Starting phenix.real_space_refine
on Wed Sep 17 02:57:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6tgp_10500/09_2025/6tgp_10500.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6tgp_10500/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6tgp_10500/09_2025/6tgp_10500.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6tgp_10500/09_2025/6tgp_10500.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6tgp_10500/09_2025/6tgp_10500.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6tgp_10500/09_2025/6tgp_10500.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 0.35, per 1000 atoms: 0.26
  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: 0.05
  Conformation dependent library (CDL) restraints added in 30.6 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.03
  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: 0.08

  Time building geometry restraints manager: 0.07 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: 0.00
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:             0.070
  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:          0.010
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     2.040
  Find NCS groups from input model:        0.010
  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:0.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    2.860
-------------------------------------------------------------------------------
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= 0.745
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.029   0.005   ARG A  19 
 TYR   0.059   0.020   TYR B  14 
 PHE   0.042   0.010   PHE B  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.01327 ( 1356)
  covalent geometry    : angle       1.89863 ( 1832)
  hydrogen bonds       : bond        0.26560 (   35)
  hydrogen bonds       : angle       9.99816 (   81)

*********************** 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  : 0.099 
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: 0.9228 (mmt)
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: 0.0846
  time to fit residues: 3.9551
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  : 0.034 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:   50.0000
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:   50.0000
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    0.5980
   chunk 11 optimal weight:    7.9990
   chunk 6 optimal weight:   30.0000
   chunk 4 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:   20.0000
   overall best weight:    5.7188

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.061745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.053088 restraints weight = 12578.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.053944 restraints weight = 9758.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.054561 restraints weight = 8116.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.055003 restraints weight = 7130.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.055271 restraints weight = 6460.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   1356  Z= 0.128
  Angle     :  0.564   6.013   1832  Z= 0.307
  Chirality :  0.041   0.129    220
  Planarity :  0.002   0.014    240
  Dihedral  :  5.051  16.455    186
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.38 (0.57), residues: 172
  helix: -2.93 (0.57), residues: 48
  sheet: -0.16 (0.75), residues: 56
  loop : -1.61 (0.55), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  20 
 TYR   0.008   0.002   TYR B  58 
 PHE   0.010   0.001   PHE B  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 1356)
  covalent geometry    : angle       0.56439 ( 1832)
  hydrogen bonds       : bond        0.03033 (   35)
  hydrogen bonds       : angle       6.25027 (   81)

*********************** 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
  24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ASP cc_start: 0.9112 (p0) cc_final: 0.8861 (p0)
REVERT: B   35 MET cc_start: 0.9374 (tpp) cc_final: 0.7709 (tpp)
REVERT: B   39 LYS cc_start: 0.9401 (ptpp) cc_final: 0.8734 (ptpp)
REVERT: B   72 ASN cc_start: 0.9186 (m-40) cc_final: 0.8843 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0542
  time to fit residues: 1.4217
Evaluate side-chains
  17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 1 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   chunk 13 optimal weight:   50.0000
   chunk 12 optimal weight:   40.0000
   chunk 5 optimal weight:   40.0000
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:   40.0000
   chunk 10 optimal weight:    0.0170
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    0.0770
   overall best weight:    4.8182

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.059902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.051324 restraints weight = 12731.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.052272 restraints weight = 9399.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.052908 restraints weight = 7539.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.053389 restraints weight = 6469.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.053705 restraints weight = 5783.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.4672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   1356  Z= 0.100
  Angle     :  0.498   4.917   1832  Z= 0.267
  Chirality :  0.039   0.107    220
  Planarity :  0.002   0.019    240
  Dihedral  :  4.507  12.878    186
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.32 (0.60), residues: 172
  helix: -2.28 (0.64), residues: 40
  sheet:  0.53 (0.76), residues: 56
  loop : -1.07 (0.60), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  20 
 TYR   0.008   0.001   TYR B  58 
 PHE   0.006   0.001   PHE A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 1356)
  covalent geometry    : angle       0.49802 ( 1832)
  hydrogen bonds       : bond        0.02546 (   35)
  hydrogen bonds       : angle       5.84102 (   81)

*********************** 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
  24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.9270 (m-40) cc_final: 0.8977 (m110)
REVERT: B   72 ASN cc_start: 0.9214 (m-40) cc_final: 0.8754 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0640
  time to fit residues: 1.6646
Evaluate side-chains
  17 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 8 optimal weight:   90.0000
   chunk 7 optimal weight:   50.0000
   chunk 10 optimal weight:    0.7980
   chunk 15 optimal weight:    0.4980
   chunk 14 optimal weight:   50.0000
   chunk 3 optimal weight:   40.0000
   chunk 13 optimal weight:    7.9990
   chunk 11 optimal weight:   10.0000
   chunk 5 optimal weight:   50.0000
   chunk 1 optimal weight:   40.0000
   chunk 12 optimal weight:   30.0000
   overall best weight:    9.8590

