Starting phenix.real_space_refine
on Tue Feb  3 13:55:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ute_64490/02_2026/9ute_64490.cif"
  }
  resolution = 3.26
  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=   0.027
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      17      5.16       5
     C    2230      2.51       5
     N     525      2.21       5
     O     552      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 3324
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 426, 3324
          Classifications: {'peptide': 426}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 15, 'TRANS': 410}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 86
          Unresolved non-hydrogen angles: 108
          Unresolved non-hydrogen dihedrals: 82
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'TRP:plan': 2, 'ARG:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 48
  Time building chain proxies: 0.91, per 1000 atoms: 0.27
  Number of scatterers: 3324
  At special positions: 0
  Unit cell: (80.75, 62.9, 69.7, 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      17     16.00
     O     552      8.00
     N     525      7.00
     C    2230      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 464 " - pdb=" SG  CYS A 467 " distance=2.03

  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: 0.27
  Conformation dependent library (CDL) restraints added in 125.2 milliseconds
  

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  792

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 1 sheets defined
      80.0% alpha, 0.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 64
      removed outlier: 3.599A  pdb=" N   ASP A  50 " --> pdb=" O   GLY A  46 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ALA A  51 " --> pdb=" O   SER A  47 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ALA A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 75
      removed outlier: 3.787A  pdb=" N   SER A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 75 through 112
WARNING: missing atoms!
      removed outlier: 3.622A  pdb=" N   LYS A 110 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   GLU A 111 " --> pdb=" O   ARG A 107 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A 112 " --> pdb=" O   LYS A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 130
    Processing helix  chain 'A' and resid 131 through 165
      removed outlier: 3.906A  pdb=" N   LYS A 135 " --> pdb=" O   GLY A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 183
      removed outlier: 3.675A  pdb=" N   ALA A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   CYS A 180 " --> pdb=" O   ILE A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 219
      removed outlier: 3.967A  pdb=" N   TRP A 196 " --> pdb=" O   ASN A 192 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   GLY A 202 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   TYR A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY A 219 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 246
      removed outlier: 3.512A  pdb=" N   TYR A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   THR A 245 " --> pdb=" O   ASN A 241 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   PHE A 246 " --> pdb=" O   ILE A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 259
      removed outlier: 4.325A  pdb=" N   MET A 259 " --> pdb=" O   MET A 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 256 through 259'
    Processing helix  chain 'A' and resid 267 through 292
      Proline residue:  A 282  - end of helix
    Processing helix  chain 'A' and resid 293 through 296
    Processing helix  chain 'A' and resid 300 through 304
    Processing helix  chain 'A' and resid 308 through 342
      removed outlier: 3.736A  pdb=" N   PHE A 326 " --> pdb=" O   GLN A 322 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY A 327 " --> pdb=" O   PHE A 323 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   THR A 331 " --> pdb=" O   GLY A 327 " (cutoff:3.500A)
      Proline residue:  A 332  - end of helix
    Processing helix  chain 'A' and resid 348 through 370
      removed outlier: 3.632A  pdb=" N   ARG A 352 " --> pdb=" O   SER A 348 " (cutoff:3.500A)
      Proline residue:  A 358  - end of helix
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 374 through 389
      removed outlier: 4.027A  pdb=" N   SER A 378 " --> pdb=" O   GLY A 374 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   SER A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   PHE A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 401
      removed outlier: 3.986A  pdb=" N   SER A 394 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   TYR A 401 " --> pdb=" O   HIS A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 409
      removed outlier: 3.638A  pdb=" N   ASN A 409 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 438
      removed outlier: 3.650A  pdb=" N   MET A 424 " --> pdb=" O   SER A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 459
      removed outlier: 3.546A  pdb=" N   TRP A 445 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 121

    227 hydrogen bonds defined for protein.
    672 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: 0.47

