Starting phenix.real_space_refine
on Tue Feb  3 14:39:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j06_61050/02_2026/9j06_61050.map"
  }
  resolution = 3.68
  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=   0.001 sd=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     S      31      5.16       5
     Cl      1      4.86       5
     C    2465      2.51       5
     N     639      2.21       5
     O     661      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3797
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3764
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3764
          Classifications: {'peptide': 488}
          Link IDs: {'PTRANS': 26, 'TRANS': 461}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'GBM': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.10, per 1000 atoms: 0.29
  Number of scatterers: 3797
  At special positions: 0
  Unit cell: (103.7, 56.1, 68.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      31     16.00
     O     661      8.00
     N     639      7.00
     C    2465      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: 0.30
  Conformation dependent library (CDL) restraints added in 92.7 milliseconds
  

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  904

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 1 sheets defined
      77.3% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 11
    Processing helix  chain 'A' and resid 14 through 26
      removed outlier: 4.336A  pdb=" N   THR A  22 " --> pdb=" O   GLN A  18 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 27 through 29
      No H-bonds generated for 'chain 'A' and resid 27 through 29'
    Processing helix  chain 'A' and resid 30 through 36
    Processing helix  chain 'A' and resid 119 through 125
    Processing helix  chain 'A' and resid 131 through 155
      removed outlier: 4.588A  pdb=" N   GLN A 135 " --> pdb=" O   ARG A 131 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   VAL A 145 " --> pdb=" O   TYR A 141 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 146 " --> pdb=" O   MET A 142 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 4.489A  pdb=" N   GLY A 148 " --> pdb=" O   GLY A 144 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 160
      removed outlier: 3.621A  pdb=" N   GLY A 160 " --> pdb=" O   ALA A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 178
      removed outlier: 3.571A  pdb=" N   ALA A 173 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   GLY A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   CYS A 178 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 182
    Processing helix  chain 'A' and resid 184 through 214
      removed outlier: 3.567A  pdb=" N   TYR A 188 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLY A 201 " --> pdb=" O   MET A 197 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   MET A 207 " --> pdb=" O   SER A 203 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   TRP A 213 " --> pdb=" O   LEU A 209 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   MET A 214 " --> pdb=" O   ASN A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 217
      No H-bonds generated for 'chain 'A' and resid 215 through 217'
    Processing helix  chain 'A' and resid 218 through 232
      removed outlier: 4.158A  pdb=" N   VAL A 222 " --> pdb=" O   THR A 218 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   GLY A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 244
      removed outlier: 3.762A  pdb=" N   LEU A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 256
    Processing helix  chain 'A' and resid 256 through 264
      removed outlier: 4.222A  pdb=" N   ALA A 260 " --> pdb=" O   ALA A 256 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR A 264 " --> pdb=" O   ALA A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 279
    Processing helix  chain 'A' and resid 280 through 296
      removed outlier: 3.841A  pdb=" N   THR A 284 " --> pdb=" O   ARG A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 325 through 330
      removed outlier: 3.682A  pdb=" N   LEU A 329 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 357
      removed outlier: 3.904A  pdb=" N   LEU A 338 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   CYS A 341 " --> pdb=" O   HIS A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 376
      removed outlier: 3.552A  pdb=" N   VAL A 372 " --> pdb=" O   TYR A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 392
      removed outlier: 3.803A  pdb=" N   LEU A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   ASN A 390 " --> pdb=" O   PHE A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 412
      removed outlier: 3.556A  pdb=" N   ASN A 412 " --> pdb=" O   CYS A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 421 through 449
      removed outlier: 3.755A  pdb=" N   LEU A 443 " --> pdb=" O   ASN A 439 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TYR A 449 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 477
      removed outlier: 3.893A  pdb=" N   ARG A 466 " --> pdb=" O   SER A 462 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   VAL A 467 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLY A 468 " --> pdb=" O   MET A 464 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   SER A 469 " --> pdb=" O   ALA A 465 " (cutoff:3.500A)
      Proline residue:  A 473  - end of helix
      removed outlier: 3.706A  pdb=" N   MET A 477 " --> pdb=" O   PRO A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 481
    Processing helix  chain 'A' and resid 484 through 499
      removed outlier: 3.693A  pdb=" N   VAL A 493 " --> pdb=" O   ILE A 489 " (cutoff:3.500A)
      Proline residue:  A 494  - end of helix
      removed outlier: 3.860A  pdb=" N   ALA A 499 " --> pdb=" O   VAL A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 504
      removed outlier: 3.506A  pdb=" N   LEU A 503 " --> pdb=" O   VAL A 500 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LEU A 504 " --> pdb=" O   THR A 501 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 500 through 504'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
      removed outlier: 3.720A  pdb=" N   HIS A  48 " --> pdb=" O   ILE A 110 " (cutoff:3.500A)

