Starting phenix.real_space_refine
on Tue Aug  4 21:28:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lje_63146/08_2026/9lje_63146.map"
  }
  resolution = 2.75
  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=   0.063
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: 6
    Type Number    sf(0)   Gaussians
     P     158      5.49       5
     Mg      1      5.21       5
     S      13      5.16       5
     C    3714      2.51       5
     N    1204      2.21       5
     O    1720      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6810
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 417, 3441
          Classifications: {'peptide': 417}
          Link IDs: {'PTRANS': 13, 'TRANS': 403}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 153, 3264
          Classifications: {'RNA': 153}
          Modifications used: {'p5*END': 1, 'rna2p_pur': 19, 'rna2p_pyr': 14, 'rna3p_pur': 61, 'rna3p_pyr': 59}
          Link IDs: {'rna2p': 32, 'rna3p': 120}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 104
          Classifications: {'DNA': 5}
          Link IDs: {'rna3p': 4}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.51, per 1000 atoms: 0.22
  Number of scatterers: 6810
  At special positions: 0
  Unit cell: (68.641, 141.417, 114.126, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      13     16.00
     P     158     15.00
     Mg      1     11.99
     O    1720      8.00
     N    1204      7.00
     C    3714      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: 0.36
  Conformation dependent library (CDL) restraints added in 202.3 milliseconds
  

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  798

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 3 sheets defined
      54.2% alpha, 12.2% beta
      46 base pairs and 65 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 32
      removed outlier: 3.736A  pdb=" N   SER A  32 " --> pdb=" O   LYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 38
      removed outlier: 3.714A  pdb=" N   ILE A  36 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 100
    Processing helix  chain 'A' and resid 116 through 132
    Processing helix  chain 'A' and resid 149 through 162
    Processing helix  chain 'A' and resid 167 through 179
    Processing helix  chain 'A' and resid 185 through 193
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 237 through 246
      removed outlier: 3.518A  pdb=" N   MET A 246 " --> pdb=" O   SER A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 259
    Processing helix  chain 'A' and resid 276 through 280
      removed outlier: 3.685A  pdb=" N   ASN A 280 " --> pdb=" O   THR A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 292
      removed outlier: 3.745A  pdb=" N   LYS A 292 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 295
      No H-bonds generated for 'chain 'A' and resid 293 through 295'
    Processing helix  chain 'A' and resid 336 through 368
      removed outlier: 3.667A  pdb=" N   LEU A 340 " --> pdb=" O   ARG A 336 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN A 367 " --> pdb=" O   ARG A 363 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   LYS A 368 " --> pdb=" O   ILE A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 385
    Processing helix  chain 'A' and resid 391 through 404
      removed outlier: 3.677A  pdb=" N   TYR A 395 " --> pdb=" O   ASN A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 413
      removed outlier: 3.969A  pdb=" N   LYS A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 425
    Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 74
      removed outlier: 5.982A  pdb=" N   PHE A  44 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 267
    Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323

    184 hydrogen bonds defined for protein.
    528 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      112 hydrogen bonds
      196 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      65 stacking parallelities
  Total time for adding SS restraints: 1.08