  Time building geometry restraints manager: 0.36 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: 968
        1.34 -     1.46: 750
        1.46 -     1.57: 1692
        1.57 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 3435
  Sorted by residual:
  bond pdb=" N   ILE A 320 "
       pdb=" CA  ILE A 320 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.60e+00
  bond pdb=" N   MET A 318 "
       pdb=" CA  MET A 318 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.42e+00
  bond pdb=" N   LEU A 319 "
       pdb=" CA  LEU A 319 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.19e-02 7.06e+03 6.21e+00
  bond pdb=" N   GLN A 322 "
       pdb=" CA  GLN A 322 "
    ideal  model  delta    sigma   weight residual
    1.459  1.487 -0.028 1.21e-02 6.83e+03 5.33e+00
  bond pdb=" N   HIS A 321 "
       pdb=" CA  HIS A 321 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.026 1.19e-02 7.06e+03 4.90e+00
  ... (remaining 3430 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 4322
        1.03 -     2.05: 302
        2.05 -     3.08: 53
        3.08 -     4.11: 11
        4.11 -     5.14: 8
  Bond angle restraints: 4696
  Sorted by residual:
  angle pdb=" CA  GLN A 322 "
        pdb=" C   GLN A 322 "
        pdb=" O   GLN A 322 "
      ideal   model   delta    sigma   weight residual
     120.55  117.55    3.00 1.06e+00 8.90e-01 7.99e+00
  angle pdb=" CA  MET A 318 "
        pdb=" C   MET A 318 "
        pdb=" O   MET A 318 "
      ideal   model   delta    sigma   weight residual
     120.82  117.86    2.96 1.05e+00 9.07e-01 7.96e+00
  angle pdb=" CA  ILE A 320 "
        pdb=" C   ILE A 320 "
        pdb=" O   ILE A 320 "
      ideal   model   delta    sigma   weight residual
     121.17  118.29    2.88 1.06e+00 8.90e-01 7.37e+00
  angle pdb=" O   ILE A 320 "
        pdb=" C   ILE A 320 "
        pdb=" N   HIS A 321 "
      ideal   model   delta    sigma   weight residual
     121.91  124.55   -2.64 9.80e-01 1.04e+00 7.24e+00
  angle pdb=" CA  LEU A 319 "
        pdb=" C   LEU A 319 "
        pdb=" O   LEU A 319 "
      ideal   model   delta    sigma   weight residual
     120.82  118.02    2.80 1.05e+00 9.07e-01 7.10e+00
  ... (remaining 4691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.82: 1729
       13.82 -    27.63: 144
       27.63 -    41.45: 25
       41.45 -    55.27: 6
       55.27 -    69.08: 8
  Dihedral angle restraints: 1912
    sinusoidal: 672
      harmonic: 1240
  Sorted by residual:
  dihedral pdb=" CA  LEU A 279 "
           pdb=" C   LEU A 279 "
           pdb=" N   THR A 280 "
           pdb=" CA  THR A 280 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.78  -17.22     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" N   MET A 271 "
           pdb=" CA  MET A 271 "
           pdb=" CB  MET A 271 "
           pdb=" CG  MET A 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.24   58.24     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   MET A 318 "
           pdb=" CA  MET A 318 "
           pdb=" CB  MET A 318 "
           pdb=" CG  MET A 318 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -121.77  -58.23     3      1.50e+01 4.44e-03 9.46e+00
  ... (remaining 1909 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 376
       0.039 -    0.078: 109
       0.078 -    0.117: 35
       0.117 -    0.156: 6
       0.156 -    0.195: 3
  Chirality restraints: 529
  Sorted by residual:
  chirality pdb=" CA  ASN A 117 "
            pdb=" N   ASN A 117 "
            pdb=" C   ASN A 117 "
            pdb=" CB  ASN A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.48e-01
  chirality pdb=" CA  ILE A 320 "
            pdb=" N   ILE A 320 "
            pdb=" C   ILE A 320 "
            pdb=" CB  ILE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.19 2.00e-01 2.50e+01 9.42e-01
  chirality pdb=" CA  VAL A 119 "
            pdb=" N   VAL A 119 "
            pdb=" C   VAL A 119 "
            pdb=" CB  VAL A 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 7.44e-01
  ... (remaining 526 not shown)

