Starting phenix.real_space_refine
on Tue Feb 11 01:58:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tx7_26156/02_2025/7tx7_26156.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tx7_26156/02_2025/7tx7_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_26156/02_2025/7tx7_26156.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tx7_26156/02_2025/7tx7_26156.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tx7_26156/02_2025/7tx7_26156.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tx7_26156/02_2025/7tx7_26156.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'GLN:plan1': 1, 'ASP:plan': 3, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 1, 'ARG:plan': 11}
          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: 2.79, per 1000 atoms: 0.87
  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: 1.07
  Conformation dependent library (CDL) restraints added in 387.6 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: 0.26
  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: 0.90

  Time building geometry restraints manager: 1.14 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:             0.350
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     12.980
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.540
-------------------------------------------------------------------------------
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= 0.501
  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 : 6.28
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.77 (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
 TRP   0.007   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 118 
 PHE   0.007   0.001   PHE A 405 
 TYR   0.011   0.001   TYR A  35 
 ARG   0.001   0.000   ARG A 268 

*********************** 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  : 0.324 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8750 (t80) cc_final: 0.8369 (t80)
REVERT: A  133 ARG cc_start: 0.8603 (mtt180) cc_final: 0.8280 (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: 0.8129 (t0)
REVERT: A  305 TYR cc_start: 0.7633 (m-80) cc_final: 0.7299 (m-80)
REVERT: A  431 GLN cc_start: 0.8145 (tt0) cc_final: 0.7930 (tt0)
REVERT: A  440 LEU cc_start: 0.8233 (tt) cc_final: 0.8023 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1675
  time to fit residues: 25.7452
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  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    0.3980
   chunk 35 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.140166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126382 restraints weight = 5978.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.130171 restraints weight = 3224.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.132683 restraints weight = 1967.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7530
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3310  Z= 0.205
  Angle     :  0.734   7.750   4583  Z= 0.331
  Chirality :  0.040   0.203    585
  Planarity :  0.004   0.051    518
  Dihedral  : 12.620 127.437    891
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.59 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.83 (0.43), residues: 393
  helix:  3.00 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop : -0.13 (0.85), residues: 64

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 107 
 HIS   0.002   0.001   HIS A 118 
 PHE   0.018   0.002   PHE A 351 
 TYR   0.015   0.002   TYR A 366 
 ARG   0.006   0.001   ARG A 151 

*********************** 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
  116 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 110
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8789 (t80) cc_final: 0.8089 (t80)
REVERT: A  133 ARG cc_start: 0.8434 (mtt180) cc_final: 0.7615 (mtt90)
REVERT: A  195 PHE cc_start: 0.7390 (t80) cc_final: 0.6563 (t80)
REVERT: A  300 ASN cc_start: 0.8375 (t0) cc_final: 0.8081 (t0)
  outliers start: 6
  outliers final: 6
  residues processed: 113
  average time/residue: 0.1332
  time to fit residues: 18.7218
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  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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
Chi-restraints excluded: chain A residue  428 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 24 optimal weight:    4.9990
   chunk 36 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.139377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125595 restraints weight = 5886.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.129349 restraints weight = 3185.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.131946 restraints weight = 1942.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7536
moved from start:          0.3265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3310  Z= 0.185
  Angle     :  0.622   6.770   4583  Z= 0.298
  Chirality :  0.036   0.118    585
  Planarity :  0.004   0.048    518
  Dihedral  : 10.089 130.761    891
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.27 %
    Favored  : 98.73 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 20.20 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.80 (0.43), residues: 393
  helix:  3.05 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -0.31 (0.82), residues: 69

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 118 
 PHE   0.012   0.001   PHE A 103 
 TYR   0.015   0.002   TYR A  35 
 ARG   0.004   0.000   ARG A 151 

