Starting phenix.real_space_refine
on Tue Mar  3 11:51:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tx7_26156/03_2026/7tx7_26156.cif"
  }
  resolution = 3.8
  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=   0.002 sd=   0.033
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       7      5.16       5
     C    2158      2.51       5
     N     487      2.21       5
     O     551      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3203
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3042
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 397, 3042
          Classifications: {'peptide': 397}
          Incomplete info: {'truncation_to_alanine': 34}
          Link IDs: {'PTRANS': 13, 'TRANS': 383}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 142
          Unresolved non-hydrogen angles: 172
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'ARG:plan': 11, 'GLU:plan': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 86
    Chain: "A"
      Number of atoms: 161
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 161
          Unusual residues: {'AJP': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 196
          Unresolved non-hydrogen angles: 294
          Unresolved non-hydrogen dihedrals: 422
          Unresolved non-hydrogen chiralities: 81
  Time building chain proxies: 0.94, per 1000 atoms: 0.29
  Number of scatterers: 3203
  At special positions: 0
  Unit cell: (73.44, 65.88, 79.92, 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       7     16.00
     O     551      8.00
     N     487      7.00
     C    2158      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.31
  Conformation dependent library (CDL) restraints added in 122.3 milliseconds
  

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 0 sheets defined
      88.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 40
      removed outlier: 3.990A  pdb=" N   HIS A  27 " --> pdb=" O   ARG A  23 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU A  28 " --> pdb=" O   SER A  24 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   CYS A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 46
      No H-bonds generated for 'chain 'A' and resid 44 through 46'
    Processing helix  chain 'A' and resid 47 through 53
    Processing helix  chain 'A' and resid 60 through 90
      removed outlier: 5.052A  pdb=" N   THR A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
      Proline residue:  A  70  - end of helix
      removed outlier: 4.890A  pdb=" N   VAL A  81 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
    Processing helix  chain 'A' and resid 91 through 113
      removed outlier: 3.958A  pdb=" N   VAL A  95 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 132
      removed outlier: 3.621A  pdb=" N   VAL A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 144
      removed outlier: 3.742A  pdb=" N   SER A 138 " --> pdb=" O   ILE A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 179
      removed outlier: 3.793A  pdb=" N   SER A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   VAL A 169 " --> pdb=" O   PHE A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 203
      removed outlier: 4.104A  pdb=" N   PHE A 202 " --> pdb=" O   VAL A 198 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU A 203 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
      removed outlier: 3.644A  pdb=" N   ARG A 263 " --> pdb=" O   GLY A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 296
      removed outlier: 4.147A  pdb=" N   ARG A 268 " --> pdb=" O   ARG A 264 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   LEU A 269 " --> pdb=" O   PRO A 265 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   TRP A 270 " --> pdb=" O   GLN A 266 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 278 " --> pdb=" O   TRP A 274 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA A 279 " --> pdb=" O   VAL A 275 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   HIS A 289 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.819A  pdb=" N   ILE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 327
      removed outlier: 3.672A  pdb=" N   GLY A 325 " --> pdb=" O   SER A 321 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   PHE A 326 " --> pdb=" O   PHE A 322 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A 327 " --> pdb=" O   ALA A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 335 through 356
    Processing helix  chain 'A' and resid 358 through 360
      No H-bonds generated for 'chain 'A' and resid 358 through 360'
    Processing helix  chain 'A' and resid 361 through 391
      removed outlier: 3.646A  pdb=" N   LEU A 379 " --> pdb=" O   SER A 375 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   VAL A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
      removed outlier: 4.516A  pdb=" N   SER A 390 " --> pdb=" O   GLN A 386 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LEU A 391 " --> pdb=" O   ILE A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 419
      removed outlier: 4.016A  pdb=" N   ALA A 397 " --> pdb=" O   LYS A 393 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   LEU A 398 " --> pdb=" O   GLU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 459
      removed outlier: 3.515A  pdb=" N   VAL A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ARG A 456 " --> pdb=" O   LEU A 452 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   GLN A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)

    244 hydrogen bonds defined for protein.
    732 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: 0.46