  Time building geometry restraints manager: 0.49 seconds

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

  Histogram of bond lengths:
        1.17 -     1.29: 707
        1.29 -     1.42: 2827
        1.42 -     1.55: 3408
        1.55 -     1.68: 312
        1.68 -     1.80: 22
  Bond restraints: 7276
  Sorted by residual:
  bond pdb=" C2    C B 215 "
       pdb=" O2    C B 215 "
    ideal  model  delta    sigma   weight residual
    1.240  1.167  0.073 9.00e-03 1.23e+04 6.63e+01
  bond pdb=" C2    C B 216 "
       pdb=" O2    C B 216 "
    ideal  model  delta    sigma   weight residual
    1.240  1.200  0.040 9.00e-03 1.23e+04 2.00e+01
  bond pdb=" N3    C B 215 "
       pdb=" C4    C B 215 "
    ideal  model  delta    sigma   weight residual
    1.335  1.306  0.029 7.00e-03 2.04e+04 1.72e+01
  bond pdb=" N9    A B 208 "
       pdb=" C4    A B 208 "
    ideal  model  delta    sigma   weight residual
    1.374  1.352  0.022 6.00e-03 2.78e+04 1.34e+01
  bond pdb=" C2    C B 215 "
       pdb=" N3    C B 215 "
    ideal  model  delta    sigma   weight residual
    1.353  1.328  0.025 8.00e-03 1.56e+04 1.01e+01
  ... (remaining 7271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 10219
        2.41 -     4.82: 319
        4.82 -     7.22: 23
        7.22 -     9.63: 2
        9.63 -    12.04: 4
  Bond angle restraints: 10567
  Sorted by residual:
  angle pdb=" O2    C B 215 "
        pdb=" C2    C B 215 "
        pdb=" N3    C B 215 "
      ideal   model   delta    sigma   weight residual
     121.90  112.25    9.65 7.00e-01 2.04e+00 1.90e+02
  angle pdb=" C2    C B 215 "
        pdb=" N1    C B 215 "
        pdb=" C6    C B 215 "
      ideal   model   delta    sigma   weight residual
     120.30  115.05    5.25 4.00e-01 6.25e+00 1.72e+02
  angle pdb=" N4    C B 215 "
        pdb=" C4    C B 215 "
        pdb=" C5    C B 215 "
      ideal   model   delta    sigma   weight residual
     120.20  127.37   -7.17 7.00e-01 2.04e+00 1.05e+02
  angle pdb=" C1'   U B 205 "
        pdb=" N1    U B 205 "
        pdb=" C2    U B 205 "
      ideal   model   delta    sigma   weight residual
     117.70  129.74  -12.04 1.20e+00 6.94e-01 1.01e+02
  angle pdb=" N1    C B 218 "
        pdb=" C2    C B 218 "
        pdb=" O2    C B 218 "
      ideal   model   delta    sigma   weight residual
     118.90  123.69   -4.79 6.00e-01 2.78e+00 6.38e+01
  ... (remaining 10562 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.80: 4066
       35.80 -    71.60: 472
       71.60 -   107.40: 35
      107.40 -   143.21: 3
      143.21 -   179.01: 7
  Dihedral angle restraints: 4583
    sinusoidal: 3345
      harmonic: 1238
  Sorted by residual:
  dihedral pdb=" O4'   C B 216 "
           pdb=" C1'   C B 216 "
           pdb=" N1    C B 216 "
           pdb=" C2    C B 216 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   25.70  174.30     1      1.50e+01 4.44e-03 8.51e+01
  dihedral pdb=" O4'   U B 205 "
           pdb=" C1'   U B 205 "
           pdb=" N1    U B 205 "
           pdb=" C2    U B 205 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    9.06 -169.06     1      1.50e+01 4.44e-03 8.46e+01
  dihedral pdb=" O4'   C B 215 "
           pdb=" C1'   C B 215 "
           pdb=" N1    C B 215 "
           pdb=" C2    C B 215 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   38.45  161.55     1      1.50e+01 4.44e-03 8.31e+01
  ... (remaining 4580 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 935
       0.050 -    0.101: 187
       0.101 -    0.151: 152
       0.151 -    0.202: 10
       0.202 -    0.252: 3
  Chirality restraints: 1287
  Sorted by residual:
  chirality pdb=" C3'   G B 277 "
            pdb=" C4'   G B 277 "
            pdb=" O3'   G B 277 "
            pdb=" C2'   G B 277 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.49   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CG  LEU A 393 "
            pdb=" CB  LEU A 393 "
            pdb=" CD1 LEU A 393 "
            pdb=" CD2 LEU A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" C3'   A B 198 "
            pdb=" C4'   A B 198 "
            pdb=" O3'   A B 198 "
            pdb=" C2'   A B 198 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.52   -0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1284 not shown)

