARG B  81 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 661.96 seconds
wall clock time: 12 minutes 31.49 seconds (751.49 seconds total)