-------------------------------------------------------------------------------
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 = 0.3461 r_free = 0.3461 target = 0.058582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.050357 restraints weight = 13004.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.051265 restraints weight = 9585.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.051868 restraints weight = 7737.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.052307 restraints weight = 6649.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.052307 restraints weight = 5984.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.5107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1356  Z= 0.134
  Angle     :  0.540   5.970   1832  Z= 0.283
  Chirality :  0.040   0.124    220
  Planarity :  0.002   0.010    240
  Dihedral  :  4.290  11.294    186
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.75
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.32 (0.65), residues: 172
  helix: -1.05 (0.81), residues: 40
  sheet:  1.07 (0.76), residues: 56
  loop : -0.64 (0.68), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  20 
 TYR   0.005   0.001   TYR B  58 
 PHE   0.007   0.001   PHE B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 1356)
  covalent geometry    : angle       0.54008 ( 1832)
  hydrogen bonds       : bond        0.02835 (   35)
  hydrogen bonds       : angle       5.97601 (   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
  24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.029 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.9326 (m-40) cc_final: 0.9078 (m110)
REVERT: B   35 MET cc_start: 0.8229 (mtt) cc_final: 0.7876 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0504
  time to fit residues: 1.3306
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  : 0.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 11 optimal weight:   20.0000
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:   50.0000
   chunk 14 optimal weight:   20.0000
   chunk 9 optimal weight:   50.0000
   chunk 2 optimal weight:   40.0000
   chunk 7 optimal weight:    0.9980
   chunk 10 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:   40.0000
   overall best weight:   12.5994

-------------------------------------------------------------------------------
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 = 0.3403 r_free = 0.3403 target = 0.056856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.048794 restraints weight = 13284.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.049682 restraints weight = 9802.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.050297 restraints weight = 7904.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 18)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.050531 restraints weight = 6776.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.050945 restraints weight = 6186.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.5568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   1356  Z= 0.143
  Angle     :  0.532   5.068   1832  Z= 0.279
  Chirality :  0.039   0.115    220
  Planarity :  0.002   0.014    240
  Dihedral  :  4.122  11.009    186
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.66), residues: 172
  helix: -0.87 (0.81), residues: 42
  sheet:  0.83 (0.71), residues: 60
  loop : -0.20 (0.75), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.005   0.001   TYR A  58 
 PHE   0.004   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 1356)
  covalent geometry    : angle       0.53169 ( 1832)
  hydrogen bonds       : bond        0.02615 (   35)
  hydrogen bonds       : angle       5.47966 (   81)

*********************** 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
  24 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 24
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.9401 (m-40) cc_final: 0.9148 (m110)
REVERT: B   83 LYS cc_start: 0.8829 (pttp) cc_final: 0.8384 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 24
  average time/residue: 0.0704
  time to fit residues: 1.8498
Evaluate side-chains
  16 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 16
  time to evaluate  : 0.030 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 1 optimal weight:   50.0000
   chunk 3 optimal weight:    6.9990
   chunk 14 optimal weight:    7.9990
   chunk 8 optimal weight:   90.0000
   chunk 10 optimal weight:   50.0000
   chunk 0 optimal weight:   20.0000
   chunk 7 optimal weight:   50.0000
   chunk 11 optimal weight:   20.0000
   chunk 12 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   overall best weight:   12.9996