  Planarity restraints: 755
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 216 "    0.005 2.00e-02 2.50e+03   5.76e-02 7.46e+01
        pdb=" N1    C B 216 "    0.013 2.00e-02 2.50e+03
        pdb=" C2    C B 216 "   -0.142 2.00e-02 2.50e+03
        pdb=" O2    C B 216 "    0.081 2.00e-02 2.50e+03
        pdb=" N3    C B 216 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    C B 216 "   -0.037 2.00e-02 2.50e+03
        pdb=" N4    C B 216 "    0.029 2.00e-02 2.50e+03
        pdb=" C5    C B 216 "    0.013 2.00e-02 2.50e+03
        pdb=" C6    C B 216 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C B 215 "    0.001 2.00e-02 2.50e+03   5.69e-02 7.29e+01
        pdb=" N1    C B 215 "    0.015 2.00e-02 2.50e+03
        pdb=" C2    C B 215 "   -0.144 2.00e-02 2.50e+03
        pdb=" O2    C B 215 "    0.079 2.00e-02 2.50e+03
        pdb=" N3    C B 215 "    0.021 2.00e-02 2.50e+03
        pdb=" C4    C B 215 "   -0.020 2.00e-02 2.50e+03
        pdb=" N4    C B 215 "    0.020 2.00e-02 2.50e+03
        pdb=" C5    C B 215 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C B 215 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 206 "   -0.004 2.00e-02 2.50e+03   2.82e-02 2.39e+01
        pdb=" N9    G B 206 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8    G B 206 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    G B 206 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B 206 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    G B 206 "    0.052 2.00e-02 2.50e+03
        pdb=" O6    G B 206 "   -0.036 2.00e-02 2.50e+03
        pdb=" N1    G B 206 "   -0.015 2.00e-02 2.50e+03
        pdb=" C2    G B 206 "    0.057 2.00e-02 2.50e+03
        pdb=" N2    G B 206 "   -0.043 2.00e-02 2.50e+03
        pdb=" N3    G B 206 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    G B 206 "    0.001 2.00e-02 2.50e+03
  ... (remaining 752 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 333
        2.69 -     3.24: 5853
        3.24 -     3.79: 12317
        3.79 -     4.35: 15800
        4.35 -     4.90: 22820
  Nonbonded interactions: 57123
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 140 "
            pdb="MG    MG A 501 "
     model   vdw
     2.133 2.170
  nonbonded pdb=" OH  TYR A 245 "
            pdb=" O   LEU A 294 "
     model   vdw
     2.171 3.040
  nonbonded pdb=" OG  SER A 235 "
            pdb=" OG  SER A 238 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   TYR A 174 "
            pdb=" OG1 THR A 178 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" NH2 ARG A 217 "
            pdb=" O6    G B  22 "
     model   vdw
     2.228 3.120
  ... (remaining 57118 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             2.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.060
  Find NCS groups from input model:        0.020
  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:5.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7524
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      :  0.004   0.073   7276  Z= 0.333
  Angle     :  0.866  12.040  10567  Z= 0.770
  Chirality :  0.059   0.252   1287
  Planarity :  0.006   0.058    755
  Dihedral  : 24.025 179.007   3785
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 32.71 %
    Favored  : 65.15 %
  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 are not related in a simple way.
  whole:  0.52 (0.41), residues: 413
  helix:  0.91 (0.35), residues: 206
  sheet: -0.31 (0.65), residues: 50
  loop : -0.00 (0.53), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 410 
 TYR   0.028   0.002   TYR A 201 
 PHE   0.014   0.002   PHE A 328 
 TRP   0.011   0.002   TRP A 157 
 HIS   0.003   0.001   HIS A  93 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.33 ( 7276)
  covalent geometry    : angle       0.86631 /  0.77 (10567)
  hydrogen bonds       : bond        0.12692 /  7.74 (  296)
  hydrogen bonds       : angle       6.12474 /  4.11 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7148 (m-30) cc_final: 0.6623 (t0)
REVERT: A    9 PHE cc_start: 0.6939 (t80) cc_final: 0.6723 (t80)
REVERT: A   19 GLU cc_start: 0.6104 (tt0) cc_final: 0.4919 (tt0)
REVERT: A   24 LYS cc_start: 0.7370 (mtpm) cc_final: 0.6635 (mmtm)
REVERT: A   28 LYS cc_start: 0.7402 (mtmt) cc_final: 0.7099 (mmtm)
REVERT: A   35 LYS cc_start: 0.7425 (mmtp) cc_final: 0.7176 (mttt)
REVERT: A   97 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7597 (mt)
REVERT: A  105 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7279 (mp0)
REVERT: A  107 ILE cc_start: 0.8124 (pt) cc_final: 0.7865 (pp)
REVERT: A  159 LYS cc_start: 0.7607 (ttpt) cc_final: 0.6882 (mmtm)
REVERT: A  174 TYR cc_start: 0.7401 (t80) cc_final: 0.7052 (t80)
REVERT: A  311 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7664 (mmtt)
REVERT: A  328 PHE cc_start: 0.7667 (t80) cc_final: 0.7306 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 102
  average time/residue: 0.5226
  time to fit residues: 55.6483
Evaluate side-chains
  73 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 69
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue   97 LEU
Chi-restraints excluded: chain A residue  108 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 54 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    1.2982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 ASN
A 202 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4429 r_free = 0.4429 target = 0.220333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.166596 restraints weight = 6396.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3926 rms_B_bonded: 1.07
r_work: 0.3707 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3570 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.1648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7276  Z= 0.209
  Angle     :  0.640   8.841  10567  Z= 0.360
  Chirality :  0.048   0.514   1287
  Planarity :  0.006   0.050    755
  Dihedral  : 24.515 178.606   2904
  Min Nonbonded Distance : 2.083

Molprobity Statistics.
  All-atom Clashscore : 10.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 30.03 %
    Favored  : 64.34 %
  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 are not related in a simple way.
  whole:  0.56 (0.41), residues: 413
  helix:  1.00 (0.35), residues: 208
  sheet: -0.21 (0.66), residues: 50
  loop : -0.14 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 254 
 TYR   0.016   0.002   TYR A  74 
 PHE   0.020   0.002   PHE A 328 
 TRP   0.014   0.002   TRP A 157 
 HIS   0.007   0.002   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00437 /  0.21 ( 7276)
  covalent geometry    : angle       0.64037 /  0.36 (10567)
  hydrogen bonds       : bond        0.07593 /  4.39 (  296)
  hydrogen bonds       : angle       4.82547 /  3.32 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 73
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7302 (m-30) cc_final: 0.6540 (t0)
REVERT: A   19 GLU cc_start: 0.6020 (tt0) cc_final: 0.5697 (tt0)
REVERT: A   24 LYS cc_start: 0.7611 (mtpm) cc_final: 0.6558 (mmtm)
REVERT: A   28 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.6836 (mptt)
REVERT: A   35 LYS cc_start: 0.7729 (mmtp) cc_final: 0.7233 (mttt)
REVERT: A  105 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7233 (mp0)
REVERT: A  123 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7521 (ttp-110)
REVERT: A  142 SER cc_start: 0.7377 (OUTLIER) cc_final: 0.6890 (t)
REVERT: A  159 LYS cc_start: 0.7708 (ttpt) cc_final: 0.7217 (ttpp)
REVERT: A  174 TYR cc_start: 0.7869 (t80) cc_final: 0.7463 (t80)
REVERT: A  253 MET cc_start: 0.8092 (mmp) cc_final: 0.7748 (mmt)
REVERT: A  259 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6461 (mt-10)
REVERT: A  290 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7794 (ttm170)
REVERT: A  311 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7062 (mptt)
REVERT: A  328 PHE cc_start: 0.7841 (t80) cc_final: 0.7557 (t80)
  outliers start: 21
  outliers final: 3
  residues processed: 82
  average time/residue: 0.5050
  time to fit residues: 43.2777
Evaluate side-chains
  72 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  105 GLU
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  319 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 19 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 48 optimal weight:    9.9990
   overall best weight:    1.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.218012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.164400 restraints weight = 6367.480|
|-----------------------------------------------------------------------------|
r_work (start): 0.3900 rms_B_bonded: 0.99
r_work: 0.3687 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3549 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7276  Z= 0.190
  Angle     :  0.599   9.078  10567  Z= 0.336
  Chirality :  0.046   0.535   1287
  Planarity :  0.005   0.050    755
  Dihedral  : 24.359 177.339   2899
  Min Nonbonded Distance : 2.084

