Starting phenix.real_space_refine
on Fri Aug 22 13:51:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sib_40505/08_2025/8sib_40505.map"
  }
  resolution = 2.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      18      5.16       5
     C    2261      2.51       5
     N     619      2.21       5
     O     646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3544
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3544
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3544
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 17, 'TRANS': 436}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
  Time building chain proxies: 1.26, per 1000 atoms: 0.36
  Number of scatterers: 3544
  At special positions: 0
  Unit cell: (66.4, 94.62, 74.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      18     16.00
     O     646      8.00
     N     619      7.00
     C    2261      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  16 " - pdb=" SG  CYS A  44 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  36 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A  44 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 152.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  840

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      38.5% alpha, 9.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.07
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 11
    Processing helix  chain 'A' and resid 116 through 125
      removed outlier: 3.534A  pdb=" N   LEU A 121 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 167
      removed outlier: 3.511A  pdb=" N   LEU A 155 " --> pdb=" O   ARG A 151 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   LYS A 158 " --> pdb=" O   GLN A 154 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   THR A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 4.447A  pdb=" N   HIS A 183 " --> pdb=" O   GLY A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 216
    Processing helix  chain 'A' and resid 258 through 273
      removed outlier: 4.302A  pdb=" N   LEU A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.755A  pdb=" N   GLN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 331
      removed outlier: 3.624A  pdb=" N   GLN A 331 " --> pdb=" O   TYR A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 354
      removed outlier: 3.832A  pdb=" N   THR A 349 " --> pdb=" O   ASP A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 372
    Processing helix  chain 'A' and resid 373 through 375
      No H-bonds generated for 'chain 'A' and resid 373 through 375'
    Processing helix  chain 'A' and resid 390 through 398
      removed outlier: 3.538A  pdb=" N   ALA A 394 " --> pdb=" O   ASP A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 418
    Processing helix  chain 'A' and resid 419 through 426
      removed outlier: 3.943A  pdb=" N   ALA A 423 " --> pdb=" O   ARG A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 449
      removed outlier: 3.507A  pdb=" N   LEU A 444 " --> pdb=" O   GLU A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 460
    Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16
      removed outlier: 3.823A  pdb=" N   GLU A  15 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 94
      removed outlier: 6.479A  pdb=" N   LYS A 107 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 7.474A  pdb=" N   LEU A 247 " --> pdb=" O   LYS A 107 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   VAL A 109 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ASP A 249 " --> pdb=" O   VAL A 109 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   LEU A 111 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   THR A 201 " --> pdb=" O   HIS A 244 " (cutoff:3.500A)
      removed outlier: 7.770A  pdb=" N   ILE A 246 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   GLY A 203 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   VAL A 248 " --> pdb=" O   GLY A 203 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   ALA A 205 " --> pdb=" O   VAL A 248 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   CYS A 200 " --> pdb=" O   ALA A 169 " (cutoff:3.500A)
      removed outlier: 6.630A  pdb=" N   LEU A 135 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 135 " (cutoff:3.500A)
      removed outlier: 6.576A  pdb=" N   ILE A 137 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   VAL A 312 " --> pdb=" O   THR A 379 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   PHE A 381 " --> pdb=" O   VAL A 312 " (cutoff:3.500A)
      removed outlier: 6.810A  pdb=" N   VAL A 314 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)

    117 hydrogen bonds defined for protein.