  Planarity restraints: 568
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 187 "    0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO A 188 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 188 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 188 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 374 "   -0.027 5.00e-02 4.00e+02   4.02e-02 2.58e+00
        pdb=" N   PRO A 375 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 392 "   -0.025 5.00e-02 4.00e+02   3.74e-02 2.24e+00
        pdb=" N   PRO A 393 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 393 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 393 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 565 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 964
        2.81 -     3.33: 3152
        3.33 -     3.86: 5171
        3.86 -     4.38: 5868
        4.38 -     4.90: 10530
  Nonbonded interactions: 25685
  Sorted by model distance:
  nonbonded pdb=" O   THR A  66 "
            pdb=" OG1 THR A  66 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" NE2 GLN A  62 "
            pdb=" OH  TYR A 244 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OG  SER A  70 "
            pdb=" ND2 ASN A 241 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" N   ASN A 308 "
            pdb=" OD1 ASN A 308 "
     model   vdw
     2.354 3.120
  nonbonded pdb=" NE  ARG A 105 "
            pdb=" OE2 GLU A 109 "
     model   vdw
     2.368 3.120
  ... (remaining 25680 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:             2.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.390
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
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   0.037   3436  Z= 0.248
  Angle     :  0.619   5.136   4698  Z= 0.377
  Chirality :  0.044   0.195    529
  Planarity :  0.005   0.054    568
  Dihedral  : 11.793  69.082   1117
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  :  5.99 %
    Favored  : 91.32 %
  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: -1.42 (0.38), residues: 424
  helix: -0.28 (0.27), residues: 315
  sheet:  None (None), residues: 0
  loop : -2.67 (0.54), residues: 109