    220 hydrogen bonds defined for protein.
    648 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: 0.54

  Time building geometry restraints manager: 0.38 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 581
        1.31 -     1.43: 1061
        1.43 -     1.56: 2195
        1.56 -     1.69: 0
        1.69 -     1.82: 50
  Bond restraints: 3887
  Sorted by residual:
  bond pdb=" C17 GBM A 601 "
       pdb=" N8  GBM A 601 "
    ideal  model  delta    sigma   weight residual
    1.340  1.457 -0.117 2.00e-02 2.50e+03 3.43e+01
  bond pdb=" C26 GBM A 601 "
       pdb=" N10 GBM A 601 "
    ideal  model  delta    sigma   weight residual
    1.342  1.452 -0.110 2.00e-02 2.50e+03 3.04e+01
  bond pdb=" N   SER A 472 "
       pdb=" CA  SER A 472 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 7.70e-03 1.69e+04 1.19e+01
  bond pdb=" C17 GBM A 601 "
       pdb=" N9  GBM A 601 "
    ideal  model  delta    sigma   weight residual
    1.394  1.457 -0.063 2.00e-02 2.50e+03 9.93e+00
  bond pdb=" C28 GBM A 601 "
       pdb=" O7  GBM A 601 "
    ideal  model  delta    sigma   weight residual
    1.339  1.400 -0.061 2.00e-02 2.50e+03 9.33e+00
  ... (remaining 3882 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.77: 5249
        3.77 -     7.54: 39
        7.54 -    11.31: 2
       11.31 -    15.08: 0
       15.08 -    18.85: 1
  Bond angle restraints: 5291
  Sorted by residual:
  angle pdb=" O4  GBM A 601 "
        pdb=" S2  GBM A 601 "
        pdb=" O5  GBM A 601 "
      ideal   model   delta    sigma   weight residual
     119.60  100.75   18.85 3.00e+00 1.11e-01 3.95e+01
  angle pdb=" CA  GLY A 108 "
        pdb=" C   GLY A 108 "
        pdb=" O   GLY A 108 "
      ideal   model   delta    sigma   weight residual
     121.75  116.58    5.17 1.02e+00 9.61e-01 2.57e+01
  angle pdb=" CA  LEU A 474 "
        pdb=" C   LEU A 474 "
        pdb=" O   LEU A 474 "
      ideal   model   delta    sigma   weight residual
     120.82  115.67    5.15 1.05e+00 9.07e-01 2.41e+01
  angle pdb=" CA  GLN A 419 "
        pdb=" C   GLN A 419 "
        pdb=" O   GLN A 419 "
      ideal   model   delta    sigma   weight residual
     121.87  116.70    5.17 1.16e+00 7.43e-01 1.99e+01
  angle pdb=" N   VAL A 145 "
        pdb=" CA  VAL A 145 "
        pdb=" C   VAL A 145 "
      ideal   model   delta    sigma   weight residual
     111.90  108.51    3.39 8.10e-01 1.52e+00 1.75e+01
  ... (remaining 5286 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.04: 2206
       35.04 -    70.07: 76
       70.07 -   105.11: 8
      105.11 -   140.15: 2
      140.15 -   175.19: 2
  Dihedral angle restraints: 2294
    sinusoidal: 890
      harmonic: 1404
  Sorted by residual:
  dihedral pdb=" C13 GBM A 601 "
           pdb=" C11 GBM A 601 "
           pdb=" N8  GBM A 601 "
           pdb=" C17 GBM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      77.89 -106.92 -175.19     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C23 GBM A 601 "
           pdb=" C19 GBM A 601 "
           pdb=" C20 GBM A 601 "
           pdb=" C25 GBM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     269.70   99.44  170.26     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C15 GBM A 601 "
           pdb=" C11 GBM A 601 "
           pdb=" C13 GBM A 601 "
           pdb=" N8  GBM A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     181.51   68.63  112.88     1      3.00e+01 1.11e-03 1.48e+01
  ... (remaining 2291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.008: 613
       1.008 -    2.016: 0
       2.016 -    3.024: 0
       3.024 -    4.033: 0
       4.033 -    5.041: 1
  Chirality restraints: 614
  Sorted by residual:
  chirality pdb=" C11 GBM A 601 "
            pdb=" C12 GBM A 601 "
            pdb=" C13 GBM A 601 "
            pdb=" N8  GBM A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48   -2.56    5.04 2.00e-01 2.50e+01 6.35e+02
  chirality pdb=" CG  LEU A 199 "
            pdb=" CB  LEU A 199 "
            pdb=" CD1 LEU A 199 "
            pdb=" CD2 LEU A 199 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  GLN A 419 "
            pdb=" N   GLN A 419 "
            pdb=" C   GLN A 419 "
            pdb=" CB  GLN A 419 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.68   -0.17 2.00e-01 2.50e+01 7.23e-01
  ... (remaining 611 not shown)