  Time building geometry restraints manager: 0.41 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 909
        1.34 -     1.46: 569
        1.46 -     1.57: 1817
        1.57 -     1.69: 4
        1.69 -     1.81: 11
  Bond restraints: 3310
  Sorted by residual:
  bond pdb=" C23 AJP A 703 "
       pdb=" C24 AJP A 703 "
    ideal  model  delta    sigma   weight residual
    1.522  1.613 -0.091 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" C05 AJP A 704 "
       pdb=" C06 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.534  1.445  0.089 2.00e-02 2.50e+03 1.96e+01
  bond pdb=" C23 AJP A 704 "
       pdb=" C24 AJP A 704 "
    ideal  model  delta    sigma   weight residual
    1.522  1.609 -0.087 2.00e-02 2.50e+03 1.91e+01
  bond pdb=" C23 AJP A 701 "
       pdb=" C24 AJP A 701 "
    ideal  model  delta    sigma   weight residual
    1.522  1.609 -0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C23 AJP A 702 "
       pdb=" C24 AJP A 702 "
    ideal  model  delta    sigma   weight residual
    1.522  1.606 -0.084 2.00e-02 2.50e+03 1.77e+01
  ... (remaining 3305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 4384
        1.63 -     3.27: 138
        3.27 -     4.90: 46
        4.90 -     6.53: 13
        6.53 -     8.17: 2
  Bond angle restraints: 4583
  Sorted by residual:
  angle pdb=" N   ALA A 131 "
        pdb=" CA  ALA A 131 "
        pdb=" C   ALA A 131 "
      ideal   model   delta    sigma   weight residual
     111.28  116.70   -5.42 1.09e+00 8.42e-01 2.47e+01
  angle pdb=" N   ALA A 132 "
        pdb=" CA  ALA A 132 "
        pdb=" C   ALA A 132 "
      ideal   model   delta    sigma   weight residual
     113.02  117.20   -4.18 1.20e+00 6.94e-01 1.21e+01
  angle pdb=" C07 AJP A 701 "
        pdb=" C06 AJP A 701 "
        pdb=" C83 AJP A 701 "
      ideal   model   delta    sigma   weight residual
     114.76  106.59    8.17 3.00e+00 1.11e-01 7.41e+00
  angle pdb=" C07 AJP A 703 "
        pdb=" C06 AJP A 703 "
        pdb=" C83 AJP A 703 "
      ideal   model   delta    sigma   weight residual
     114.76  107.70    7.06 3.00e+00 1.11e-01 5.53e+00
  angle pdb=" C07 AJP A 702 "
        pdb=" C06 AJP A 702 "
        pdb=" C83 AJP A 702 "
      ideal   model   delta    sigma   weight residual
     114.76  108.24    6.52 3.00e+00 1.11e-01 4.72e+00
  ... (remaining 4578 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.62: 2133
       30.62 -    61.24: 54
       61.24 -    91.85: 19
       91.85 -   122.47: 19
      122.47 -   153.09: 8
  Dihedral angle restraints: 2233
    sinusoidal: 1065
      harmonic: 1168
  Sorted by residual:
  dihedral pdb=" O31 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.28  -29.63 -153.09     1      3.00e+01 1.11e-03 2.02e+01
  dihedral pdb=" C29 AJP A 702 "
           pdb=" C30 AJP A 702 "
           pdb=" C32 AJP A 702 "
           pdb=" O33 AJP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.96   90.80 -151.76     1      3.00e+01 1.11e-03 2.01e+01
  dihedral pdb=" C21 AJP A 704 "
           pdb=" C22 AJP A 704 "
           pdb=" C23 AJP A 704 "
           pdb=" O25 AJP A 704 "
      ideal   model   delta sinusoidal    sigma   weight residual
     176.32   50.06  126.26     1      3.00e+01 1.11e-03 1.70e+01
  ... (remaining 2230 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 499
       0.064 -    0.128: 50
       0.128 -    0.192: 8
       0.192 -    0.256: 13
       0.256 -    0.320: 15
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" C19 AJP A 702 "
            pdb=" C18 AJP A 702 "
            pdb=" C20 AJP A 702 "
            pdb=" C24 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.75   -0.32 2.00e-01 2.50e+01 2.56e+00
  chirality pdb=" C11 AJP A 702 "
            pdb=" C10 AJP A 702 "
            pdb=" C12 AJP A 702 "
            pdb=" C16 AJP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.52   -0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" C11 AJP A 704 "
            pdb=" C10 AJP A 704 "
            pdb=" C12 AJP A 704 "
            pdb=" C16 AJP A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.20    2.51   -0.31 2.00e-01 2.50e+01 2.40e+00
  ... (remaining 582 not shown)