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 311 
 TYR   0.019   0.002   TYR A  69 
 PHE   0.014   0.002   PHE A 148 
 TRP   0.013   0.001   TRP A 196 
 HIS   0.003   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 3435)
  covalent geometry    : angle       0.61878 ( 4696)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       0.31316 (    2)
  hydrogen bonds       : bond        0.13212 (  227)
  hydrogen bonds       : angle       5.06721 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  305 MET cc_start: 0.8899 (mmm) cc_final: 0.8348 (mmt)
  outliers start: 9
  outliers final: 6
  residues processed: 56
  average time/residue: 0.0706
  time to fit residues: 4.8780
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 THR
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  195 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  308 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
A  59 GLN
A 121 GLN
A 454 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.140248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114130 restraints weight = 4263.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 1.94
r_work: 0.2919 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3436  Z= 0.129
  Angle     :  0.492   5.716   4698  Z= 0.268
  Chirality :  0.038   0.161    529
  Planarity :  0.004   0.047    568
  Dihedral  :  5.686  57.871    467
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  :  9.58 %
    Favored  : 88.62 %
  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:  0.26 (0.41), residues: 424
  helix:  1.04 (0.29), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.50 (0.56), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.016   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 3435)
  covalent geometry    : angle       0.49230 ( 4696)
  SS BOND              : bond        0.00114 (    1)
  SS BOND              : angle       0.17143 (    2)
  hydrogen bonds       : bond        0.05567 (  227)
  hydrogen bonds       : angle       3.81386 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  305 MET cc_start: 0.8994 (mmm) cc_final: 0.8550 (mmt)
REVERT: A  354 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7684 (tt)
  outliers start: 6
  outliers final: 3
  residues processed: 55
  average time/residue: 0.0610
  time to fit residues: 4.2677
Evaluate side-chains
  49 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 45
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.138897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.112637 restraints weight = 4319.457|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 1.97
r_work: 0.2906 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3436  Z= 0.147
  Angle     :  0.506   5.751   4698  Z= 0.275
  Chirality :  0.038   0.153    529
  Planarity :  0.004   0.046    568
  Dihedral  :  4.887  59.708    459
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 10.18 %
    Favored  : 87.72 %
  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:  0.74 (0.42), residues: 424
  helix:  1.39 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.37 (0.55), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.013   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 3435)
  covalent geometry    : angle       0.50593 ( 4696)
  SS BOND              : bond        0.00022 (    1)
  SS BOND              : angle       0.31508 (    2)
  hydrogen bonds       : bond        0.05947 (  227)
  hydrogen bonds       : angle       3.77701 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  354 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7701 (tt)
  outliers start: 7
  outliers final: 4
  residues processed: 48
  average time/residue: 0.0664
  time to fit residues: 4.0429
Evaluate side-chains
  49 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0370
   chunk 23 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.139814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.113604 restraints weight = 4271.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3004 rms_B_bonded: 1.97
r_work: 0.2890 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3436  Z= 0.136
  Angle     :  0.489   5.722   4698  Z= 0.265
  Chirality :  0.038   0.151    529
  Planarity :  0.004   0.044    568
  Dihedral  :  4.719  55.792    459
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  :  9.28 %
    Favored  : 88.02 %
  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:  1.03 (0.42), residues: 424
  helix:  1.59 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.21 (0.56), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.012   0.001   TRP A 196 
 HIS   0.002   0.000   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 3435)
  covalent geometry    : angle       0.48895 ( 4696)
  SS BOND              : bond        0.00034 (    1)
  SS BOND              : angle       0.27577 (    2)
  hydrogen bonds       : bond        0.05614 (  227)
  hydrogen bonds       : angle       3.71826 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.120 
Fit side-chains
REVERT: A  354 LEU cc_start: 0.8011 (OUTLIER) cc_final: 0.7647 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 48
  average time/residue: 0.0673
  time to fit residues: 4.0974
Evaluate side-chains
  51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 43
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  455 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    0.6980
   chunk 30 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3559 r_free = 0.3559 target = 0.139036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.112935 restraints weight = 4213.646|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 1.95
r_work: 0.2881 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.1505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3436  Z= 0.144
  Angle     :  0.495   5.708   4698  Z= 0.269
  Chirality :  0.038   0.149    529
  Planarity :  0.004   0.044    568
  Dihedral  :  4.665  53.162    459
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  :  9.58 %
    Favored  : 87.43 %
  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:  1.15 (0.42), residues: 424
  helix:  1.66 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.09 (0.57), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 105 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.014   0.001   PHE A 416 
 TRP   0.012   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 3435)
  covalent geometry    : angle       0.49547 ( 4696)
  SS BOND              : bond        0.00037 (    1)
  SS BOND              : angle       0.21280 (    2)
  hydrogen bonds       : bond        0.05828 (  227)
  hydrogen bonds       : angle       3.73659 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 43
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  115 PHE cc_start: 0.6625 (OUTLIER) cc_final: 0.5833 (m-80)
REVERT: A  118 HIS cc_start: 0.6540 (OUTLIER) cc_final: 0.5986 (t70)
REVERT: A  354 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7681 (tt)
REVERT: A  464 CYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7370 (t)
  outliers start: 10
  outliers final: 5
  residues processed: 49
  average time/residue: 0.0665
  time to fit residues: 4.1285
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 30 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.139425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.113277 restraints weight = 4275.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 1.97
r_work: 0.2881 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2764 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3436  Z= 0.140
  Angle     :  0.487   5.690   4698  Z= 0.264
  Chirality :  0.038   0.149    529
  Planarity :  0.004   0.043    568
  Dihedral  :  4.608  51.049    459
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  :  9.88 %
    Favored  : 86.83 %
  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:  1.23 (0.42), residues: 424
  helix:  1.71 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -2.03 (0.57), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.012   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3435)
  covalent geometry    : angle       0.48745 ( 4696)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       0.20376 (    2)
  hydrogen bonds       : bond        0.05691 (  227)
  hydrogen bonds       : angle       3.69957 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  115 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5670 (m-80)
REVERT: A  118 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.6026 (t70)
REVERT: A  354 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7694 (tt)
REVERT: A  464 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7387 (t)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0632
  time to fit residues: 4.0118
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 1 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3557 r_free = 0.3557 target = 0.138601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.112407 restraints weight = 4321.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 1.98
r_work: 0.2873 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   3436  Z= 0.154
  Angle     :  0.504   5.686   4698  Z= 0.274
  Chirality :  0.039   0.149    529
  Planarity :  0.004   0.043    568
  Dihedral  :  4.640  50.175    459
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  :  9.88 %
    Favored  : 86.53 %
  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:  1.23 (0.42), residues: 424
  helix:  1.70 (0.30), residues: 318
  sheet:  None (None), residues: 0
  loop : -1.98 (0.56), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 105 
 TYR   0.015   0.001   TYR A  69 
 PHE   0.015   0.001   PHE A 416 
 TRP   0.011   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 3435)
  covalent geometry    : angle       0.50452 ( 4696)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       0.22488 (    2)
  hydrogen bonds       : bond        0.05994 (  227)
  hydrogen bonds       : angle       3.75725 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.121 
Fit side-chains
REVERT: A  115 PHE cc_start: 0.6621 (OUTLIER) cc_final: 0.5674 (m-80)
REVERT: A  354 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7724 (tt)
REVERT: A  464 CYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7405 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 51
  average time/residue: 0.0437
  time to fit residues: 2.8793
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.1980
   chunk 17 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   chunk 37 optimal weight:    0.4980
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0370
   chunk 5 optimal weight:    0.5980
   overall best weight:    0.3858