  Planarity restraints: 662
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A   3 "   -0.013 2.00e-02 2.50e+03   1.56e-02 4.25e+00
        pdb=" CG  PHE A   3 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 PHE A   3 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE A   3 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE A   3 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A   3 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A   3 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 395 "    0.028 5.00e-02 4.00e+02   4.17e-02 2.79e+00
        pdb=" N   PRO A 396 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 396 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 396 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 108 "    0.007 2.00e-02 2.50e+03   1.44e-02 2.08e+00
        pdb=" C   GLY A 108 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   GLY A 108 "    0.009 2.00e-02 2.50e+03
        pdb=" N   TRP A 109 "    0.009 2.00e-02 2.50e+03
  ... (remaining 659 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 762
        2.78 -     3.31: 3824
        3.31 -     3.84: 6028
        3.84 -     4.37: 6678
        4.37 -     4.90: 11581
  Nonbonded interactions: 28873
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 362 "
            pdb=" NH2 ARG A 423 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OD1 ASP A  70 "
            pdb=" N   ARG A  71 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" N   ASP A 282 "
            pdb=" OD1 ASP A 282 "
     model   vdw
     2.390 3.120
  nonbonded pdb=" OG1 THR A 515 "
            pdb=" OE1 GLN A 517 "
     model   vdw
     2.401 3.040
  nonbonded pdb=" N   GLN A 517 "
            pdb=" OE1 GLN A 517 "
     model   vdw
     2.401 3.120
  ... (remaining 28868 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.290
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.830
  Find NCS groups from input model:        0.010
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
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      :  0.005   0.117   3887  Z= 0.288
  Angle     :  0.844  18.854   5291  Z= 0.450
  Chirality :  0.207   5.041    614
  Planarity :  0.004   0.042    662
  Dihedral  : 18.306 175.185   1390
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 22.22 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.41), residues: 480
  helix:  0.80 (0.30), residues: 326
  sheet:  None (None), residues: 0
  loop : -0.86 (0.55), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  71 
 TYR   0.017   0.002   TYR A 230 
 PHE   0.036   0.001   PHE A   3 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.003   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00523 ( 3887)
  covalent geometry    : angle       0.84359 ( 5291)
  hydrogen bonds       : bond        0.18365 (  220)
  hydrogen bonds       : angle       5.32394 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9326 (tt0) cc_final: 0.8757 (tm-30)
REVERT: A  124 TRP cc_start: 0.8305 (m-90) cc_final: 0.7727 (m-10)
REVERT: A  159 LEU cc_start: 0.9157 (mm) cc_final: 0.8790 (tt)
REVERT: A  507 THR cc_start: 0.9035 (m) cc_final: 0.8797 (m)
  outliers start: 3
  outliers final: 0
  residues processed: 108
  average time/residue: 0.0674
  time to fit residues: 9.1066
Evaluate side-chains
  98 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:   10.0000
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A 337 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.138621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.101985 restraints weight = 6679.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.105468 restraints weight = 3522.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.107743 restraints weight = 2391.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109010 restraints weight = 1901.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.109878 restraints weight = 1671.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3887  Z= 0.136
  Angle     :  0.707  12.245   5291  Z= 0.325