  Planarity restraints: 518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  93 "    0.040 5.00e-02 4.00e+02   6.14e-02 6.03e+00
        pdb=" N   PRO A  94 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO A  94 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  94 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  42 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO A  43 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 205 "    0.022 5.00e-02 4.00e+02   3.34e-02 1.79e+00
        pdb=" N   PRO A 206 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "    0.019 5.00e-02 4.00e+02
  ... (remaining 515 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 28
        2.64 -     3.20: 3257
        3.20 -     3.77: 4947
        3.77 -     4.33: 6145
        4.33 -     4.90: 10221
  Nonbonded interactions: 24598
  Sorted by model distance:
  nonbonded pdb=" O33 AJP A 701 "
            pdb=" O77 AJP A 701 "
     model   vdw
     2.072 3.040
  nonbonded pdb=" O   GLN A 433 "
            pdb=" OG  SER A 436 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   LEU A 124 "
            pdb=" OG  SER A 127 "
     model   vdw
     2.279 3.040
  nonbonded pdb=" ND1 HIS A 289 "
            pdb=" OD1 ASN A 306 "
     model   vdw
     2.410 3.120
  nonbonded pdb=" O   TYR A 126 "
            pdb=" OG1 THR A 129 "
     model   vdw
     2.421 3.040
  ... (remaining 24593 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 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:             0.780
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.310
  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:0.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
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      :  0.008   0.091   3310  Z= 0.402
  Angle     :  0.760   8.165   4583  Z= 0.336
  Chirality :  0.068   0.320    585
  Planarity :  0.005   0.061    518
  Dihedral  : 21.146 153.091   1483
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  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:  3.77 (0.42), residues: 393
  helix:  3.08 (0.27), residues: 317
  sheet:  None (None), residues: 0
  loop : -0.26 (0.80), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 268 
 TYR   0.011   0.001   TYR A  35 
 PHE   0.007   0.001   PHE A 405 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 ( 3310)
  covalent geometry    : angle       0.76037 ( 4583)
  hydrogen bonds       : bond        0.14491 (  244)
  hydrogen bonds       : angle       5.44710 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.086 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8750 (t80) cc_final: 0.8368 (t80)
REVERT: A  133 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8282 (mpt-90)
REVERT: A  195 PHE cc_start: 0.7125 (t80) cc_final: 0.6548 (t80)
REVERT: A  300 ASN cc_start: 0.8397 (t0) cc_final: 0.8127 (t0)
REVERT: A  305 TYR cc_start: 0.7633 (m-80) cc_final: 0.7300 (m-80)
REVERT: A  431 GLN cc_start: 0.8144 (tt0) cc_final: 0.7930 (tt0)
REVERT: A  440 LEU cc_start: 0.8233 (tt) cc_final: 0.8025 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0681
  time to fit residues: 10.5046
Evaluate side-chains
  103 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 277 ASN
A 346 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.139056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.125266 restraints weight = 5943.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.129035 restraints weight = 3227.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131543 restraints weight = 1969.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133360 restraints weight = 1304.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134679 restraints weight = 907.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7516
moved from start:          0.2563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3310  Z= 0.168
  Angle     :  0.757   7.428   4583  Z= 0.339
  Chirality :  0.040   0.222    585
  Planarity :  0.005   0.051    518
  Dihedral  : 12.599 126.693    891
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.24 %
    Favored  : 79.80 %
  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:  3.89 (0.43), residues: 393
  helix:  2.99 (0.28), residues: 328
  sheet:  None (None), residues: 0
  loop :  0.21 (0.89), residues: 65

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 151 
 TYR   0.014   0.002   TYR A 366 
 PHE   0.017   0.002   PHE A 351 
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3310)
  covalent geometry    : angle       0.75744 ( 4583)
  hydrogen bonds       : bond        0.05192 (  244)
  hydrogen bonds       : angle       4.26819 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.087 
Fit side-chains
REVERT: A   32 LEU cc_start: 0.8586 (mp) cc_final: 0.8323 (tp)
REVERT: A   51 TYR cc_start: 0.8812 (t80) cc_final: 0.8135 (t80)
REVERT: A  133 ARG cc_start: 0.8371 (mtt180) cc_final: 0.7033 (mpt-90)
REVERT: A  195 PHE cc_start: 0.7399 (t80) cc_final: 0.6581 (t80)
REVERT: A  300 ASN cc_start: 0.8300 (t0) cc_final: 0.8002 (t0)
REVERT: A  431 GLN cc_start: 0.8090 (tt0) cc_final: 0.7645 (mt0)
  outliers start: 6
  outliers final: 6
  residues processed: 110
  average time/residue: 0.0514
  time to fit residues: 7.1329
Evaluate side-chains
  101 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  134 ILE
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  193 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 21 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 15 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 4 optimal weight:    0.0470
   chunk 30 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.7078