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  5.63 %
    Allowed  : 30.29 %
    Favored  : 64.08 %
  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 are not related in a simple way.
  whole:  0.47 (0.41), residues: 413
  helix:  0.98 (0.35), residues: 209
  sheet: -0.21 (0.67), residues: 49
  loop : -0.29 (0.52), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 217 
 TYR   0.012   0.002   TYR A  74 
 PHE   0.022   0.002   PHE A 328 
 TRP   0.013   0.002   TRP A 157 
 HIS   0.007   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00403 /  0.19 ( 7276)
  covalent geometry    : angle       0.59949 /  0.34 (10567)
  hydrogen bonds       : bond        0.07106 /  4.15 (  296)
  hydrogen bonds       : angle       4.68922 /  3.22 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7395 (m-30) cc_final: 0.6611 (t0)
REVERT: A   24 LYS cc_start: 0.7590 (mtpm) cc_final: 0.6586 (mmtm)
REVERT: A   28 LYS cc_start: 0.7434 (OUTLIER) cc_final: 0.6844 (mptt)
REVERT: A   35 LYS cc_start: 0.7775 (mmtp) cc_final: 0.7245 (mttt)
REVERT: A  123 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7426 (ttp-110)
REVERT: A  142 SER cc_start: 0.7393 (OUTLIER) cc_final: 0.6891 (t)
REVERT: A  159 LYS cc_start: 0.7747 (ttpt) cc_final: 0.7238 (ttpp)
REVERT: A  174 TYR cc_start: 0.7890 (t80) cc_final: 0.7513 (t80)
REVERT: A  259 GLU cc_start: 0.6954 (OUTLIER) cc_final: 0.6327 (mt-10)
REVERT: A  260 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6491 (ttm170)
REVERT: A  290 ARG cc_start: 0.8048 (OUTLIER) cc_final: 0.7728 (ttm170)
REVERT: A  311 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7095 (mptt)
REVERT: A  418 ARG cc_start: 0.6893 (mtt-85) cc_final: 0.6635 (mtm180)
  outliers start: 21
  outliers final: 8
  residues processed: 76
  average time/residue: 0.5635
  time to fit residues: 44.7348
Evaluate side-chains
  75 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 60
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue   28 LYS
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  151 GLN
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  405 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 47 optimal weight:   50.0000
   chunk 34 optimal weight:    0.7980
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    0.5980
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 9 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4420 r_free = 0.4420 target = 0.219191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.165781 restraints weight = 6453.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 1.04
r_work: 0.3704 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.2428