    342 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: 0.35

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1156
        1.34 -     1.47: 780
        1.47 -     1.59: 1652
        1.59 -     1.71: 0
        1.71 -     1.83: 26
  Bond restraints: 3614
  Sorted by residual:
  bond pdb=" C   GLU A 343 "
       pdb=" N   PRO A 344 "
    ideal  model  delta    sigma   weight residual
    1.336  1.370 -0.034 1.25e-02 6.40e+03 7.38e+00
  bond pdb=" N   SER A 101 "
       pdb=" CA  SER A 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.492 -0.035 1.29e-02 6.01e+03 7.16e+00
  bond pdb=" C   LEU A  30 "
       pdb=" N   PRO A  31 "
    ideal  model  delta    sigma   weight residual
    1.334  1.381 -0.047 2.34e-02 1.83e+03 4.04e+00
  bond pdb=" C   SER A 307 "
       pdb=" N   PRO A 308 "
    ideal  model  delta    sigma   weight residual
    1.329  1.353 -0.024 1.18e-02 7.18e+03 4.02e+00
  bond pdb=" CB  ILE A 412 "
       pdb=" CG2 ILE A 412 "
    ideal  model  delta    sigma   weight residual
    1.521  1.461  0.060 3.30e-02 9.18e+02 3.36e+00
  ... (remaining 3609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.66: 4661
        2.66 -     5.32: 200
        5.32 -     7.98: 21
        7.98 -    10.64: 10
       10.64 -    13.30: 4
  Bond angle restraints: 4896
  Sorted by residual:
  angle pdb=" C   ARG A  46 "
        pdb=" N   LEU A  47 "
        pdb=" CA  LEU A  47 "
      ideal   model   delta    sigma   weight residual
     121.54  133.47  -11.93 1.91e+00 2.74e-01 3.90e+01
  angle pdb=" C   GLU A  76 "
        pdb=" N   GLU A  77 "
        pdb=" CA  GLU A  77 "
      ideal   model   delta    sigma   weight residual
     122.46  129.98   -7.52 1.41e+00 5.03e-01 2.84e+01
  angle pdb=" C   CYS A  36 "
        pdb=" N   GLN A  37 "
        pdb=" CA  GLN A  37 "
      ideal   model   delta    sigma   weight residual
     121.54  131.32   -9.78 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" C   VAL A  48 "
        pdb=" N   LYS A  49 "
        pdb=" CA  LYS A  49 "
      ideal   model   delta    sigma   weight residual
     121.54  130.64   -9.10 1.91e+00 2.74e-01 2.27e+01
  angle pdb=" C   GLY A 100 "
        pdb=" N   SER A 101 "
        pdb=" CA  SER A 101 "
      ideal   model   delta    sigma   weight residual
     121.54  130.39   -8.85 1.91e+00 2.74e-01 2.15e+01
  ... (remaining 4891 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.41: 2018
       15.41 -    30.83: 117
       30.83 -    46.24: 29
       46.24 -    61.66: 8
       61.66 -    77.07: 7
  Dihedral angle restraints: 2179
    sinusoidal: 877
      harmonic: 1302
  Sorted by residual:
  dihedral pdb=" CA  SER A 307 "
           pdb=" C   SER A 307 "
           pdb=" N   PRO A 308 "
           pdb=" CA  PRO A 308 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -123.29  -56.71     0      5.00e+00 4.00e-02 1.29e+02
  dihedral pdb=" CA  LEU A  30 "
           pdb=" C   LEU A  30 "
           pdb=" N   PRO A  31 "
           pdb=" CA  PRO A  31 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -126.99  -53.01     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  ILE A 383 "
           pdb=" C   ILE A 383 "
           pdb=" N   GLY A 384 "
           pdb=" CA  GLY A 384 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -131.62  -48.38     0      5.00e+00 4.00e-02 9.36e+01
  ... (remaining 2176 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 438
       0.065 -    0.130: 103
       0.130 -    0.195: 19
       0.195 -    0.260: 1
       0.260 -    0.325: 5
  Chirality restraints: 566
  Sorted by residual:
  chirality pdb=" CB  VAL A 176 "
            pdb=" CA  VAL A 176 "
            pdb=" CG1 VAL A 176 "
            pdb=" CG2 VAL A 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.65e+00
  chirality pdb=" CG  LEU A  47 "
            pdb=" CB  LEU A  47 "
            pdb=" CD1 LEU A  47 "
            pdb=" CD2 LEU A  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.30   -0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" CB  ILE A 383 "
            pdb=" CA  ILE A 383 "
            pdb=" CG1 ILE A 383 "
            pdb=" CG2 ILE A 383 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.93   -0.29 2.00e-01 2.50e+01 2.08e+00
  ... (remaining 563 not shown)

  Planarity restraints: 622
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A  95 "    0.018 2.00e-02 2.50e+03   3.59e-02 1.29e+01
        pdb=" C   ILE A  95 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   ILE A  95 "    0.023 2.00e-02 2.50e+03
        pdb=" N   ASN A  96 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  30 "   -0.058 5.00e-02 4.00e+02   8.82e-02 1.24e+01
        pdb=" N   PRO A  31 "    0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A  31 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A  31 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A  31 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   PRO A  31 "    0.055 2.00e-02 2.50e+03