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3732 r_free = 0.3732 target = 0.138551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.124697 restraints weight = 5971.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128562 restraints weight = 3202.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.131052 restraints weight = 1933.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132925 restraints weight = 1280.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.134123 restraints weight = 882.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.3183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3310  Z= 0.138
  Angle     :  0.639   6.593   4583  Z= 0.300
  Chirality :  0.037   0.156    585
  Planarity :  0.004   0.047    518
  Dihedral  : 10.301 129.857    891
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 18.89 %
    Favored  : 78.50 %
  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:  3.84 (0.43), residues: 393
  helix:  3.05 (0.28), residues: 325
  sheet:  None (None), residues: 0
  loop : -0.18 (0.83), residues: 68

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 151 
 TYR   0.019   0.002   TYR A 366 
 PHE   0.017   0.001   PHE A 103 
 TRP   0.006   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3310)
  covalent geometry    : angle       0.63944 ( 4583)
  hydrogen bonds       : bond        0.04647 (  244)
  hydrogen bonds       : angle       3.91981 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8925 (t80) cc_final: 0.8671 (t80)
REVERT: A   51 TYR cc_start: 0.8732 (t80) cc_final: 0.8003 (t80)
REVERT: A  133 ARG cc_start: 0.8376 (mtt180) cc_final: 0.7627 (mtt90)
REVERT: A  195 PHE cc_start: 0.7233 (t80) cc_final: 0.6415 (t80)
REVERT: A  300 ASN cc_start: 0.8173 (t0) cc_final: 0.7813 (t0)
REVERT: A  336 LYS cc_start: 0.8374 (mttt) cc_final: 0.8093 (mmtm)
REVERT: A  431 GLN cc_start: 0.7985 (tt0) cc_final: 0.7667 (mt0)
  outliers start: 8
  outliers final: 6
  residues processed: 105
  average time/residue: 0.0519
  time to fit residues: 6.8877
Evaluate side-chains
  100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 12 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.138194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124407 restraints weight = 5917.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.128269 restraints weight = 3162.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.130737 restraints weight = 1904.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.132530 restraints weight = 1255.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.133795 restraints weight = 873.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3310  Z= 0.142
  Angle     :  0.639   7.643   4583  Z= 0.305
  Chirality :  0.036   0.151    585
  Planarity :  0.004   0.045    518
  Dihedral  :  9.372 118.959    891
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 19.87 %
    Favored  : 76.55 %
  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:  3.67 (0.43), residues: 393
  helix:  2.91 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.52 (0.83), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 151 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.014   0.001   PHE A 326 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 3310)
  covalent geometry    : angle       0.63924 ( 4583)
  hydrogen bonds       : bond        0.04536 (  244)
  hydrogen bonds       : angle       3.86753 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
REVERT: A   34 PHE cc_start: 0.8984 (t80) cc_final: 0.8760 (t80)
REVERT: A   45 GLU cc_start: 0.9011 (tt0) cc_final: 0.8666 (tt0)
REVERT: A   51 TYR cc_start: 0.8732 (t80) cc_final: 0.8038 (t80)
REVERT: A  195 PHE cc_start: 0.7206 (t80) cc_final: 0.6390 (t80)
REVERT: A  294 GLU cc_start: 0.7901 (tp30) cc_final: 0.7647 (tp30)
REVERT: A  300 ASN cc_start: 0.8216 (t0) cc_final: 0.7900 (t0)
REVERT: A  336 LYS cc_start: 0.8386 (mttt) cc_final: 0.8084 (mmtm)
REVERT: A  431 GLN cc_start: 0.8091 (tt0) cc_final: 0.7744 (mt0)
  outliers start: 11
  outliers final: 8
  residues processed: 105
  average time/residue: 0.0531
  time to fit residues: 7.0599
Evaluate side-chains
  96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 88
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 HIS
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 14 optimal weight:    4.9990
   chunk 34 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3740 r_free = 0.3740 target = 0.138915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125216 restraints weight = 5822.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.129080 restraints weight = 3113.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131558 restraints weight = 1875.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.133384 restraints weight = 1231.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.134598 restraints weight = 851.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.3932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   3310  Z= 0.140
  Angle     :  0.639   7.372   4583  Z= 0.308
  Chirality :  0.038   0.187    585