*********************** 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
  107 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   34 PHE cc_start: 0.8981 (t80) cc_final: 0.8766 (t80)
REVERT: A   51 TYR cc_start: 0.8707 (t80) cc_final: 0.7970 (t80)
REVERT: A  133 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7589 (mtt90)
REVERT: A  195 PHE cc_start: 0.7229 (t80) cc_final: 0.6453 (t80)
REVERT: A  300 ASN cc_start: 0.8332 (t0) cc_final: 0.7913 (t0)
REVERT: A  336 LYS cc_start: 0.8378 (mttt) cc_final: 0.8103 (mmtm)
  outliers start: 7
  outliers final: 5
  residues processed: 105
  average time/residue: 0.1273
  time to fit residues: 16.6389
Evaluate side-chains
  97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 92
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
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  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 20 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 31 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.138624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.124738 restraints weight = 5967.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.128555 restraints weight = 3214.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.131061 restraints weight = 1958.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3310  Z= 0.192
  Angle     :  0.627   8.306   4583  Z= 0.301
  Chirality :  0.036   0.126    585
  Planarity :  0.004   0.045    518
  Dihedral  :  9.192 115.678    891
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 17.92 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.63 (0.43), residues: 393
  helix:  2.93 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -0.71 (0.82), residues: 63

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 355 
 PHE   0.014   0.001   PHE A 326 
 TYR   0.020   0.002   TYR A 366 
 ARG   0.004   0.000   ARG A  61 

*********************** 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
  110 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 GLU cc_start: 0.8932 (tt0) cc_final: 0.8588 (tt0)
REVERT: A   51 TYR cc_start: 0.8683 (t80) cc_final: 0.8078 (t80)
REVERT: A  195 PHE cc_start: 0.7205 (t80) cc_final: 0.6383 (t80)
REVERT: A  300 ASN cc_start: 0.8296 (t0) cc_final: 0.8092 (t0)
REVERT: A  336 LYS cc_start: 0.8365 (mttt) cc_final: 0.8078 (mmtm)
  outliers start: 12
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1270
  time to fit residues: 16.6843
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  : 0.348 
-------------------------------------------------------------------------------
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  203 LEU
Chi-restraints excluded: chain A residue  335 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 4 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0370
   chunk 31 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.3436

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.142041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.128019 restraints weight = 5880.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.131868 restraints weight = 3170.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.134454 restraints weight = 1927.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7502
moved from start:          0.4050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3310  Z= 0.167
  Angle     :  0.617   7.425   4583  Z= 0.298
  Chirality :  0.036   0.114    585
  Planarity :  0.004   0.042    518
  Dihedral  :  7.001  73.804    891
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 20.52 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.52 (0.43), residues: 393
  helix:  2.81 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -0.59 (0.85), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A  27 
 PHE   0.029   0.001   PHE A  34 
 TYR   0.025   0.002   TYR A 366 
 ARG   0.003   0.000   ARG A 151 

*********************** 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
  100 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8626 (t80) cc_final: 0.8096 (t80)
REVERT: A  101 LEU cc_start: 0.8892 (mt) cc_final: 0.8611 (mt)
REVERT: A  195 PHE cc_start: 0.7199 (t80) cc_final: 0.6494 (t80)
REVERT: A  300 ASN cc_start: 0.8306 (t0) cc_final: 0.8042 (t0)
REVERT: A  336 LYS cc_start: 0.8282 (mttt) cc_final: 0.8001 (mmtm)
REVERT: A  338 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8100 (tt)
  outliers start: 10
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1393
  time to fit residues: 16.6257
Evaluate side-chains
  89 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  203 LEU
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  428 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 25 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0570
   chunk 21 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5700

-------------------------------------------------------------------------------
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 = 0.3758 r_free = 0.3758 target = 0.140163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126126 restraints weight = 6001.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.130007 restraints weight = 3229.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132638 restraints weight = 1953.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.4258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3310  Z= 0.177
  Angle     :  0.615   7.962   4583  Z= 0.299
  Chirality :  0.036   0.176    585
  Planarity :  0.004   0.040    518
  Dihedral  :  5.533  51.879    891
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 22.15 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.29 (0.43), residues: 393
  helix:  2.69 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -0.92 (0.80), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A 355 
 PHE   0.020   0.001   PHE A  34 
 TYR   0.012   0.001   TYR A  35 
 ARG   0.003   0.000   ARG A  61 