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7276  Z= 0.150
  Angle     :  0.550   8.208  10567  Z= 0.313
  Chirality :  0.043   0.472   1287
  Planarity :  0.005   0.045    755
  Dihedral  : 24.232 178.079   2899
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 30.29 %
    Favored  : 64.34 %
  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 are not related in a simple way.
  whole:  0.55 (0.41), residues: 413
  helix:  1.08 (0.35), residues: 208
  sheet: -0.39 (0.70), residues: 50
  loop : -0.20 (0.51), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 217 
 TYR   0.017   0.002   TYR A 256 
 PHE   0.024   0.002   PHE A 328 
 TRP   0.010   0.002   TRP A 157 
 HIS   0.007   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.15 ( 7276)
  covalent geometry    : angle       0.55031 /  0.31 (10567)
  hydrogen bonds       : bond        0.06748 /  3.82 (  296)
  hydrogen bonds       : angle       4.47494 /  3.08 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7483 (m-30) cc_final: 0.6716 (t0)
REVERT: A   24 LYS cc_start: 0.7516 (mtpm) cc_final: 0.6518 (mmtm)
REVERT: A   28 LYS cc_start: 0.7371 (mtmt) cc_final: 0.6747 (mptt)
REVERT: A   35 LYS cc_start: 0.7821 (mmtp) cc_final: 0.7348 (mmtt)
REVERT: A  108 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7786 (mt)
REVERT: A  123 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7404 (ttp-110)
REVERT: A  142 SER cc_start: 0.7240 (OUTLIER) cc_final: 0.6753 (t)
REVERT: A  159 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7225 (ttpp)
REVERT: A  174 TYR cc_start: 0.7852 (t80) cc_final: 0.7524 (t80)
REVERT: A  259 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6235 (mt-10)
REVERT: A  260 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.5906 (ttm-80)
REVERT: A  290 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7735 (ttm170)
REVERT: A  311 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7103 (mptt)
REVERT: A  416 GLN cc_start: 0.7408 (OUTLIER) cc_final: 0.6838 (tm-30)
REVERT: A  418 ARG cc_start: 0.6904 (mtt-85) cc_final: 0.6627 (mmt90)
  outliers start: 20
  outliers final: 6
  residues processed: 75
  average time/residue: 0.4891
  time to fit residues: 38.3850
Evaluate side-chains
  74 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  107 ILE
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 49 optimal weight:   10.0000
   chunk 46 optimal weight:   50.0000
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 101 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.218883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.165415 restraints weight = 6442.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3912 rms_B_bonded: 1.02
r_work: 0.3699 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3561 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.2606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7276  Z= 0.144
  Angle     :  0.540   8.234  10567  Z= 0.307
  Chirality :  0.042   0.471   1287
  Planarity :  0.004   0.045    755
  Dihedral  : 24.109 178.543   2899
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  4.83 %
    Allowed  : 32.17 %
    Favored  : 63.00 %
  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 are not related in a simple way.
  whole:  0.62 (0.41), residues: 413
  helix:  1.13 (0.36), residues: 208
  sheet: -0.34 (0.70), residues: 50
  loop : -0.17 (0.51), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 410 
 TYR   0.015   0.002   TYR A 256 
 PHE   0.025   0.002   PHE A 328 
 TRP   0.009   0.002   TRP A 157 
 HIS   0.005   0.001   HIS A  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 7276)
  covalent geometry    : angle       0.54039 /  0.31 (10567)
  hydrogen bonds       : bond        0.06542 /  3.74 (  296)
  hydrogen bonds       : angle       4.36950 /  3.00 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 62
  time to evaluate  : 0.175 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7518 (m-30) cc_final: 0.6715 (t0)
REVERT: A   24 LYS cc_start: 0.7479 (mtpm) cc_final: 0.6493 (mmtm)
REVERT: A   28 LYS cc_start: 0.7430 (mtmt) cc_final: 0.6818 (mptt)
REVERT: A   35 LYS cc_start: 0.7899 (mmtp) cc_final: 0.7426 (mmtt)
REVERT: A   67 GLU cc_start: 0.7302 (pt0) cc_final: 0.6909 (pm20)
REVERT: A  101 ASN cc_start: 0.7349 (OUTLIER) cc_final: 0.7124 (t0)
REVERT: A  108 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7722 (mt)
REVERT: A  123 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7424 (ttp-110)
REVERT: A  142 SER cc_start: 0.7168 (OUTLIER) cc_final: 0.6713 (t)
REVERT: A  159 LYS cc_start: 0.7767 (ttpt) cc_final: 0.7275 (ttpp)
REVERT: A  174 TYR cc_start: 0.7874 (t80) cc_final: 0.7557 (t80)
REVERT: A  259 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6265 (mt-10)
REVERT: A  260 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6928 (ttm170)
REVERT: A  290 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7718 (ttm170)
REVERT: A  311 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7100 (mptt)
REVERT: A  416 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.6860 (tm-30)
REVERT: A  418 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6599 (ttm170)
  outliers start: 18
  outliers final: 6
  residues processed: 72
  average time/residue: 0.5511
  time to fit residues: 41.6189
Evaluate side-chains
  77 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  142 SER
Chi-restraints excluded: chain A residue  151 GLN
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  246 MET
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 48 optimal weight:   10.0000
   chunk 24 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 44 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0060
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0370
   chunk 34 optimal weight:    0.9980
   chunk 49 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.7276