  Chirality :  0.039   0.128    614
  Planarity :  0.005   0.048    662
  Dihedral  : 12.207 163.701    545
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.22 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.40), residues: 480
  helix:  0.85 (0.30), residues: 332
  sheet:  None (None), residues: 0
  loop : -1.01 (0.56), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 336 
 TYR   0.019   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A   3 
 TRP   0.016   0.001   TRP A  66 
 HIS   0.002   0.001   HIS A 337 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 3887)
  covalent geometry    : angle       0.70650 ( 5291)
  hydrogen bonds       : bond        0.04942 (  220)
  hydrogen bonds       : angle       4.01919 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9292 (tt0) cc_final: 0.8759 (tm-30)
REVERT: A   69 ARG cc_start: 0.8668 (ptp90) cc_final: 0.8389 (mtm180)
REVERT: A  336 ARG cc_start: 0.9144 (OUTLIER) cc_final: 0.8821 (ptt-90)
REVERT: A  438 PHE cc_start: 0.7198 (OUTLIER) cc_final: 0.6768 (t80)
REVERT: A  507 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8752 (m)
REVERT: A  517 GLN cc_start: 0.8913 (mp10) cc_final: 0.8659 (mp10)
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 0.0516
  time to fit residues: 7.6144
Evaluate side-chains
  109 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  507 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9980
   chunk 32 optimal weight:    0.1980
   chunk 39 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A  48 HIS
A 168 ASN
A 337 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.137706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.100681 restraints weight = 6559.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.104088 restraints weight = 3508.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.106227 restraints weight = 2410.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.107169 restraints weight = 1935.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.107993 restraints weight = 1737.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.1955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3887  Z= 0.131
  Angle     :  0.678  13.563   5291  Z= 0.313
  Chirality :  0.039   0.130    614
  Planarity :  0.004   0.037    662
  Dihedral  : 10.713 159.595    545
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 22.72 %
    Favored  : 71.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.40), residues: 480
  helix:  0.94 (0.30), residues: 333
  sheet:  None (None), residues: 0
  loop : -0.90 (0.56), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 336 
 TYR   0.014   0.001   TYR A 490 
 PHE   0.008   0.001   PHE A 351 
 TRP   0.017   0.002   TRP A 124 
 HIS   0.002   0.001   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 3887)
  covalent geometry    : angle       0.67753 ( 5291)
  hydrogen bonds       : bond        0.04401 (  220)
  hydrogen bonds       : angle       3.83256 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9375 (tt0) cc_final: 0.8969 (tm-30)
REVERT: A   10 VAL cc_start: 0.9587 (p) cc_final: 0.9219 (p)
REVERT: A   69 ARG cc_start: 0.8680 (ptp90) cc_final: 0.8380 (mtm180)
REVERT: A   76 GLU cc_start: 0.8193 (tp30) cc_final: 0.7304 (tm-30)
REVERT: A  336 ARG cc_start: 0.9199 (OUTLIER) cc_final: 0.8638 (ptt-90)
REVERT: A  438 PHE cc_start: 0.7260 (OUTLIER) cc_final: 0.6827 (t80)
REVERT: A  507 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8760 (m)
REVERT: A  517 GLN cc_start: 0.8961 (mp10) cc_final: 0.8704 (mp10)
  outliers start: 23
  outliers final: 16
  residues processed: 110
  average time/residue: 0.0429
  time to fit residues: 6.2221
Evaluate side-chains
  122 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 103
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    0.2980
   chunk 2 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0770
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.3980
   chunk 27 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0870
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.2916