  Planarity :  0.004   0.042    518
  Dihedral  :  7.357  75.342    891
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 19.22 %
    Favored  : 75.90 %
  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:  3.40 (0.43), residues: 393
  helix:  2.80 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -0.97 (0.81), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 151 
 TYR   0.014   0.001   TYR A  35 
 PHE   0.019   0.001   PHE A 103 
 TRP   0.008   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3310)
  covalent geometry    : angle       0.63862 ( 4583)
  hydrogen bonds       : bond        0.04471 (  244)
  hydrogen bonds       : angle       3.86938 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.079 
Fit side-chains
REVERT: A   45 GLU cc_start: 0.8925 (tt0) cc_final: 0.8444 (tt0)
REVERT: A   51 TYR cc_start: 0.8716 (t80) cc_final: 0.8048 (t80)
REVERT: A  195 PHE cc_start: 0.7275 (t80) cc_final: 0.6583 (t80)
REVERT: A  300 ASN cc_start: 0.8247 (t0) cc_final: 0.8000 (t0)
REVERT: A  336 LYS cc_start: 0.8361 (mttt) cc_final: 0.8085 (mmtm)
REVERT: A  338 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8105 (tt)
REVERT: A  431 GLN cc_start: 0.8057 (tt0) cc_final: 0.7738 (mt0)
  outliers start: 15
  outliers final: 10
  residues processed: 107
  average time/residue: 0.0550
  time to fit residues: 7.2817
Evaluate side-chains
  97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 86
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 25 optimal weight:    0.8980
   chunk 16 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 12 optimal weight:    0.1980
   chunk 17 optimal weight:    0.9990
   chunk 19 optimal weight:    8.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3733 r_free = 0.3733 target = 0.138327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124849 restraints weight = 5915.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.128686 restraints weight = 3180.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.131214 restraints weight = 1926.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.132913 restraints weight = 1274.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.134133 restraints weight = 887.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7565
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   3310  Z= 0.140
  Angle     :  0.671   9.107   4583  Z= 0.326
  Chirality :  0.038   0.183    585
  Planarity :  0.004   0.043    518
  Dihedral  :  5.834  51.846    891
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 22.80 %
    Favored  : 72.96 %
  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:  3.29 (0.43), residues: 393
  helix:  2.71 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.96 (0.79), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.009   0.001   TYR A  92 
 PHE   0.027   0.001   PHE A  34 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 3310)
  covalent geometry    : angle       0.67136 ( 4583)
  hydrogen bonds       : bond        0.04437 (  244)
  hydrogen bonds       : angle       3.95093 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8865 (tt0) cc_final: 0.8531 (tt0)
REVERT: A   51 TYR cc_start: 0.8665 (t80) cc_final: 0.8113 (t80)
REVERT: A   97 LEU cc_start: 0.8686 (tp) cc_final: 0.8411 (tp)
REVERT: A  119 MET cc_start: 0.8541 (mmm) cc_final: 0.8187 (mmm)
REVERT: A  134 ILE cc_start: 0.9133 (pt) cc_final: 0.8918 (mt)
REVERT: A  195 PHE cc_start: 0.7407 (t80) cc_final: 0.6666 (t80)
REVERT: A  294 GLU cc_start: 0.7954 (tp30) cc_final: 0.7750 (tp30)
REVERT: A  300 ASN cc_start: 0.8114 (t0) cc_final: 0.7889 (t0)
REVERT: A  336 LYS cc_start: 0.8349 (mttt) cc_final: 0.8083 (mmtm)
REVERT: A  338 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8043 (tt)
REVERT: A  431 GLN cc_start: 0.7987 (tt0) cc_final: 0.7708 (mt0)
  outliers start: 13
  outliers final: 11
  residues processed: 100
  average time/residue: 0.0521
  time to fit residues: 6.6149
Evaluate side-chains
  101 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 24 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 18 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.137491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.123986 restraints weight = 6067.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.127752 restraints weight = 3258.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.130266 restraints weight = 1990.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.131956 restraints weight = 1323.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.133209 restraints weight = 932.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.4375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3310  Z= 0.151
  Angle     :  0.696  11.872   4583  Z= 0.334
  Chirality :  0.038   0.165    585
  Planarity :  0.004   0.041    518
  Dihedral  :  5.619  51.734    891
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 23.13 %
    Favored  : 72.96 %
  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:  3.17 (0.43), residues: 393
  helix:  2.60 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -0.88 (0.81), residues: 62