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.056220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.048257 restraints weight = 12706.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.049187 restraints weight = 9130.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.049810 restraints weight = 7303.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.050254 restraints weight = 6186.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.050417 restraints weight = 5507.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.6276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   1356  Z= 0.147
  Angle     :  0.560   4.823   1832  Z= 0.295
  Chirality :  0.039   0.106    220
  Planarity :  0.002   0.013    240
  Dihedral  :  4.038  10.346    186
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.81
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.66), residues: 172
  helix: -0.48 (0.85), residues: 42
  sheet:  1.05 (0.70), residues: 60
  loop : -0.32 (0.74), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  20 
 TYR   0.005   0.001   TYR B  58 
 PHE   0.005   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 1356)
  covalent geometry    : angle       0.55982 ( 1832)
  hydrogen bonds       : bond        0.02844 (   35)
  hydrogen bonds       : angle       6.14419 (   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
  21 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 21
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 ASN cc_start: 0.9388 (m-40) cc_final: 0.9102 (m110)
REVERT: B   35 MET cc_start: 0.8469 (mtt) cc_final: 0.8065 (mtt)
REVERT: B   83 LYS cc_start: 0.8816 (pttp) cc_final: 0.8432 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 21
  average time/residue: 0.0910
  time to fit residues: 2.1197
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  : 0.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 9 optimal weight:    9.9990
   chunk 2 optimal weight:   50.0000
   chunk 5 optimal weight:   20.0000
   chunk 0 optimal weight:   80.0000
   chunk 14 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0470
   chunk 8 optimal weight:   50.0000
   chunk 13 optimal weight:   20.0000
   chunk 11 optimal weight:   40.0000
   chunk 1 optimal weight:    8.9990
   chunk 7 optimal weight:    9.9990
   overall best weight:    7.2086

-------------------------------------------------------------------------------
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 = 0.3477 r_free = 0.3477 target = 0.058122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.050059 restraints weight = 12762.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.051070 restraints weight = 8975.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.051779 restraints weight = 7057.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.052236 restraints weight = 5915.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.052459 restraints weight = 5207.712|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.6519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   1356  Z= 0.103
  Angle     :  0.505   5.438   1832  Z= 0.267
  Chirality :  0.040   0.102    220
  Planarity :  0.002   0.010    240
  Dihedral  :  3.831   9.713    186
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.67), residues: 172
  helix: -0.44 (0.86), residues: 42
  sheet:  1.25 (0.70), residues: 60
  loop :  0.06 (0.77), residues: 70

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B  81 
 TYR   0.006   0.001   TYR B  58 
 PHE   0.003   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 1356)
  covalent geometry    : angle       0.50508 ( 1832)
  hydrogen bonds       : bond        0.02619 (   35)
  hydrogen bonds       : angle       5.69381 (   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
  22 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.055 
Fit side-chains
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.8394 (mtt) cc_final: 0.7965 (mtt)
REVERT: B   83 LYS cc_start: 0.8899 (pttp) cc_final: 0.8451 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 22
  average time/residue: 0.0872
  time to fit residues: 2.1589
Evaluate side-chains
  13 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 7 optimal weight:   50.0000
   chunk 11 optimal weight:   50.0000
   chunk 3 optimal weight:   10.0000
   chunk 6 optimal weight:   50.0000
   chunk 4 optimal weight:    8.9990
   chunk 8 optimal weight:   80.0000
   chunk 15 optimal weight:   20.0000
   chunk 9 optimal weight:   30.0000
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 5 optimal weight:   30.0000
   overall best weight:    9.7994

-------------------------------------------------------------------------------
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 = 0.3465 r_free = 0.3465 target = 0.057313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.050042 restraints weight = 11817.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.050939 restraints weight = 8409.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.051535 restraints weight = 6652.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.051974 restraints weight = 5637.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.052285 restraints weight = 4999.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7808
moved from start:          0.6836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   1356  Z= 0.124
  Angle     :  0.557   7.490   1832  Z= 0.293
  Chirality :  0.038   0.110    220
  Planarity :  0.002   0.017    240
  Dihedral  :  3.962  10.464    186
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.70), residues: 172
  helix:  0.18 (0.95), residues: 36
  sheet:  1.42 (0.70), residues: 60
  loop :  0.61 (0.82), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  81 
 TYR   0.005   0.001   TYR A  58 
 PHE   0.004   0.001   PHE A  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 1356)
  covalent geometry    : angle       0.55731 ( 1832)
  hydrogen bonds       : bond        0.02429 (   35)
  hydrogen bonds       : angle       5.57086 (   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
  20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.8349 (mtt) cc_final: 0.7853 (mtt)
REVERT: B   83 LYS cc_start: 0.8610 (pttp) cc_final: 0.8305 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0935
  time to fit residues: 2.0691
Evaluate side-chains
  12 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.058 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 1 optimal weight:   50.0000
   chunk 8 optimal weight:   90.0000
   chunk 11 optimal weight:   50.0000
   chunk 5 optimal weight:   20.0000
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:   30.0000
   chunk 12 optimal weight:    1.9990
   chunk 7 optimal weight:   30.0000
   chunk 0 optimal weight:   20.0000
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    7.3390