        pdb=" O   PRO A  31 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   GLY A  32 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 619 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 836
        2.79 -     3.32: 3127
        3.32 -     3.85: 5541
        3.85 -     4.37: 6449
        4.37 -     4.90: 11243
  Nonbonded interactions: 27196
  Sorted by model distance:
  nonbonded pdb=" O   PHE A 290 "
            pdb=" OG1 THR A 318 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ALA A 163 "
            pdb=" OG1 THR A 167 "
     model   vdw
     2.324 3.040
  nonbonded pdb=" OH  TYR A 108 "
            pdb=" O   LEU A 216 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" NH1 ARG A  41 "
            pdb=" O   ARG A  46 "
     model   vdw
     2.348 3.120
  nonbonded pdb=" N   LEU A  30 "
            pdb=" O   LEU A  30 "
     model   vdw
     2.374 2.496
  ... (remaining 27191 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.280
  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:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
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      :  0.007   0.060   3617  Z= 0.320
  Angle     :  1.312  13.305   4902  Z= 0.756
  Chirality :  0.064   0.325    566
  Planarity :  0.008   0.088    622
  Dihedral  : 11.699  75.711   1330
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  1.33 %
    Allowed  : 12.89 %
    Favored  : 85.78 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  3.88 %
    Favored  : 95.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 17.65 %
    Twisted General : 0.92 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.28 (0.28), residues: 450
  helix: -4.12 (0.18), residues: 167
  sheet: -1.75 (0.55), residues: 62
  loop : -3.55 (0.33), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 320 
 TYR   0.028   0.003   TYR A 108 
 PHE   0.021   0.004   PHE A 381 
 TRP   0.021   0.003   TRP A   6 
 HIS   0.012   0.002   HIS A 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 ( 3614)
  covalent geometry    : angle       1.30401 ( 4896)
  SS BOND              : bond        0.00735 (    3)
  SS BOND              : angle       4.21702 (    6)
  hydrogen bonds       : bond        0.31640 (  117)
  hydrogen bonds       : angle       9.31291 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
REVERT: A  102 HIS cc_start: 0.7321 (m-70) cc_final: 0.6998 (m170)
REVERT: A  198 LYS cc_start: 0.8504 (mmtt) cc_final: 0.7943 (ttpp)
REVERT: A  211 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7185 (mm-30)
REVERT: A  352 LYS cc_start: 0.9076 (mtmm) cc_final: 0.8615 (mttp)
REVERT: A  370 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8435 (mm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 80
  average time/residue: 0.5645
  time to fit residues: 46.2904
Evaluate side-chains
  43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  236 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0570
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.0770
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
A  38 GLN
A  86 GLN
A 144 GLN
A 154 GLN
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 276 HIS
A 404 ASN
A 432 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.128626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.097869 restraints weight = 6500.463|
|-----------------------------------------------------------------------------|
r_work (start): 0.3518 rms_B_bonded: 3.88
r_work: 0.3365 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3365
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   3617  Z= 0.161
  Angle     :  0.839  11.174   4902  Z= 0.428
  Chirality :  0.047   0.246    566
  Planarity :  0.006   0.073    622
  Dihedral  :  7.579  42.577    483
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.89 %
    Allowed  : 12.89 %
    Favored  : 86.22 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 11.37 %
    Favored  : 85.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.69 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.57 (0.33), residues: 450
  helix: -1.54 (0.33), residues: 178
  sheet: -1.96 (0.61), residues: 49
  loop : -3.23 (0.35), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 274 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.010   0.001   PHE A 146 
 TRP   0.009   0.001   TRP A  78 
 HIS   0.006   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3614)
  covalent geometry    : angle       0.82900 ( 4896)
  SS BOND              : bond        0.00982 (    3)
  SS BOND              : angle       3.73604 (    6)
  hydrogen bonds       : bond        0.04027 (  117)