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

Flipped N/Q/H residues before XYZ refinement:
A 168 ASN
A 371 GLN
A 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.139995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.103256 restraints weight = 6451.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.106815 restraints weight = 3347.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.109109 restraints weight = 2256.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110356 restraints weight = 1793.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.111285 restraints weight = 1580.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3887  Z= 0.112
  Angle     :  0.651  11.959   5291  Z= 0.298
  Chirality :  0.038   0.121    614
  Planarity :  0.004   0.033    662
  Dihedral  :  9.969 156.505    545
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 25.43 %
    Favored  : 69.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.40), residues: 480
  helix:  1.02 (0.30), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.84 (0.56), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 336 
 TYR   0.018   0.002   TYR A 242 
 PHE   0.008   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 3887)
  covalent geometry    : angle       0.65122 ( 5291)
  hydrogen bonds       : bond        0.03668 (  220)
  hydrogen bonds       : angle       3.69945 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9420 (tt0) cc_final: 0.8883 (tm-30)
REVERT: A   69 ARG cc_start: 0.8654 (ptp90) cc_final: 0.8367 (mtm180)
REVERT: A   76 GLU cc_start: 0.8303 (tp30) cc_final: 0.7519 (tm-30)
REVERT: A  285 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9339 (pp)
REVERT: A  297 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7680 (mmmm)
REVERT: A  438 PHE cc_start: 0.7139 (OUTLIER) cc_final: 0.6787 (t80)
REVERT: A  507 THR cc_start: 0.8999 (OUTLIER) cc_final: 0.8789 (m)
REVERT: A  517 GLN cc_start: 0.8935 (mp10) cc_final: 0.8694 (mp10)
  outliers start: 21
  outliers final: 14
  residues processed: 122
  average time/residue: 0.0506
  time to fit residues: 8.0440
Evaluate side-chains
  122 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0030
   chunk 14 optimal weight:    0.9990
   chunk 12 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:   10.0000
   chunk 31 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0980
   overall best weight:    0.3390

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A 168 ASN
A 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.139725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.102947 restraints weight = 6458.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.106485 restraints weight = 3365.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.108780 restraints weight = 2270.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.109883 restraints weight = 1804.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.110799 restraints weight = 1599.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   3887  Z= 0.113
  Angle     :  0.668   9.846   5291  Z= 0.304
  Chirality :  0.039   0.119    614
  Planarity :  0.004   0.032    662
  Dihedral  :  9.499 156.889    545
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 25.43 %
    Favored  : 69.14 %
  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:  0.78 (0.41), residues: 480
  helix:  1.11 (0.30), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.75 (0.57), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 336 
 TYR   0.011   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A   3 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 3887)
  covalent geometry    : angle       0.66760 ( 5291)
  hydrogen bonds       : bond        0.03553 (  220)
  hydrogen bonds       : angle       3.67643 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 104
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9415 (tt0) cc_final: 0.8881 (tm-30)
REVERT: A   69 ARG cc_start: 0.8685 (ptp90) cc_final: 0.8382 (mtm180)
REVERT: A   76 GLU cc_start: 0.8321 (tp30) cc_final: 0.7497 (tm-30)
REVERT: A  237 LEU cc_start: 0.8475 (tp) cc_final: 0.7920 (tt)
REVERT: A  285 LEU cc_start: 0.9590 (tt) cc_final: 0.9333 (pp)
REVERT: A  297 LYS cc_start: 0.7929 (mmtm) cc_final: 0.7513 (mmmm)
REVERT: A  336 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8625 (ptt-90)
REVERT: A  438 PHE cc_start: 0.7175 (OUTLIER) cc_final: 0.6899 (t80)
REVERT: A  507 THR cc_start: 0.8973 (OUTLIER) cc_final: 0.8760 (m)
REVERT: A  517 GLN cc_start: 0.8958 (mp10) cc_final: 0.8744 (mp10)
  outliers start: 22
  outliers final: 15
  residues processed: 115
  average time/residue: 0.0542
  time to fit residues: 8.2032
Evaluate side-chains
  119 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 19 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0050
   chunk 38 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0670
   chunk 1 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   overall best weight:    0.3932