-------------------------------------------------------------------------------
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 = 0.3491 r_free = 0.3491 target = 0.058082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.050582 restraints weight = 12317.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.051452 restraints weight = 9045.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.052093 restraints weight = 7304.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.052445 restraints weight = 6244.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.052676 restraints weight = 5610.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.6974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   1356  Z= 0.109
  Angle     :  0.575   7.396   1832  Z= 0.299
  Chirality :  0.039   0.102    220
  Planarity :  0.002   0.018    240
  Dihedral  :  3.917  12.538    186
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 10.70
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.70), residues: 172
  helix:  0.07 (0.91), residues: 36
  sheet:  1.72 (0.70), residues: 60
  loop :  0.83 (0.84), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  81 
 TYR   0.005   0.001   TYR A  58 
 PHE   0.004   0.001   PHE A  21 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 1356)
  covalent geometry    : angle       0.57469 ( 1832)
  hydrogen bonds       : bond        0.02488 (   35)
  hydrogen bonds       : angle       5.94728 (   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
  20 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 20
  time to evaluate  : 0.070 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   35 MET cc_start: 0.8353 (mtt) cc_final: 0.7916 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 20
  average time/residue: 0.0939
  time to fit residues: 2.0795
Evaluate side-chains
  12 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 12
  time to evaluate  : 0.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 12 optimal weight:   40.0000
   chunk 6 optimal weight:   50.0000
   chunk 1 optimal weight:   40.0000
   chunk 0 optimal weight:   30.0000
   chunk 10 optimal weight:   20.0000
   chunk 15 optimal weight:    8.9990
   chunk 7 optimal weight:   20.0000
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:   30.0000
   chunk 13 optimal weight:    8.9990
   chunk 8 optimal weight:   80.0000
   overall best weight:   12.9994

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.055491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.048150 restraints weight = 12661.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.048961 restraints weight = 9283.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.049530 restraints weight = 7481.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.049954 restraints weight = 6390.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.050267 restraints weight = 5700.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.7239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   1356  Z= 0.149
  Angle     :  0.620   6.725   1832  Z= 0.324
  Chirality :  0.039   0.102    220
  Planarity :  0.002   0.018    240
  Dihedral  :  4.009  10.057    186
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.18
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.70), residues: 172
  helix: -0.16 (0.84), residues: 36
  sheet:  1.79 (0.68), residues: 60
  loop :  0.96 (0.86), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  81 
 TYR   0.004   0.001   TYR A  58 
 PHE   0.005   0.001   PHE A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 1356)
  covalent geometry    : angle       0.61968 ( 1832)
  hydrogen bonds       : bond        0.02649 (   35)
  hydrogen bonds       : angle       6.09703 (   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  : 0.055 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.7687 (mtt) cc_final: 0.7257 (mtt)
REVERT: A   71 ASP cc_start: 0.8487 (m-30) cc_final: 0.8242 (t70)
REVERT: A   72 ASN cc_start: 0.9503 (m-40) cc_final: 0.9116 (m110)
REVERT: B   35 MET cc_start: 0.8435 (mtt) cc_final: 0.7920 (mtt)
REVERT: B   83 LYS cc_start: 0.8608 (pttp) cc_final: 0.8320 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 18
  average time/residue: 0.1045
  time to fit residues: 2.0821
Evaluate side-chains
  13 residues out of total 144 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 13
  time to evaluate  : 0.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 16
   random chunks:
   chunk 7 optimal weight:   40.0000
   chunk 12 optimal weight:   50.0000
   chunk 6 optimal weight:    9.9990
   chunk 3 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 8 optimal weight:   80.0000
   chunk 9 optimal weight:   20.0000
   chunk 4 optimal weight:    0.0070
   chunk 14 optimal weight:   50.0000
   chunk 13 optimal weight:   10.0000
   chunk 2 optimal weight:    2.9990
   overall best weight:    6.2008

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.057114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.049508 restraints weight = 12499.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.050339 restraints weight = 9325.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.050899 restraints weight = 7567.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.051334 restraints weight = 6490.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.051341 restraints weight = 5793.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7874
moved from start:          0.7294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   1356  Z= 0.101
  Angle     :  0.536   6.740   1832  Z= 0.281
  Chirality :  0.039   0.111    220
  Planarity :  0.002   0.016    240
  Dihedral  :  3.779   9.017    186
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.82 (0.72), residues: 172
  helix:  0.04 (0.90), residues: 36
  sheet:  2.15 (0.69), residues: 60
  loop :  1.19 (0.88), residues: 76

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 1356)
  covalent geometry    : angle       0.53579 ( 1832)
  hydrogen bonds       : bond        0.02384 (   35)
  hydrogen bonds       : angle       5.73825 (   81)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 357.35 seconds
wall clock time: 7 minutes 4.72 seconds (424.72 seconds total)