  hydrogen bonds       : angle       4.89195 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 51
  time to evaluate  : 0.085 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLN cc_start: 0.6691 (OUTLIER) cc_final: 0.6441 (mm-40)
REVERT: A  102 HIS cc_start: 0.7124 (m-70) cc_final: 0.6756 (t-90)
REVERT: A  131 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8099 (mm-30)
REVERT: A  198 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8292 (tttt)
REVERT: A  340 ASP cc_start: 0.8690 (t70) cc_final: 0.8402 (p0)
REVERT: A  349 THR cc_start: 0.8757 (m) cc_final: 0.8447 (t)
REVERT: A  352 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8778 (mppt)
REVERT: A  370 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: A  460 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8247 (tm-30)
  outliers start: 13
  outliers final: 1
  residues processed: 61
  average time/residue: 0.4779
  time to fit residues: 29.9368
Evaluate side-chains
  42 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLN
Chi-restraints excluded: chain A residue   87 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0870
   chunk 35 optimal weight:    2.9990
   chunk 13 optimal weight:    4.9990
   chunk 33 optimal weight:    0.0980
   chunk 12 optimal weight:    0.0470
   overall best weight:    0.2856

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.128554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.098772 restraints weight = 6196.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 3.54
r_work: 0.3305 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   3617  Z= 0.147
  Angle     :  0.817  14.219   4902  Z= 0.405
  Chirality :  0.046   0.178    566
  Planarity :  0.004   0.039    622
  Dihedral  :  6.991  43.903    481
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 12.89 %
    Favored  : 86.44 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 13.18 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.76 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.37), residues: 450
  helix: -0.10 (0.39), residues: 178
  sheet: -1.79 (0.61), residues: 49
  loop : -3.05 (0.37), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  46 
 TYR   0.009   0.001   TYR A 327 
 PHE   0.007   0.001   PHE A 146 
 TRP   0.009   0.001   TRP A  78 
 HIS   0.006   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3614)
  covalent geometry    : angle       0.80199 ( 4896)
  SS BOND              : bond        0.01738 (    3)
  SS BOND              : angle       4.53799 (    6)
  hydrogen bonds       : bond        0.03095 (  117)
  hydrogen bonds       : angle       4.02509 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 HIS cc_start: 0.7173 (m-70) cc_final: 0.6937 (t-90)
REVERT: A  198 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8291 (tttt)
REVERT: A  211 GLU cc_start: 0.8453 (tp30) cc_final: 0.8017 (mm-30)
REVERT: A  327 TYR cc_start: 0.8932 (t80) cc_final: 0.8687 (t80)
REVERT: A  331 GLN cc_start: 0.8576 (mt0) cc_final: 0.8323 (mt0)
REVERT: A  460 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8282 (tm-30)
  outliers start: 12
  outliers final: 1
  residues processed: 53
  average time/residue: 0.4329
  time to fit residues: 23.6889
Evaluate side-chains
  37 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 36
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.2980
   chunk 1 optimal weight:    6.9990
   chunk 9 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0170
   chunk 13 optimal weight:    0.0070
   overall best weight:    0.3436

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.126677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.096514 restraints weight = 6381.950|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.63
r_work: 0.3292 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8204
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3617  Z= 0.143
  Angle     :  0.781  12.427   4902  Z= 0.391
  Chirality :  0.046   0.181    566
  Planarity :  0.004   0.040    622
  Dihedral  :  6.567  39.375    481
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 11.78 %
    Favored  : 87.56 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 16.02 %
    Favored  : 80.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 11.76 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.39), residues: 450
  helix:  0.43 (0.40), residues: 179
  sheet: -1.69 (0.63), residues: 51
  loop : -2.79 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  28 
 TYR   0.007   0.001   TYR A 327 
 PHE   0.005   0.001   PHE A 245 
 TRP   0.008   0.001   TRP A 207 
 HIS   0.005   0.001   HIS A  51 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3614)
  covalent geometry    : angle       0.76476 ( 4896)
  SS BOND              : bond        0.01644 (    3)
  SS BOND              : angle       4.59601 (    6)