*********************** 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
  97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8633 (t80) cc_final: 0.8149 (t80)
REVERT: A  101 LEU cc_start: 0.8931 (mt) cc_final: 0.8658 (mt)
REVERT: A  133 ARG cc_start: 0.8530 (mtt-85) cc_final: 0.8209 (mtt90)
REVERT: A  300 ASN cc_start: 0.8173 (t0) cc_final: 0.7925 (t0)
REVERT: A  336 LYS cc_start: 0.8314 (mttt) cc_final: 0.8077 (mmtm)
REVERT: A  338 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8067 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 93
  average time/residue: 0.1282
  time to fit residues: 14.8705
Evaluate side-chains
  90 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  203 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  428 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.9380

-------------------------------------------------------------------------------
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 = 0.3727 r_free = 0.3727 target = 0.137788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124195 restraints weight = 5863.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.127958 restraints weight = 3220.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.130522 restraints weight = 1977.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.4424

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= 0.212
  Angle     :  0.651   9.565   4583  Z= 0.315
  Chirality :  0.037   0.172    585
  Planarity :  0.004   0.040    518
  Dihedral  :  5.494  51.616    891
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 21.17 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.31 (0.43), residues: 393
  helix:  2.72 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.05 (0.82), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 355 
 PHE   0.020   0.001   PHE A 103 
 TYR   0.012   0.001   TYR A  92 
 ARG   0.005   0.000   ARG A  61 

*********************** 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
  102 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   51 TYR cc_start: 0.8671 (t80) cc_final: 0.8177 (t80)
REVERT: A   59 PHE cc_start: 0.8304 (OUTLIER) cc_final: 0.7691 (m-80)
REVERT: A  300 ASN cc_start: 0.8231 (t0) cc_final: 0.8012 (t0)
REVERT: A  336 LYS cc_start: 0.8365 (mttt) cc_final: 0.8108 (mmtm)
REVERT: A  338 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.8085 (tt)
  outliers start: 12
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1288
  time to fit residues: 15.5318
Evaluate side-chains
  96 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
Chi-restraints excluded: chain A residue  137 SER
Chi-restraints excluded: chain A residue  194 THR
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  338 LEU
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  394 GLU
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 30 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   chunk 23 optimal weight:    0.0060
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.4996

-------------------------------------------------------------------------------
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 = 0.3760 r_free = 0.3760 target = 0.140275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126458 restraints weight = 5867.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.130242 restraints weight = 3208.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.132718 restraints weight = 1979.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4556

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3310  Z= 0.179
  Angle     :  0.679   9.195   4583  Z= 0.321
  Chirality :  0.038   0.191    585
  Planarity :  0.004   0.041    518
  Dihedral  :  5.311  51.690    891
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 24.43 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.18 (0.43), residues: 393
  helix:  2.63 (0.28), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.03 (0.80), residues: 61

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A 355 
 PHE   0.017   0.001   PHE A 326 
 TYR   0.009   0.001   TYR A  35 
 ARG   0.003   0.000   ARG A  61 

*********************** 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
  99 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8621 (t80) cc_final: 0.8218 (t80)
REVERT: A   72 LEU cc_start: 0.8991 (tt) cc_final: 0.8726 (tt)
REVERT: A   97 LEU cc_start: 0.8628 (tp) cc_final: 0.8335 (tp)
REVERT: A  119 MET cc_start: 0.8676 (mmm) cc_final: 0.8325 (mmm)
REVERT: A  286 TYR cc_start: 0.8653 (m-10) cc_final: 0.8441 (m-10)
REVERT: A  300 ASN cc_start: 0.8232 (t0) cc_final: 0.8015 (t0)
REVERT: A  336 LYS cc_start: 0.8321 (mttt) cc_final: 0.8099 (mmtm)
REVERT: A  338 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8046 (tt)
  outliers start: 7
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1436
  time to fit residues: 17.0805
Evaluate side-chains
  94 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  338 LEU
Chi-restraints excluded: chain A residue  364 LEU
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 10 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 15 optimal weight:    1.9990
   chunk 28 optimal weight:    0.3980
   chunk 2 optimal weight:    0.0470
   chunk 30 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    0.4980
   overall best weight:    0.4478