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.142899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.116550 restraints weight = 4354.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.02
r_work: 0.2927 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.1842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3436  Z= 0.111
  Angle     :  0.457   5.618   4698  Z= 0.247
  Chirality :  0.037   0.148    529
  Planarity :  0.004   0.043    568
  Dihedral  :  4.428  47.672    459
  Min Nonbonded Distance : 2.651

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 10.48 %
    Favored  : 86.23 %
  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:  1.55 (0.42), residues: 424
  helix:  1.88 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.79 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 105 
 TYR   0.012   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.013   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 3435)
  covalent geometry    : angle       0.45666 ( 4696)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.31274 (    2)
  hydrogen bonds       : bond        0.04800 (  227)
  hydrogen bonds       : angle       3.56151 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.6519 (OUTLIER) cc_final: 0.5492 (m-80)
REVERT: A  118 HIS cc_start: 0.6475 (OUTLIER) cc_final: 0.6070 (t70)
REVERT: A  323 PHE cc_start: 0.7789 (t80) cc_final: 0.7137 (t80)
REVERT: A  354 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7627 (tt)
REVERT: A  402 ARG cc_start: 0.7398 (ptt-90) cc_final: 0.7185 (ptt-90)
  outliers start: 11
  outliers final: 7
  residues processed: 50
  average time/residue: 0.0516
  time to fit residues: 3.2274
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3574 r_free = 0.3574 target = 0.140320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.114039 restraints weight = 4313.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.00
r_work: 0.2900 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2782 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3436  Z= 0.133
  Angle     :  0.477   5.628   4698  Z= 0.258
  Chirality :  0.038   0.148    529
  Planarity :  0.004   0.043    568
  Dihedral  :  4.460  47.555    459
  Min Nonbonded Distance : 2.648