  hydrogen bonds       : bond        0.02741 (  117)
  hydrogen bonds       : angle       3.83515 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  102 HIS cc_start: 0.7196 (m-70) cc_final: 0.6994 (t-90)
REVERT: A  198 LYS cc_start: 0.8741 (mmtt) cc_final: 0.8296 (tttt)
REVERT: A  211 GLU cc_start: 0.8417 (tp30) cc_final: 0.7955 (mm-30)
REVERT: A  291 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7395 (tt0)
REVERT: A  302 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7150 (pp20)
REVERT: A  460 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8324 (tm-30)
  outliers start: 12
  outliers final: 4
  residues processed: 49
  average time/residue: 0.4746
  time to fit residues: 24.0002
Evaluate side-chains
  41 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  194 ARG
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  392 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0980
   chunk 10 optimal weight:    0.4980
   chunk 1 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.0970
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN
A 240 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.124886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.095053 restraints weight = 6350.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 3.62
r_work: 0.3343 rms_B_bonded: 4.24 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3617  Z= 0.141
  Angle     :  0.774  13.421   4902  Z= 0.385
  Chirality :  0.046   0.177    566
  Planarity :  0.005   0.075    622
  Dihedral  :  6.413  38.068    481
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 12.22 %
    Favored  : 87.11 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 16.80 %
    Favored  : 79.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.81 (0.40), residues: 450
  helix:  0.56 (0.41), residues: 179
  sheet: -1.62 (0.65), residues: 51
  loop : -2.72 (0.39), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  46 
 TYR   0.010   0.001   TYR A 327 
 PHE   0.006   0.001   PHE A 356 
 TRP   0.008   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 3614)
  covalent geometry    : angle       0.75845 ( 4896)
  SS BOND              : bond        0.01444 (    3)
  SS BOND              : angle       4.51271 (    6)
  hydrogen bonds       : bond        0.02752 (  117)
  hydrogen bonds       : angle       3.80548 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A   92 TYR cc_start: 0.8911 (p90) cc_final: 0.7965 (p90)
REVERT: A  102 HIS cc_start: 0.7241 (m-70) cc_final: 0.7017 (t-90)
REVERT: A  198 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8294 (tttt)
REVERT: A  211 GLU cc_start: 0.8452 (tp30) cc_final: 0.7956 (mm-30)
REVERT: A  291 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7440 (tt0)
REVERT: A  302 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7260 (pp20)
REVERT: A  352 LYS cc_start: 0.9142 (mtmm) cc_final: 0.8531 (mtmt)
REVERT: A  460 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8343 (tm-30)
  outliers start: 14
  outliers final: 4
  residues processed: 48
  average time/residue: 0.4655
  time to fit residues: 23.1208
Evaluate side-chains
  43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue   71 PHE
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  392 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  37 GLN
A 154 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.129538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.100933 restraints weight = 6671.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.74
r_work: 0.3388 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.4224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3617  Z= 0.204
  Angle     :  0.821  13.685   4902  Z= 0.407
  Chirality :  0.048   0.194    566
  Planarity :  0.005   0.065    622
  Dihedral  :  6.463  39.096    481
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 13.33 %
    Favored  : 86.00 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 19.12 %
    Favored  : 77.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.89 (0.40), residues: 450
  helix:  0.52 (0.41), residues: 179
  sheet: -1.68 (0.64), residues: 51
  loop : -2.77 (0.40), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  46 
 TYR   0.008   0.001   TYR A  92 
 PHE   0.022   0.002   PHE A  71 
 TRP   0.014   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3614)
  covalent geometry    : angle       0.80702 ( 4896)
  SS BOND              : bond        0.01304 (    3)
  SS BOND              : angle       4.43372 (    6)
  hydrogen bonds       : bond        0.03191 (  117)
  hydrogen bonds       : angle       3.98001 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 39
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8837 (p90) cc_final: 0.8026 (p90)
REVERT: A  102 HIS cc_start: 0.7243 (m-70) cc_final: 0.6877 (t-90)