-------------------------------------------------------------------------------
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 = 0.3769 r_free = 0.3769 target = 0.140374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.126720 restraints weight = 5970.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.130489 restraints weight = 3236.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.133014 restraints weight = 1981.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.4737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3310  Z= 0.184
  Angle     :  0.734  15.793   4583  Z= 0.338
  Chirality :  0.038   0.194    585
  Planarity :  0.004   0.039    518
  Dihedral  :  5.191  51.093    891
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 26.38 %
    Favored  : 70.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.06 (0.43), residues: 393
  helix:  2.47 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.90 (0.82), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 270 
 HIS   0.002   0.001   HIS A 118 
 PHE   0.030   0.001   PHE A  34 
 TYR   0.010   0.001   TYR A  35 
 ARG   0.002   0.000   ARG A  61 

*********************** 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
  103 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8598 (t80) cc_final: 0.8180 (t80)
REVERT: A   59 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7722 (m-80)
REVERT: A   72 LEU cc_start: 0.8956 (tt) cc_final: 0.8735 (tt)
REVERT: A  336 LYS cc_start: 0.8326 (mttt) cc_final: 0.8107 (mmtm)
REVERT: A  338 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8033 (tt)
  outliers start: 9
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1454
  time to fit residues: 17.9924
Evaluate side-chains
  97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 PHE
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  338 LEU
Chi-restraints excluded: chain A residue  364 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 6 optimal weight:    0.0000
   chunk 34 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0870
   chunk 29 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0870
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.3540

-------------------------------------------------------------------------------
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 = 0.3791 r_free = 0.3791 target = 0.142251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.128400 restraints weight = 5783.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.132108 restraints weight = 3174.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.134623 restraints weight = 1966.998|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3310  Z= 0.177
  Angle     :  0.751  17.067   4583  Z= 0.344
  Chirality :  0.038   0.197    585
  Planarity :  0.004   0.039    518
  Dihedral  :  5.061  50.559    891
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 27.69 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.16 (0.43), residues: 393
  helix:  2.54 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.96 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 270 
 HIS   0.001   0.000   HIS A 289 
 PHE   0.027   0.001   PHE A  34 
 TYR   0.038   0.001   TYR A 366 
 ARG   0.002   0.000   ARG A  61 

********************** 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
  97 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 90
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 TYR cc_start: 0.8580 (t80) cc_final: 0.8170 (t80)
REVERT: A   72 LEU cc_start: 0.8944 (tt) cc_final: 0.8729 (tt)
REVERT: A  336 LYS cc_start: 0.8323 (mttt) cc_final: 0.8064 (mmtm)
REVERT: A  338 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.8011 (tt)
  outliers start: 7
  outliers final: 6
  residues processed: 95
  average time/residue: 0.1428
  time to fit residues: 16.5948
Evaluate side-chains
  93 residues out of total 341 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 SER
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  338 LEU
Chi-restraints excluded: chain A residue  364 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 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 11 optimal weight:    0.0050
   chunk 1 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0980
   chunk 33 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.4794

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.141906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.128161 restraints weight = 5862.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.131861 restraints weight = 3201.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134289 restraints weight = 1975.843|
|-----------------------------------------------------------------------------|
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.5031

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= 0.183
  Angle     :  0.755  16.253   4583  Z= 0.347
  Chirality :  0.038   0.196    585
  Planarity :  0.004   0.038    518
  Dihedral  :  5.040  49.830    891
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 27.36 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.12 (0.43), residues: 393
  helix:  2.51 (0.28), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.93 (0.80), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 107 
 HIS   0.001   0.000   HIS A 355 
 PHE   0.028   0.001   PHE A  34 
 TYR   0.008   0.001   TYR A  35 
 ARG   0.002   0.000   ARG A 268 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1290.76 seconds
wall clock time: 23 minutes 43.18 seconds (1423.18 seconds total)