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 10.18 %
    Favored  : 86.53 %
  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:  1.60 (0.42), residues: 424
  helix:  1.90 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.69 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 105 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A 416 
 TRP   0.011   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3435)
  covalent geometry    : angle       0.47700 ( 4696)
  SS BOND              : bond        0.00001 (    1)
  SS BOND              : angle       0.39367 (    2)
  hydrogen bonds       : bond        0.05422 (  227)
  hydrogen bonds       : angle       3.63055 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.6545 (OUTLIER) cc_final: 0.5543 (m-80)
REVERT: A  118 HIS cc_start: 0.6490 (OUTLIER) cc_final: 0.6075 (t70)
REVERT: A  323 PHE cc_start: 0.7820 (t80) cc_final: 0.7162 (t80)
REVERT: A  354 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7686 (tt)
  outliers start: 11
  outliers final: 7
  residues processed: 49
  average time/residue: 0.0528
  time to fit residues: 3.2962
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 6 optimal weight:    0.8980
   chunk 8 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3429 r_free = 0.3429 target = 0.131166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.104788 restraints weight = 4297.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.81
r_work: 0.2933 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3436  Z= 0.135
  Angle     :  0.483   5.632   4698  Z= 0.262
  Chirality :  0.038   0.148    529
  Planarity :  0.004   0.042    568
  Dihedral  :  4.479  47.307    459
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 10.48 %
    Favored  : 86.23 %
  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:  1.61 (0.42), residues: 424
  helix:  1.90 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.65 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 105 
 TYR   0.014   0.001   TYR A  69 
 PHE   0.012   0.001   PHE A  85 
 TRP   0.011   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 3435)
  covalent geometry    : angle       0.48326 ( 4696)
  SS BOND              : bond        0.00021 (    1)
  SS BOND              : angle       0.38565 (    2)
  hydrogen bonds       : bond        0.05516 (  227)
  hydrogen bonds       : angle       3.64693 (  672)

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

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

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  848 Ramachandran restraints generated.
    424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: A  115 PHE cc_start: 0.6484 (OUTLIER) cc_final: 0.5482 (m-80)
REVERT: A  118 HIS cc_start: 0.6373 (OUTLIER) cc_final: 0.5923 (t70)
REVERT: A  323 PHE cc_start: 0.7830 (t80) cc_final: 0.7178 (t80)
REVERT: A  354 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7729 (tt)
  outliers start: 11
  outliers final: 8
  residues processed: 49
  average time/residue: 0.0392
  time to fit residues: 2.4581
Evaluate side-chains
  52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 41
  time to evaluate  : 0.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 PHE
Chi-restraints excluded: chain A residue  118 HIS
Chi-restraints excluded: chain A residue  176 ILE
Chi-restraints excluded: chain A residue  227 SER
Chi-restraints excluded: chain A residue  255 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 THR
Chi-restraints excluded: chain A residue  338 GLU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  464 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 12 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 32 optimal weight:    0.2980
   chunk 21 optimal weight:    0.0270
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.140993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.114754 restraints weight = 4309.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.00
r_work: 0.2906 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8409
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3436  Z= 0.127
  Angle     :  0.475   5.613   4698  Z= 0.257
  Chirality :  0.038   0.147    529
  Planarity :  0.004   0.043    568
  Dihedral  :  4.437  46.692    459
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 10.18 %
    Favored  : 86.23 %
  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:  1.71 (0.42), residues: 424
  helix:  1.97 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -1.61 (0.57), residues: 104

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 402 
 TYR   0.013   0.001   TYR A  69 
 PHE   0.013   0.001   PHE A  85 
 TRP   0.011   0.001   TRP A 196 
 HIS   0.002   0.001   HIS A 321 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 3435)
  covalent geometry    : angle       0.47549 ( 4696)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.36339 (    2)
  hydrogen bonds       : bond        0.05310 (  227)
  hydrogen bonds       : angle       3.60207 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 908.92 seconds
wall clock time: 16 minutes 12.81 seconds (972.81 seconds total)