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
A   8 GLN
A 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.141889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.104877 restraints weight = 6485.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.108335 restraints weight = 3403.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.110515 restraints weight = 2311.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.111699 restraints weight = 1851.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.112256 restraints weight = 1642.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3887  Z= 0.108
  Angle     :  0.637   8.733   5291  Z= 0.296
  Chirality :  0.038   0.120    614
  Planarity :  0.004   0.028    662
  Dihedral  :  9.299 157.987    545
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 26.42 %
    Favored  : 67.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.41), residues: 480
  helix:  1.17 (0.30), residues: 335
  sheet:  None (None), residues: 0
  loop : -0.68 (0.58), residues: 145

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.014   0.001   TYR A 169 
 PHE   0.007   0.001   PHE A 351 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 3887)
  covalent geometry    : angle       0.63658 ( 5291)
  hydrogen bonds       : bond        0.03499 (  220)
  hydrogen bonds       : angle       3.67817 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   18 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.8306 (mp10)
REVERT: A   69 ARG cc_start: 0.8686 (ptp90) cc_final: 0.8362 (mtm180)
REVERT: A   76 GLU cc_start: 0.8355 (tp30) cc_final: 0.7519 (tm-30)
REVERT: A  285 LEU cc_start: 0.9574 (tt) cc_final: 0.9347 (pp)
REVERT: A  336 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8645 (ptt-90)
REVERT: A  438 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: A  454 ARG cc_start: 0.8499 (ttm170) cc_final: 0.8175 (ttm-80)
REVERT: A  507 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8775 (m)
REVERT: A  517 GLN cc_start: 0.8966 (mp10) cc_final: 0.8740 (mp10)
  outliers start: 24
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0551
  time to fit residues: 8.3403
Evaluate side-chains
  122 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 102
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  507 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    0.0020
   chunk 45 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.6988

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

Flipped N/Q/H residues before XYZ refinement:
A   8 GLN
A 398 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.140116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.103592 restraints weight = 6581.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.107117 restraints weight = 3342.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109235 restraints weight = 2229.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.110679 restraints weight = 1772.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.111275 restraints weight = 1542.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3887  Z= 0.120
  Angle     :  0.686  12.803   5291  Z= 0.315
  Chirality :  0.040   0.140    614
  Planarity :  0.004   0.031    662
  Dihedral  :  9.259 160.439    545
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  6.91 %
    Allowed  : 26.91 %
    Favored  : 66.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.41), residues: 480
  helix:  1.13 (0.30), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.60 (0.59), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.016   0.001   TYR A 490 
 PHE   0.011   0.001   PHE A   3 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.001   0.000   HIS A 246 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 3887)
  covalent geometry    : angle       0.68605 ( 5291)
  hydrogen bonds       : bond        0.03821 (  220)
  hydrogen bonds       : angle       3.76161 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 110
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9394 (tt0) cc_final: 0.9035 (tm-30)
REVERT: A   18 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8306 (mp10)
REVERT: A   76 GLU cc_start: 0.8377 (tp30) cc_final: 0.7535 (tm-30)
REVERT: A  213 TRP cc_start: 0.8531 (m100) cc_final: 0.8260 (m100)
REVERT: A  285 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9307 (pp)
REVERT: A  336 ARG cc_start: 0.9158 (OUTLIER) cc_final: 0.8642 (ptt-90)
REVERT: A  433 CYS cc_start: 0.8349 (OUTLIER) cc_final: 0.8115 (t)
REVERT: A  438 PHE cc_start: 0.7283 (OUTLIER) cc_final: 0.7004 (t80)
REVERT: A  454 ARG cc_start: 0.8479 (ttm170) cc_final: 0.8233 (ttm-80)
REVERT: A  517 GLN cc_start: 0.8944 (mp10) cc_final: 0.8736 (mp10)
  outliers start: 28
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0527
  time to fit residues: 8.4050
Evaluate side-chains
  130 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   28 LEU
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 27 optimal weight:    7.9990
   chunk 14 optimal weight:    1.9990
   chunk 10 optimal weight:    0.3980
   chunk 46 optimal weight:    0.0470
   chunk 12 optimal weight:    0.5980
   chunk 19 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.139475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.103355 restraints weight = 6462.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.106879 restraints weight = 3314.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.109096 restraints weight = 2209.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.110310 restraints weight = 1748.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.110730 restraints weight = 1535.112|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3094