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 268 
 TYR   0.010   0.001   TYR A  35 
 PHE   0.023   0.002   PHE A  34 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3310)
  covalent geometry    : angle       0.69644 ( 4583)
  hydrogen bonds       : bond        0.04540 (  244)
  hydrogen bonds       : angle       4.05598 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.100 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7685 (mtm-85)
REVERT: A   45 GLU cc_start: 0.8817 (tt0) cc_final: 0.8184 (tt0)
REVERT: A   51 TYR cc_start: 0.8718 (t80) cc_final: 0.8172 (t80)
REVERT: A  134 ILE cc_start: 0.9150 (pt) cc_final: 0.8929 (mt)
REVERT: A  300 ASN cc_start: 0.8129 (t0) cc_final: 0.7912 (t0)
REVERT: A  336 LYS cc_start: 0.8368 (mttt) cc_final: 0.8096 (mmtm)
REVERT: A  338 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.8046 (tt)
REVERT: A  431 GLN cc_start: 0.7975 (tt0) cc_final: 0.7696 (mt0)
  outliers start: 12
  outliers final: 11
  residues processed: 99
  average time/residue: 0.0566
  time to fit residues: 6.9421
Evaluate side-chains
  102 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  394 GLU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 13 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3737 r_free = 0.3737 target = 0.138180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.124827 restraints weight = 6136.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128578 restraints weight = 3286.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131043 restraints weight = 2000.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.132830 restraints weight = 1330.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.133999 restraints weight = 920.685|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.4542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3310  Z= 0.141
  Angle     :  0.722  15.667   4583  Z= 0.337
  Chirality :  0.038   0.180    585
  Planarity :  0.004   0.041    518
  Dihedral  :  5.469  51.541    891
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 25.08 %
    Favored  : 71.66 %
  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:  3.19 (0.43), residues: 393
  helix:  2.60 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -0.89 (0.85), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.034   0.002   TYR A 366 
 PHE   0.021   0.001   PHE A  34 
 TRP   0.007   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 3310)
  covalent geometry    : angle       0.72231 ( 4583)
  hydrogen bonds       : bond        0.04402 (  244)
  hydrogen bonds       : angle       4.04702 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 ARG cc_start: 0.8239 (mtm-85) cc_final: 0.7672 (mtm-85)
REVERT: A   45 GLU cc_start: 0.8833 (tt0) cc_final: 0.8163 (tt0)
REVERT: A   51 TYR cc_start: 0.8711 (t80) cc_final: 0.8170 (t80)
REVERT: A   72 LEU cc_start: 0.9041 (tt) cc_final: 0.8769 (tt)
REVERT: A  134 ILE cc_start: 0.9188 (pt) cc_final: 0.8972 (mt)
REVERT: A  300 ASN cc_start: 0.8099 (t0) cc_final: 0.7892 (t0)
REVERT: A  336 LYS cc_start: 0.8352 (mttt) cc_final: 0.8075 (mmtm)
REVERT: A  431 GLN cc_start: 0.7909 (tt0) cc_final: 0.7662 (mt0)
  outliers start: 10
  outliers final: 9
  residues processed: 99
  average time/residue: 0.0596
  time to fit residues: 7.2848
Evaluate side-chains
  98 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  335 SER
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 172 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.137371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.124089 restraints weight = 6056.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127756 restraints weight = 3285.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.130288 restraints weight = 2011.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.131949 restraints weight = 1325.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.133168 restraints weight = 931.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3310  Z= 0.145
  Angle     :  0.734  15.692   4583  Z= 0.341
  Chirality :  0.038   0.194    585
  Planarity :  0.004   0.040    518
  Dihedral  :  5.431  51.013    891
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 25.73 %
    Favored  : 71.34 %
  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:  3.16 (0.43), residues: 393
  helix:  2.57 (0.28), residues: 334
  sheet:  None (None), residues: 0
  loop : -0.94 (0.84), residues: 59