REVERT: A  151 ARG cc_start: 0.8659 (tpt170) cc_final: 0.8453 (tpm170)
REVERT: A  198 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8268 (tttt)
REVERT: A  211 GLU cc_start: 0.8485 (tp30) cc_final: 0.7940 (mm-30)
REVERT: A  291 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7543 (tt0)
REVERT: A  302 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7278 (pp20)
REVERT: A  358 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8331 (mm110)
REVERT: A  435 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8571 (pp)
REVERT: A  460 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8345 (tm-30)
  outliers start: 13
  outliers final: 3
  residues processed: 48
  average time/residue: 0.4796
  time to fit residues: 23.7623
Evaluate side-chains
  43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  154 GLN
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 15 optimal weight:    0.5980
   chunk 1 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 21 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0970
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.130873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.102541 restraints weight = 6784.470|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 3.74
r_work: 0.3405 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3617  Z= 0.156
  Angle     :  0.809  14.459   4902  Z= 0.400
  Chirality :  0.047   0.207    566
  Planarity :  0.004   0.051    622
  Dihedral  :  6.297  37.151    481
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 12.67 %
    Favored  : 86.67 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 20.16 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.73 (0.40), residues: 450
  helix:  0.61 (0.41), residues: 180
  sheet: -1.41 (0.65), residues: 49
  loop : -2.71 (0.40), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 219 
 TYR   0.008   0.001   TYR A 327 
 PHE   0.007   0.001   PHE A 454 
 TRP   0.008   0.001   TRP A 207 
 HIS   0.006   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 3614)
  covalent geometry    : angle       0.79399 ( 4896)
  SS BOND              : bond        0.01317 (    3)
  SS BOND              : angle       4.43577 (    6)
  hydrogen bonds       : bond        0.02796 (  117)
  hydrogen bonds       : angle       3.93581 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 TYR cc_start: 0.8799 (p90) cc_final: 0.7889 (p90)
REVERT: A  102 HIS cc_start: 0.7313 (m-70) cc_final: 0.6984 (t-90)
REVERT: A  151 ARG cc_start: 0.8687 (tpt170) cc_final: 0.8255 (tpt170)
REVERT: A  155 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8512 (mt)
REVERT: A  198 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8255 (tttt)
REVERT: A  211 GLU cc_start: 0.8466 (tp30) cc_final: 0.7945 (mm-30)
REVERT: A  291 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7484 (tt0)
REVERT: A  302 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7268 (pp20)
REVERT: A  358 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8453 (mm110)
REVERT: A  435 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8519 (pp)
REVERT: A  460 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8335 (tm-30)
  outliers start: 13
  outliers final: 2
  residues processed: 50
  average time/residue: 0.4850
  time to fit residues: 25.0649
Evaluate side-chains
  43 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.129694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.101196 restraints weight = 6853.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3453 rms_B_bonded: 3.74
r_work: 0.3309 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.4442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3617  Z= 0.179
  Angle     :  0.842  17.371   4902  Z= 0.410
  Chirality :  0.048   0.251    566
  Planarity :  0.004   0.041    622
  Dihedral  :  6.229  37.761    481
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 13.11 %
    Favored  : 86.22 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.45 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.78 (0.39), residues: 450
  helix:  0.62 (0.40), residues: 179
  sheet: -1.32 (0.65), residues: 49
  loop : -2.80 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  46 
 TYR   0.008   0.001   TYR A 108 
 PHE   0.009   0.001   PHE A 454 
 TRP   0.012   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 3614)
  covalent geometry    : angle       0.82914 ( 4896)
  SS BOND              : bond        0.01119 (    3)
  SS BOND              : angle       4.32474 (    6)
  hydrogen bonds       : bond        0.03133 (  117)
  hydrogen bonds       : angle       3.95321 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A   92 TYR cc_start: 0.8766 (p90) cc_final: 0.7870 (p90)
REVERT: A  102 HIS cc_start: 0.7418 (m-70) cc_final: 0.6991 (t-90)