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.218921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.165615 restraints weight = 6458.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3916 rms_B_bonded: 0.99
r_work: 0.3704 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3565 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7276  Z= 0.144
  Angle     :  0.535   8.235  10567  Z= 0.304
  Chirality :  0.042   0.467   1287
  Planarity :  0.004   0.046    755
  Dihedral  : 24.060 178.719   2899
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 32.98 %
    Favored  : 62.73 %
  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 are not related in a simple way.
  whole:  0.69 (0.42), residues: 413
  helix:  1.17 (0.36), residues: 208
  sheet: -0.24 (0.72), residues: 50
  loop : -0.13 (0.51), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 410 
 TYR   0.015   0.002   TYR A 256 
 PHE   0.022   0.002   PHE A 328 
 TRP   0.009   0.002   TRP A 157 
 HIS   0.004   0.001   HIS A  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00297 /  0.14 ( 7276)
  covalent geometry    : angle       0.53454 /  0.30 (10567)
  hydrogen bonds       : bond        0.06341 /  3.67 (  296)
  hydrogen bonds       : angle       4.35054 /  2.98 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.118 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7521 (m-30) cc_final: 0.6722 (t0)
REVERT: A   19 GLU cc_start: 0.5950 (tt0) cc_final: 0.5620 (tt0)
REVERT: A   24 LYS cc_start: 0.7468 (mtpm) cc_final: 0.6467 (mmtm)
REVERT: A   28 LYS cc_start: 0.7413 (mtmt) cc_final: 0.6785 (mptt)
REVERT: A   35 LYS cc_start: 0.7921 (mmtp) cc_final: 0.7436 (mmtt)
REVERT: A   67 GLU cc_start: 0.7318 (pt0) cc_final: 0.6934 (pm20)
REVERT: A  108 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7750 (mt)
REVERT: A  123 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7402 (ttp-110)
REVERT: A  159 LYS cc_start: 0.7725 (ttpt) cc_final: 0.7225 (ttpp)
REVERT: A  174 TYR cc_start: 0.7865 (t80) cc_final: 0.7521 (t80)
REVERT: A  259 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6258 (mt-10)
REVERT: A  260 ARG cc_start: 0.7845 (OUTLIER) cc_final: 0.6788 (ttm170)
REVERT: A  290 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7700 (ttm170)
REVERT: A  311 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7086 (mptt)
REVERT: A  416 GLN cc_start: 0.7454 (OUTLIER) cc_final: 0.6861 (tm-30)
REVERT: A  418 ARG cc_start: 0.6828 (mtt-85) cc_final: 0.6495 (ttm170)
REVERT: A  425 LYS cc_start: 0.6920 (pptt) cc_final: 0.6546 (tptp)
  outliers start: 16
  outliers final: 5
  residues processed: 72
  average time/residue: 0.5582
  time to fit residues: 42.0437
Evaluate side-chains
  72 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  131 MET
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 25 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9980
   chunk 50 optimal weight:   10.0000
   chunk 16 optimal weight:    0.1980
   chunk 8 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.1784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.215070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.161077 restraints weight = 6379.068|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.02
r_work: 0.3648 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3511 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7276  Z= 0.184
  Angle     :  0.584   9.205  10567  Z= 0.326
  Chirality :  0.045   0.535   1287
  Planarity :  0.005   0.050    755
  Dihedral  : 24.035 178.650   2899
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  5.09 %
    Allowed  : 32.98 %
    Favored  : 61.93 %
  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 are not related in a simple way.
  whole:  0.59 (0.41), residues: 413
  helix:  1.07 (0.36), residues: 210
  sheet: -0.13 (0.73), residues: 50
  loop : -0.24 (0.51), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 390 
 TYR   0.018   0.002   TYR A 256 
 PHE   0.029   0.002   PHE A 328 
 TRP   0.013   0.003   TRP A 157 
 HIS   0.006   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00398 /  0.18 ( 7276)
  covalent geometry    : angle       0.58413 /  0.33 (10567)
  hydrogen bonds       : bond        0.06478 /  3.92 (  296)
  hydrogen bonds       : angle       4.42640 /  3.03 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 59
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A    5 ASP cc_start: 0.7565 (m-30) cc_final: 0.6726 (t0)
REVERT: A   19 GLU cc_start: 0.6184 (tt0) cc_final: 0.5751 (tt0)
REVERT: A   24 LYS cc_start: 0.7542 (mtpm) cc_final: 0.6608 (mmtm)
REVERT: A   28 LYS cc_start: 0.7430 (mtmt) cc_final: 0.6890 (mptt)
REVERT: A   35 LYS cc_start: 0.8052 (mmtp) cc_final: 0.7578 (mmtt)
REVERT: A   67 GLU cc_start: 0.7463 (pt0) cc_final: 0.7010 (pm20)
REVERT: A  123 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7418 (ttp-110)
REVERT: A  159 LYS cc_start: 0.7696 (ttpt) cc_final: 0.7107 (ttpp)
REVERT: A  173 ILE cc_start: 0.7789 (OUTLIER) cc_final: 0.7580 (mm)
REVERT: A  174 TYR cc_start: 0.7938 (t80) cc_final: 0.7580 (t80)
REVERT: A  211 ASP cc_start: 0.7766 (m-30) cc_final: 0.7496 (t0)
REVERT: A  259 GLU cc_start: 0.7001 (OUTLIER) cc_final: 0.6403 (mt-10)
REVERT: A  260 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7103 (ttm170)
REVERT: A  290 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7655 (ttm170)
REVERT: A  311 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7132 (mptt)
REVERT: A  416 GLN cc_start: 0.7545 (OUTLIER) cc_final: 0.6923 (tm-30)
REVERT: A  418 ARG cc_start: 0.6900 (mtt-85) cc_final: 0.5810 (mtm-85)
REVERT: A  425 LYS cc_start: 0.6824 (pptt) cc_final: 0.5841 (ptpt)
  outliers start: 19
  outliers final: 7
  residues processed: 73
  average time/residue: 0.5838
  time to fit residues: 44.6765
Evaluate side-chains
  73 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 59
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  151 GLN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 54 optimal weight:    9.9990
   chunk 15 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  16 HIS
A 386 HIS
A 421 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.208978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.155289 restraints weight = 6414.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 0.99
r_work: 0.3591 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3455 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.087   7276  Z= 0.304
  Angle     :  0.742  11.365  10567  Z= 0.403
  Chirality :  0.055   0.728   1287
  Planarity :  0.006   0.059    755
  Dihedral  : 24.184 177.502   2899
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 9.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 32.44 %
    Favored  : 63.54 %
