Starting phenix.real_space_refine
on Fri Aug 22 12:55:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k5d_36902/08_2025/8k5d_36902.map"
  }
  resolution = 3.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      17      5.16       5
     Cl      1      4.86       5
     C    1561      2.51       5
     N     394      2.21       5
     O     372      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2345
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2328
          Classifications: {'peptide': 291}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 280}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 62
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 58
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'OKL': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 0.89, per 1000 atoms: 0.38
  Number of scatterers: 2345
  At special positions: 0
  Unit cell: (69.72, 62.25, 79.68, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      17     16.00
     O     372      8.00
     N     394      7.00
     C    1561      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A 183 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 100 " - pdb=" SG  CYS A 177 " 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: 0.14
  Conformation dependent library (CDL) restraints added in 56.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  558

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 2 sheets defined
      75.9% alpha, 2.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 54
      removed outlier: 4.068A  pdb=" N   LEU A  43 " --> pdb=" O   ILE A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 89
      Proline residue:  A  81  - end of helix
    Processing helix  chain 'A' and resid 97 through 130
    Processing helix  chain 'A' and resid 134 through 138
    Processing helix  chain 'A' and resid 140 through 166
      removed outlier: 5.124A  pdb=" N   HIS A 161 " --> pdb=" O   GLY A 157 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   LEU A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
      removed outlier: 4.881A  pdb=" N   LYS A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 218
      removed outlier: 3.816A  pdb=" N   ALA A 191 " --> pdb=" O   GLN A 187 " (cutoff:3.500A)
      Proline residue:  A 200  - end of helix
    Processing helix  chain 'A' and resid 223 through 260
      removed outlier: 3.717A  pdb=" N   LYS A 227 " --> pdb=" O   HIS A 223 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ARG A 228 " --> pdb=" O   ALA A 224 " (cutoff:3.500A)
      Proline residue:  A 246  - end of helix
    Processing helix  chain 'A' and resid 266 through 294
      removed outlier: 3.597A  pdb=" N   ARG A 270 " --> pdb=" O   CYS A 266 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   VAL A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ALA A 275 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ILE A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   THR A 279 " --> pdb=" O   ALA A 275 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   THR A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   TYR A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   MET A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ASN A 286 " --> pdb=" O   PHE A 282 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A 287 " --> pdb=" O   THR A 283 " (cutoff:3.500A)
      Proline residue:  A 291  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12
    Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171

    165 hydrogen bonds defined for protein.
    483 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: 0.25

  Time building geometry restraints manager: 0.18 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: 713
        1.34 -     1.46: 438
        1.46 -     1.58: 1236
        1.58 -     1.69: 0
        1.69 -     1.81: 26
  Bond restraints: 2413
  Sorted by residual:
  bond pdb=" C07 OKL A 401 "
       pdb=" O08 OKL A 401 "
    ideal  model  delta    sigma   weight residual
    1.214  1.398 -0.184 2.00e-02 2.50e+03 8.47e+01
  bond pdb=" C10 OKL A 401 "
       pdb=" O11 OKL A 401 "
    ideal  model  delta    sigma   weight residual
    1.215  1.396 -0.181 2.00e-02 2.50e+03 8.20e+01
  bond pdb=" C15 OKL A 401 "
       pdb="CL17 OKL A 401 "
    ideal  model  delta    sigma   weight residual
    1.692  1.784 -0.092 2.00e-02 2.50e+03 2.11e+01
  bond pdb=" C10 OKL A 401 "
       pdb=" N09 OKL A 401 "
    ideal  model  delta    sigma   weight residual
    1.390  1.325  0.065 2.00e-02 2.50e+03 1.07e+01
  bond pdb=" C07 OKL A 401 "
       pdb=" N09 OKL A 401 "
    ideal  model  delta    sigma   weight residual
    1.384  1.328  0.056 2.00e-02 2.50e+03 7.72e+00
  ... (remaining 2408 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 3204
        1.90 -     3.81: 50
        3.81 -     5.71: 22
        5.71 -     7.62: 4
        7.62 -     9.52: 4
  Bond angle restraints: 3284
  Sorted by residual:
  angle pdb=" N   VAL A  27 "
        pdb=" CA  VAL A  27 "
        pdb=" C   VAL A  27 "
      ideal   model   delta    sigma   weight residual
     111.91  108.72    3.19 8.90e-01 1.26e+00 1.28e+01
  angle pdb=" N   PRO A  31 "
        pdb=" CA  PRO A  31 "
        pdb=" C   PRO A  31 "
      ideal   model   delta    sigma   weight residual
     110.70  114.65   -3.95 1.22e+00 6.72e-01 1.05e+01
  angle pdb=" CA  PRO A  31 "
        pdb=" C   PRO A  31 "
        pdb=" N   PRO A  32 "
      ideal   model   delta    sigma   weight residual
     117.93  121.72   -3.79 1.20e+00 6.94e-01 9.98e+00
  angle pdb=" C07 OKL A 401 "
        pdb=" N09 OKL A 401 "
        pdb=" C10 OKL A 401 "
      ideal   model   delta    sigma   weight residual
     129.77  120.31    9.46 3.00e+00 1.11e-01 9.94e+00
  angle pdb=" C12 OKL A 401 "
        pdb=" C10 OKL A 401 "
        pdb=" N09 OKL A 401 "
      ideal   model   delta    sigma   weight residual
     109.84  119.23   -9.39 3.00e+00 1.11e-01 9.80e+00
  ... (remaining 3279 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.19: 1261
       27.19 -    54.38: 120
       54.38 -    81.58: 7
       81.58 -   108.77: 0
      108.77 -   135.96: 1
  Dihedral angle restraints: 1389
    sinusoidal: 535
      harmonic: 854
  Sorted by residual:
  dihedral pdb=" C03 OKL A 401 "
           pdb=" C04 OKL A 401 "
           pdb=" C05 OKL A 401 "
           pdb=" N06 OKL A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     183.45   47.49  135.96     1      3.00e+01 1.11e-03 1.83e+01
  dihedral pdb=" CA  LYS A 164 "
           pdb=" C   LYS A 164 "
           pdb=" N   LYS A 165 "
           pdb=" CA  LYS A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.75  -17.25     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  GLU A 196 "
           pdb=" C   GLU A 196 "
           pdb=" N   PHE A 197 "
           pdb=" CA  PHE A 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.64   16.36     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 1386 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 261
       0.037 -    0.074: 82
       0.074 -    0.110: 28
       0.110 -    0.147: 4
       0.147 -    0.184: 3
  Chirality restraints: 378
  Sorted by residual:
  chirality pdb=" CA  ASN A 110 "
            pdb=" N   ASN A 110 "
            pdb=" C   ASN A 110 "
            pdb=" CB  ASN A 110 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.43e-01
  chirality pdb=" CA  PRO A  31 "
            pdb=" N   PRO A  31 "
            pdb=" C   PRO A  31 "
            pdb=" CB  PRO A  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.54    0.18 2.00e-01 2.50e+01 7.95e-01
  chirality pdb=" CA  THR A 159 "
            pdb=" N   THR A 159 "
            pdb=" C   THR A 159 "
            pdb=" CB  THR A 159 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.37    0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 375 not shown)