REVERT: A  114 ASP cc_start: 0.8788 (t70) cc_final: 0.8461 (t0)
REVERT: A  198 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8251 (tttt)
REVERT: A  291 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7697 (tt0)
REVERT: A  302 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7272 (pp20)
REVERT: A  358 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8541 (mm110)
REVERT: A  435 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  460 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8324 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 52
  average time/residue: 0.4988
  time to fit residues: 26.8375
Evaluate side-chains
  48 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 35 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0670
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A  50 GLN
A 154 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.130077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.101764 restraints weight = 6633.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 3.68
r_work: 0.3376 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   3617  Z= 0.161
  Angle     :  0.854  17.433   4902  Z= 0.412
  Chirality :  0.048   0.233    566
  Planarity :  0.004   0.042    622
  Dihedral  :  6.178  33.293    481
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 12.89 %
    Favored  : 86.44 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 22.48 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.72 (0.39), residues: 450
  helix:  0.69 (0.41), residues: 179
  sheet: -1.34 (0.65), residues: 49
  loop : -2.77 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.009   0.001   TYR A 327 
 PHE   0.010   0.001   PHE A 381 
 TRP   0.008   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3614)
  covalent geometry    : angle       0.84091 ( 4896)
  SS BOND              : bond        0.01210 (    3)
  SS BOND              : angle       4.33513 (    6)
  hydrogen bonds       : bond        0.02957 (  117)
  hydrogen bonds       : angle       3.97561 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.141 
Fit side-chains
REVERT: A   92 TYR cc_start: 0.8795 (p90) cc_final: 0.7858 (p90)
REVERT: A  102 HIS cc_start: 0.7413 (m-70) cc_final: 0.6976 (t-90)
REVERT: A  114 ASP cc_start: 0.8749 (t70) cc_final: 0.8428 (t0)
REVERT: A  155 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8448 (mp)
REVERT: A  198 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8245 (tttt)
REVERT: A  291 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7546 (tt0)
REVERT: A  302 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7216 (pp20)
REVERT: A  358 GLN cc_start: 0.8982 (mm-40) cc_final: 0.8552 (mm110)
REVERT: A  435 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8447 (pp)
REVERT: A  460 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8335 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 50
  average time/residue: 0.5048
  time to fit residues: 26.1940
Evaluate side-chains
  49 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 41
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 36 optimal weight:    0.4980
   chunk 17 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 19 optimal weight:    0.0770
   chunk 31 optimal weight:    0.4980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
A 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.130367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.102268 restraints weight = 6765.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 3.70
r_work: 0.3396 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.4706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   3617  Z= 0.151
  Angle     :  0.860  19.059   4902  Z= 0.413
  Chirality :  0.049   0.230    566
  Planarity :  0.004   0.041    622
  Dihedral  :  6.193  33.324    481
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.67 %
    Allowed  : 12.44 %
    Favored  : 86.89 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 21.96 %
    Favored  : 75.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.39), residues: 450
  helix:  0.70 (0.40), residues: 179
  sheet: -1.35 (0.65), residues: 49
  loop : -2.77 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.009   0.001   TYR A 108 
 PHE   0.014   0.001   PHE A 356 
 TRP   0.007   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 3614)
  covalent geometry    : angle       0.84770 ( 4896)
  SS BOND              : bond        0.01144 (    3)
  SS BOND              : angle       4.23628 (    6)
  hydrogen bonds       : bond        0.02979 (  117)
  hydrogen bonds       : angle       3.95229 (  342)

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

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

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  900 Ramachandran restraints generated.