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 151 
 TYR   0.034   0.002   TYR A 366 
 PHE   0.022   0.001   PHE A 103 
 TRP   0.007   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 3310)
  covalent geometry    : angle       0.73429 ( 4583)
  hydrogen bonds       : bond        0.04387 (  244)
  hydrogen bonds       : angle       4.06910 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 0.117 
Fit side-chains
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8735 (t80) cc_final: 0.8164 (t80)
REVERT: A  133 ARG cc_start: 0.8449 (mtt180) cc_final: 0.7951 (mtt90)
REVERT: A  134 ILE cc_start: 0.9191 (pt) cc_final: 0.8976 (mt)
REVERT: A  336 LYS cc_start: 0.8370 (mttt) cc_final: 0.8073 (mmtm)
REVERT: A  431 GLN cc_start: 0.7862 (tt0) cc_final: 0.7619 (mt0)
  outliers start: 9
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0579
  time to fit residues: 6.9902
Evaluate side-chains
  100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  421 VAL
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 12 optimal weight:    1.9990
   chunk 3 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 31 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 172 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.140035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126596 restraints weight = 5914.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.130321 restraints weight = 3191.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.132890 restraints weight = 1960.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134622 restraints weight = 1290.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.135819 restraints weight = 892.071|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.4821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3310  Z= 0.131
  Angle     :  0.728  16.346   4583  Z= 0.338
  Chirality :  0.038   0.186    585
  Planarity :  0.004   0.040    518
  Dihedral  :  5.176  50.874    891
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 26.38 %
    Favored  : 71.01 %
  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:  3.19 (0.43), residues: 393
  helix:  2.58 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.89 (0.82), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  42 
 TYR   0.011   0.001   TYR A 366 
 PHE   0.019   0.001   PHE A 103 
 TRP   0.009   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A 289 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3310)
  covalent geometry    : angle       0.72759 ( 4583)
  hydrogen bonds       : bond        0.04200 (  244)
  hydrogen bonds       : angle       3.97627 (  732)

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

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

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  786 Ramachandran restraints generated.
    393 Oldfield, 0 Emsley, 393 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 92
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8333 (mtm-85) cc_final: 0.7846 (mtm-85)
REVERT: A   51 TYR cc_start: 0.8669 (t80) cc_final: 0.8089 (t80)
REVERT: A  133 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8047 (mtt90)
REVERT: A  172 GLN cc_start: 0.7538 (OUTLIER) cc_final: 0.7236 (tp40)
REVERT: A  336 LYS cc_start: 0.8339 (mttt) cc_final: 0.8084 (mmtm)
  outliers start: 8
  outliers final: 5
  residues processed: 98
  average time/residue: 0.0645
  time to fit residues: 7.6302
Evaluate side-chains
  92 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 86
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 GLN
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  203 LEU
Chi-restraints excluded: chain A residue  284 VAL
Chi-restraints excluded: chain A residue  337 LEU
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 35 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 120 GLN ** 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 = 0.3765 r_free = 0.3765 target = 0.140666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.126810 restraints weight = 6063.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.130643 restraints weight = 3293.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.133113 restraints weight = 2020.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134853 restraints weight = 1349.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.136201 restraints weight = 955.953|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7547
moved from start:          0.4896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.323   3310  Z= 0.488
  Angle     :  1.395  65.757   4583  Z= 0.827
  Chirality :  0.041   0.461    585
  Planarity :  0.013   0.292    518
  Dihedral  :  5.178  50.861    891
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 28.01 %
    Favored  : 69.71 %
  Cbeta Deviations :  0.27 %
  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:  3.16 (0.43), residues: 393
  helix:  2.56 (0.28), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.90 (0.81), residues: 58

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  61 
 TYR   0.007   0.001   TYR A  35 
 PHE   0.028   0.001   PHE A 141 
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 

Details of bonding type rmsd
  covalent geometry    : bond        0.01080 ( 3310)
  covalent geometry    : angle       1.39473 ( 4583)
  hydrogen bonds       : bond        0.04208 (  244)
  hydrogen bonds       : angle       3.98676 (  732)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 658.52 seconds
wall clock time: 11 minutes 59.74 seconds (719.74 seconds total)