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3887  Z= 0.123
  Angle     :  0.744  11.320   5291  Z= 0.343
  Chirality :  0.040   0.136    614
  Planarity :  0.004   0.031    662
  Dihedral  :  9.191 160.579    545
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.14 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.41), residues: 480
  helix:  1.03 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.53 (0.60), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.016   0.001   TYR A 490 
 PHE   0.009   0.001   PHE A   3 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 3887)
  covalent geometry    : angle       0.74384 ( 5291)
  hydrogen bonds       : bond        0.03772 (  220)
  hydrogen bonds       : angle       3.87715 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9398 (tt0) cc_final: 0.8933 (tm-30)
REVERT: A   18 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8286 (mp10)
REVERT: A   76 GLU cc_start: 0.8357 (tp30) cc_final: 0.7496 (tm-30)
REVERT: A  285 LEU cc_start: 0.9553 (tt) cc_final: 0.9326 (pp)
REVERT: A  336 ARG cc_start: 0.9147 (OUTLIER) cc_final: 0.8507 (ptt-90)
REVERT: A  433 CYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8122 (t)
REVERT: A  438 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7052 (t80)
REVERT: A  454 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8181 (ttm-80)
REVERT: A  517 GLN cc_start: 0.8957 (mp10) cc_final: 0.8741 (mp10)
  outliers start: 21
  outliers final: 15
  residues processed: 120
  average time/residue: 0.0499
  time to fit residues: 7.8120
Evaluate side-chains
  125 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 106
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 9 optimal weight:    0.3980
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0670
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.6722

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.140092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.101561 restraints weight = 6728.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.105239 restraints weight = 3521.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.107467 restraints weight = 2368.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.108581 restraints weight = 1894.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.109405 restraints weight = 1690.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3546
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3887  Z= 0.128
  Angle     :  0.764  14.652   5291  Z= 0.343
  Chirality :  0.040   0.168    614
  Planarity :  0.004   0.030    662
  Dihedral  :  9.086 161.507    545
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 28.64 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.41), residues: 480
  helix:  1.01 (0.29), residues: 338
  sheet:  None (None), residues: 0
  loop : -0.46 (0.61), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.011   0.001   TYR A 169 
 PHE   0.008   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A  66 
 HIS   0.001   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3887)
  covalent geometry    : angle       0.76352 ( 5291)
  hydrogen bonds       : bond        0.03875 (  220)
  hydrogen bonds       : angle       3.98376 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9430 (tt0) cc_final: 0.8996 (tm-30)
REVERT: A   18 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8302 (mp10)
REVERT: A   76 GLU cc_start: 0.8387 (tp30) cc_final: 0.7521 (tm-30)
REVERT: A  237 LEU cc_start: 0.8568 (tp) cc_final: 0.7988 (tt)
REVERT: A  285 LEU cc_start: 0.9562 (tt) cc_final: 0.9336 (pp)
REVERT: A  336 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8489 (ptt-90)
REVERT: A  433 CYS cc_start: 0.8340 (OUTLIER) cc_final: 0.8110 (t)
REVERT: A  438 PHE cc_start: 0.7386 (OUTLIER) cc_final: 0.7075 (t80)
REVERT: A  454 ARG cc_start: 0.8526 (ttm170) cc_final: 0.7984 (ttm170)
  outliers start: 22
  outliers final: 16
  residues processed: 116
  average time/residue: 0.0408
  time to fit residues: 6.3118
Evaluate side-chains
  124 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 29 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9990
   chunk 46 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 7 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A   4 ASN
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 168 ASN
A 398 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.140628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.102171 restraints weight = 6726.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.105876 restraints weight = 3493.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.107944 restraints weight = 2352.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.109339 restraints weight = 1893.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.109888 restraints weight = 1670.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.3363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3887  Z= 0.130
  Angle     :  0.799  12.810   5291  Z= 0.362
  Chirality :  0.041   0.155    614
  Planarity :  0.004   0.029    662
  Dihedral  :  8.930 161.188    545
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 29.14 %
    Favored  : 65.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.82 (0.41), residues: 480
  helix:  1.04 (0.30), residues: 337
  sheet:  None (None), residues: 0
  loop : -0.51 (0.60), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.016   0.001   TYR A 169 
 PHE   0.009   0.001   PHE A 351 
 TRP   0.011   0.001   TRP A 213 
 HIS   0.001   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 3887)
  covalent geometry    : angle       0.79869 ( 5291)
  hydrogen bonds       : bond        0.03861 (  220)
  hydrogen bonds       : angle       4.04408 (  648)