  Planarity restraints: 398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 167 "    0.030 5.00e-02 4.00e+02   4.52e-02 3.27e+00
        pdb=" N   PRO A 168 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 168 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 168 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A  31 "   -0.029 5.00e-02 4.00e+02   4.33e-02 3.00e+00
        pdb=" N   PRO A  32 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A  32 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A  32 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 131 "    0.026 5.00e-02 4.00e+02   3.94e-02 2.48e+00
        pdb=" N   PRO A 132 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 132 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 132 "    0.022 5.00e-02 4.00e+02
  ... (remaining 395 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 258
        2.74 -     3.28: 2460
        3.28 -     3.82: 3903
        3.82 -     4.36: 4195
        4.36 -     4.90: 7307
  Nonbonded interactions: 18123
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 278 "
            pdb=" OG  SER A 281 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OD1 ASN A  68 "
            pdb=" NE1 TRP A 152 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" N   SER A 179 "
            pdb=" O08 OKL A 401 "
     model   vdw
     2.326 3.120
  nonbonded pdb=" NH2 ARG A 111 "
            pdb=" O11 OKL A 401 "
     model   vdw
     2.330 3.120
  nonbonded pdb=" N   ASP A 221 "
            pdb=" OD1 ASP A 221 "
     model   vdw
     2.345 3.120
  ... (remaining 18118 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     3.680
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    5.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
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   0.184   2415  Z= 0.332
  Angle     :  0.755   9.520   3288  Z= 0.371
  Chirality :  0.043   0.184    378
  Planarity :  0.005   0.045    398
  Dihedral  : 19.082 135.960    825
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 41.70 %
    Favored  : 57.89 %
  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 aren not related in a simple way.
  whole:  0.46 (0.51), residues: 289
  helix:  1.39 (0.37), residues: 202
  sheet:  None (None), residues: 0
  loop : -2.40 (0.68), residues: 87

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  22 
 TYR   0.005   0.001   TYR A 126 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.003   0.001   TRP A  93 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00673 ( 2413)
  covalent geometry    : angle       0.75568 ( 3284)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.34041 (    4)
  hydrogen bonds       : bond        0.12440 (  165)
  hydrogen bonds       : angle       5.08309 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.087 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.4006 (OUTLIER) cc_final: 0.3713 (m-10)
REVERT: A  103 MET cc_start: 0.7450 (tpp) cc_final: 0.7040 (tpp)
REVERT: A  170 GLN cc_start: 0.8195 (tp40) cc_final: 0.7866 (tp40)
  outliers start: 1
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0278
  time to fit residues: 2.5386
Evaluate side-chains
  68 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 67
  time to evaluate  : 0.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0980
   chunk 13 optimal weight:    1.9990
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    0.5382