  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 are not related in a simple way.
  whole: -0.05 (0.40), residues: 413
  helix:  0.51 (0.35), residues: 210
  sheet: -0.17 (0.76), residues: 48
  loop : -0.58 (0.49), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 390 
 TYR   0.020   0.003   TYR A  86 
 PHE   0.039   0.003   PHE A 328 
 TRP   0.014   0.003   TRP A 157 
 HIS   0.008   0.002   HIS A  77 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00675 /  0.30 ( 7276)
  covalent geometry    : angle       0.74192 /  0.40 (10567)
  hydrogen bonds       : bond        0.07498 /  4.78 (  296)
  hydrogen bonds       : angle       4.76610 /  3.25 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 ASP cc_start: 0.7612 (m-30) cc_final: 0.6828 (t0)
REVERT: A   19 GLU cc_start: 0.6316 (tt0) cc_final: 0.5771 (tt0)
REVERT: A   24 LYS cc_start: 0.7582 (mtpm) cc_final: 0.6541 (mmtm)
REVERT: A   28 LYS cc_start: 0.7478 (mtmt) cc_final: 0.6938 (mptt)
REVERT: A   35 LYS cc_start: 0.8173 (mmtp) cc_final: 0.7749 (mttt)
REVERT: A   67 GLU cc_start: 0.7447 (pt0) cc_final: 0.6996 (pm20)
REVERT: A  123 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7413 (ttp-110)
REVERT: A  142 SER cc_start: 0.7680 (p) cc_final: 0.7233 (t)
REVERT: A  159 LYS cc_start: 0.7643 (ttpt) cc_final: 0.7064 (ttpp)
REVERT: A  173 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7603 (mm)
REVERT: A  259 GLU cc_start: 0.7014 (OUTLIER) cc_final: 0.6359 (mt-10)
REVERT: A  260 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7357 (ttm170)
REVERT: A  290 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7712 (ttm170)
REVERT: A  311 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7225 (mptt)
REVERT: A  405 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8416 (t)
REVERT: A  416 GLN cc_start: 0.7655 (OUTLIER) cc_final: 0.7019 (tm-30)
REVERT: A  418 ARG cc_start: 0.6963 (mtt-85) cc_final: 0.6560 (mmt90)
REVERT: A  425 LYS cc_start: 0.6633 (pptt) cc_final: 0.5615 (ptpt)
  outliers start: 15
  outliers final: 5
  residues processed: 66
  average time/residue: 0.7252
  time to fit residues: 49.9281
Evaluate side-chains
  66 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 53
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  260 ARG
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  405 SER
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 55 optimal weight:   10.0000
   chunk 42 optimal weight:   20.0000
   chunk 51 optimal weight:   10.0000
   chunk 18 optimal weight:    0.5980
   chunk 46 optimal weight:   50.0000
   chunk 37 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 43 optimal weight:    6.9990
   overall best weight:    1.8384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.210156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.156890 restraints weight = 6378.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3833 rms_B_bonded: 1.01
r_work: 0.3615 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3481 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.3579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   7276  Z= 0.238
  Angle     :  0.638   9.885  10567  Z= 0.354
  Chirality :  0.049   0.605   1287
  Planarity :  0.005   0.056    755
  Dihedral  : 24.118 177.690   2899
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 33.24 %
    Favored  : 63.27 %
  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 are not related in a simple way.
  whole: -0.01 (0.41), residues: 413
  helix:  0.54 (0.35), residues: 210
  sheet: -0.22 (0.79), residues: 48
  loop : -0.53 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 390 
 TYR   0.022   0.003   TYR A 256 
 PHE   0.031   0.002   PHE A 328 
 TRP   0.017   0.003   TRP A 157 
 HIS   0.011   0.002   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00523 /  0.24 ( 7276)
  covalent geometry    : angle       0.63760 /  0.35 (10567)
  hydrogen bonds       : bond        0.06630 /  4.12 (  296)
  hydrogen bonds       : angle       4.61766 /  3.14 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLU cc_start: 0.6316 (tt0) cc_final: 0.5906 (tt0)
REVERT: A   24 LYS cc_start: 0.7547 (mtpm) cc_final: 0.6491 (mmtm)
REVERT: A   28 LYS cc_start: 0.7458 (mtmt) cc_final: 0.6909 (mptt)
REVERT: A   35 LYS cc_start: 0.8144 (mmtp) cc_final: 0.7729 (mttt)
REVERT: A   67 GLU cc_start: 0.7470 (pt0) cc_final: 0.6999 (pm20)
REVERT: A  123 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7389 (ttp-110)
REVERT: A  142 SER cc_start: 0.7629 (p) cc_final: 0.7206 (t)
REVERT: A  159 LYS cc_start: 0.7738 (ttpt) cc_final: 0.7165 (ttpp)
REVERT: A  259 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6422 (mt-10)
REVERT: A  290 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7706 (ttm170)
REVERT: A  311 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7219 (mptt)
REVERT: A  416 GLN cc_start: 0.7497 (OUTLIER) cc_final: 0.6869 (tm-30)
REVERT: A  418 ARG cc_start: 0.6958 (mtt-85) cc_final: 0.6615 (mmt90)
REVERT: A  425 LYS cc_start: 0.6455 (pptt) cc_final: 0.5591 (ptpt)
  outliers start: 13
  outliers final: 5
  residues processed: 64
  average time/residue: 0.6914
  time to fit residues: 46.1828
Evaluate side-chains
  66 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 55 optimal weight:   10.0000
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 43 optimal weight:    7.9990
   chunk 20 optimal weight:    0.5980
   chunk 38 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 48 optimal weight:    5.9990
   overall best weight:    0.6580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.214176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.161516 restraints weight = 6387.925|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.02
r_work: 0.3672 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3541 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3541
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7276  Z= 0.142
  Angle     :  0.551   8.395  10567  Z= 0.313
  Chirality :  0.042   0.475   1287
  Planarity :  0.004   0.048    755
  Dihedral  : 24.000 178.482   2899
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 34.58 %
    Favored  : 63.00 %
  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 are not related in a simple way.
  whole:  0.36 (0.41), residues: 413
  helix:  0.91 (0.36), residues: 209
  sheet: -0.29 (0.78), residues: 48
  loop : -0.36 (0.50), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 204 
 TYR   0.021   0.002   TYR A 256 
 PHE   0.024   0.002   PHE A 328 
 TRP   0.014   0.002   TRP A 157 
 HIS   0.007   0.001   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 ( 7276)
  covalent geometry    : angle       0.55052 /  0.31 (10567)
  hydrogen bonds       : bond        0.06015 /  3.59 (  296)
  hydrogen bonds       : angle       4.45732 /  3.01 (  724)