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

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

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  960 Ramachandran restraints generated.
    480 Oldfield, 0 Emsley, 480 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    9 GLN cc_start: 0.9426 (tt0) cc_final: 0.8968 (tm-30)
REVERT: A   18 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8281 (mp10)
REVERT: A   76 GLU cc_start: 0.8382 (tp30) cc_final: 0.7510 (tm-30)
REVERT: A  285 LEU cc_start: 0.9558 (tt) cc_final: 0.9335 (pp)
REVERT: A  336 ARG cc_start: 0.9156 (OUTLIER) cc_final: 0.8346 (ptt180)
REVERT: A  433 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8107 (t)
REVERT: A  438 PHE cc_start: 0.7392 (OUTLIER) cc_final: 0.7120 (t80)
REVERT: A  454 ARG cc_start: 0.8549 (ttm170) cc_final: 0.8009 (ttm170)
  outliers start: 22
  outliers final: 17
  residues processed: 115
  average time/residue: 0.0495
  time to fit residues: 7.4671
Evaluate side-chains
  127 residues out of total 405 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   18 GLN
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   65 VAL
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  206 CYS
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  343 SER
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  409 ILE
Chi-restraints excluded: chain A residue  433 CYS
Chi-restraints excluded: chain A residue  438 PHE
Chi-restraints excluded: chain A residue  440 CYS
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  501 THR
Chi-restraints excluded: chain A residue  516 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0970
   chunk 25 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0070
   chunk 39 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.4596

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

Flipped N/Q/H residues before XYZ refinement:
** A   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 398 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.140386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.103888 restraints weight = 6586.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.107482 restraints weight = 3395.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.109798 restraints weight = 2276.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.111111 restraints weight = 1789.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.111736 restraints weight = 1565.913|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3887  Z= 0.126
  Angle     :  0.787  12.747   5291  Z= 0.355
  Chirality :  0.040   0.158    614
  Planarity :  0.004   0.030    662
  Dihedral  :  8.773 161.198    545
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  5.19 %
    Allowed  : 29.63 %
    Favored  : 65.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.41), residues: 480
  helix:  1.10 (0.30), residues: 337
  sheet:  None (None), residues: 0
  loop : -0.48 (0.61), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 336 
 TYR   0.014   0.001   TYR A 169 
 PHE   0.023   0.001   PHE A   3 
 TRP   0.010   0.001   TRP A  66 
 HIS   0.002   0.000   HIS A 217 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3887)
  covalent geometry    : angle       0.78735 ( 5291)
  hydrogen bonds       : bond        0.03690 (  220)
  hydrogen bonds       : angle       4.00718 (  648)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 908.71 seconds
wall clock time: 16 minutes 13.75 seconds (973.75 seconds total)