    450 Oldfield, 0 Emsley, 450 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 39
  time to evaluate  : 0.142 
Fit side-chains
REVERT: A   92 TYR cc_start: 0.8801 (p90) cc_final: 0.7817 (p90)
REVERT: A  102 HIS cc_start: 0.7419 (m-70) cc_final: 0.6979 (t-90)
REVERT: A  114 ASP cc_start: 0.8726 (t70) cc_final: 0.8421 (t0)
REVERT: A  151 ARG cc_start: 0.8667 (tpt170) cc_final: 0.8462 (tpt170)
REVERT: A  155 LEU cc_start: 0.8745 (mt) cc_final: 0.8454 (mt)
REVERT: A  198 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8246 (tttt)
REVERT: A  211 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7931 (mm-30)
REVERT: A  291 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7538 (tt0)
REVERT: A  302 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7162 (pp20)
REVERT: A  358 GLN cc_start: 0.8952 (mm-40) cc_final: 0.8634 (mm110)
REVERT: A  435 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8404 (pp)
REVERT: A  460 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8342 (tm-30)
  outliers start: 9
  outliers final: 3
  residues processed: 46
  average time/residue: 0.4679
  time to fit residues: 22.4288
Evaluate side-chains
  44 residues out of total 389 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 38
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 CYS
Chi-restraints excluded: chain A residue  291 GLU
Chi-restraints excluded: chain A residue  302 GLU
Chi-restraints excluded: chain A residue  303 TYR
Chi-restraints excluded: chain A residue  392 ASP
Chi-restraints excluded: chain A residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 28 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 3 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 9 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 154 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.130151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.101928 restraints weight = 6648.512|
|-----------------------------------------------------------------------------|
r_work (start): 0.3513 rms_B_bonded: 3.67
r_work: 0.3390 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.4749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   3617  Z= 0.161
  Angle     :  0.875  20.437   4902  Z= 0.416
  Chirality :  0.048   0.223    566
  Planarity :  0.004   0.042    622
  Dihedral  :  6.208  33.753    481
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  : 13.33 %
    Favored  : 86.44 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.45 %
    Favored  : 75.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.46 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.66 (0.40), residues: 450
  helix:  0.78 (0.41), residues: 179
  sheet: -1.33 (0.65), residues: 49
  loop : -2.78 (0.39), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 219 
 TYR   0.012   0.001   TYR A 327 
 PHE   0.015   0.001   PHE A 356 
 TRP   0.009   0.001   TRP A 207 
 HIS   0.004   0.001   HIS A 191 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 3614)
  covalent geometry    : angle       0.86225 ( 4896)
  SS BOND              : bond        0.01123 (    3)
  SS BOND              : angle       4.25853 (    6)
  hydrogen bonds       : bond        0.02980 (  117)
  hydrogen bonds       : angle       3.97837 (  342)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1256.99 seconds
wall clock time: 22 minutes 10.30 seconds (1330.30 seconds total)