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

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

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  826 Ramachandran restraints generated.
    413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   19 GLU cc_start: 0.6309 (tt0) cc_final: 0.6018 (tt0)
REVERT: A   24 LYS cc_start: 0.7469 (mtpm) cc_final: 0.6503 (mmtm)
REVERT: A   28 LYS cc_start: 0.7468 (mtmt) cc_final: 0.6959 (mptt)
REVERT: A   35 LYS cc_start: 0.8155 (mmtp) cc_final: 0.7722 (mttt)
REVERT: A   67 GLU cc_start: 0.7495 (pt0) cc_final: 0.7091 (pm20)
REVERT: A  123 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7437 (ttp-110)
REVERT: A  142 SER cc_start: 0.7497 (p) cc_final: 0.7124 (t)
REVERT: A  159 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7247 (ttpp)
REVERT: A  174 TYR cc_start: 0.7704 (t80) cc_final: 0.7401 (t80)
REVERT: A  259 GLU cc_start: 0.6967 (OUTLIER) cc_final: 0.6337 (mt-10)
REVERT: A  290 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7733 (ttm170)
REVERT: A  311 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7211 (mptt)
REVERT: A  416 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6798 (tm-30)
REVERT: A  418 ARG cc_start: 0.6934 (mtt-85) cc_final: 0.6621 (mmt90)
REVERT: A  425 LYS cc_start: 0.6374 (pptt) cc_final: 0.5547 (ptpt)
  outliers start: 9
  outliers final: 3
  residues processed: 65
  average time/residue: 0.6586
  time to fit residues: 44.6234
Evaluate side-chains
  65 residues out of total 373 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 VAL
Chi-restraints excluded: chain A residue  123 ARG
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  290 ARG
Chi-restraints excluded: chain A residue  311 LYS
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  416 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 1 optimal weight:    3.9990
   chunk 51 optimal weight:    9.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 31 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 45 optimal weight:   10.0000
   chunk 4 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   overall best weight:    1.7586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 106 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.209802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.156452 restraints weight = 6366.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3827 rms_B_bonded: 1.02
r_work: 0.3610 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3475 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069   7276  Z= 0.241
  Angle     :  0.642  10.241  10567  Z= 0.353
  Chirality :  0.049   0.611   1287
  Planarity :  0.005   0.053    755
  Dihedral  : 24.035 177.883   2899
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 34.58 %
    Favored  : 62.47 %
  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 are not related in a simple way.
  whole:  0.15 (0.41), residues: 413
  helix:  0.67 (0.35), residues: 210
  sheet: -0.14 (0.80), residues: 48
  loop : -0.45 (0.50), residues: 155

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 390 
 TYR   0.018   0.003   TYR A 245 
 PHE   0.029   0.002   PHE A 328 
 TRP   0.014   0.003   TRP A 157 
 HIS   0.009   0.002   HIS A  16 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00534 /  0.24 ( 7276)
  covalent geometry    : angle       0.64197 /  0.35 (10567)
  hydrogen bonds       : bond        0.06609 /  4.14 (  296)
  hydrogen bonds       : angle       4.57084 /  3.09 (  724)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2498.46 seconds
wall clock time: 43 minutes 13.57 seconds (2593.57 seconds total)