-------------------------------------------------------------------------------
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 = 0.3718 r_free = 0.3718 target = 0.150479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.133180 restraints weight = 3905.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.136310 restraints weight = 2314.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.138426 restraints weight = 1588.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.140051 restraints weight = 1210.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140938 restraints weight = 977.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7754
moved from start:          0.0719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2415  Z= 0.140
  Angle     :  0.588   7.404   3288  Z= 0.305
  Chirality :  0.041   0.136    378
  Planarity :  0.005   0.048    398
  Dihedral  :  9.694 144.174    319
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 33.60 %
    Favored  : 60.32 %
  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 aren not related in a simple way.
  whole:  0.35 (0.50), residues: 289
  helix:  1.19 (0.36), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.70 (0.67), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 218 
 TYR   0.008   0.001   TYR A 284 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.005   0.001   TRP A  50 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2413)
  covalent geometry    : angle       0.58834 ( 3284)
  SS BOND              : bond        0.00154 (    2)
  SS BOND              : angle       0.18330 (    4)
  hydrogen bonds       : bond        0.04348 (  165)
  hydrogen bonds       : angle       4.24072 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
REVERT: A   37 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8515 (mm-30)
REVERT: A   87 TYR cc_start: 0.8485 (m-80) cc_final: 0.8264 (m-80)
REVERT: A  290 ASP cc_start: 0.8567 (m-30) cc_final: 0.8279 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 75
  average time/residue: 0.0411
  time to fit residues: 3.9199
Evaluate side-chains
  77 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  282 PHE
Chi-restraints excluded: chain A residue  285 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3746 r_free = 0.3746 target = 0.152636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.135026 restraints weight = 3967.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.138160 restraints weight = 2401.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.140219 restraints weight = 1671.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.141937 restraints weight = 1284.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.142701 restraints weight = 1033.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2415  Z= 0.154
  Angle     :  0.599   8.148   3288  Z= 0.308
  Chirality :  0.041   0.137    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.233 143.325    317
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  7.29 %
    Allowed  : 33.60 %
    Favored  : 59.11 %
  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 aren not related in a simple way.
  whole:  0.51 (0.51), residues: 289
  helix:  1.27 (0.36), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.52 (0.71), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.008   0.002   TYR A 284 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.005   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 2413)
  covalent geometry    : angle       0.59919 ( 3284)
  SS BOND              : bond        0.00201 (    2)
  SS BOND              : angle       0.21311 (    4)
  hydrogen bonds       : bond        0.04251 (  165)
  hydrogen bonds       : angle       4.18326 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
REVERT: A   87 TYR cc_start: 0.8519 (m-80) cc_final: 0.8179 (m-80)
REVERT: A  103 MET cc_start: 0.7651 (tpp) cc_final: 0.7421 (tpp)
REVERT: A  290 ASP cc_start: 0.8625 (m-30) cc_final: 0.8148 (m-30)
  outliers start: 18
  outliers final: 12
  residues processed: 76
  average time/residue: 0.0433
  time to fit residues: 4.1362
Evaluate side-chains
  78 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  162 LEU
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  282 PHE
Chi-restraints excluded: chain A residue  285 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 2 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3735 r_free = 0.3735 target = 0.151483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.134037 restraints weight = 3953.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.137267 restraints weight = 2368.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.139306 restraints weight = 1632.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.140908 restraints weight = 1246.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.142043 restraints weight = 1010.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.1278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   2415  Z= 0.168
  Angle     :  0.607   8.004   3288  Z= 0.310
  Chirality :  0.041   0.127    378
  Planarity :  0.005   0.051    398
  Dihedral  :  9.297 144.206    317
  Min Nonbonded Distance : 2.620

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  8.50 %
    Allowed  : 32.79 %
    Favored  : 58.70 %
  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 aren not related in a simple way.
  whole:  0.51 (0.51), residues: 289
  helix:  1.34 (0.36), residues: 213
  sheet:  None (None), residues: 0
  loop : -2.65 (0.68), residues: 76

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 222 
 TYR   0.009   0.002   TYR A 284 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.005   0.001   TRP A 152 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 2413)
  covalent geometry    : angle       0.60740 ( 3284)
  SS BOND              : bond        0.00214 (    2)
  SS BOND              : angle       0.20265 (    4)
  hydrogen bonds       : bond        0.04284 (  165)
  hydrogen bonds       : angle       4.14180 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3900 (OUTLIER) cc_final: 0.3634 (m-10)
REVERT: A  290 ASP cc_start: 0.8698 (m-30) cc_final: 0.8071 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0451
  time to fit residues: 4.2448
Evaluate side-chains
  81 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 65
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  282 PHE
Chi-restraints excluded: chain A residue  285 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0000
   chunk 21 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.5584

-------------------------------------------------------------------------------
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 = 0.3748 r_free = 0.3748 target = 0.152764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135532 restraints weight = 3864.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138693 restraints weight = 2323.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.140740 restraints weight = 1606.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142359 restraints weight = 1226.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143483 restraints weight = 988.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2415  Z= 0.136
  Angle     :  0.584   7.306   3288  Z= 0.300
  Chirality :  0.040   0.137    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.192 142.680    317
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  8.50 %
    Allowed  : 32.39 %
    Favored  : 59.11 %
  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 aren not related in a simple way.
  whole:  0.57 (0.51), residues: 289
  helix:  1.35 (0.36), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.59 (0.69), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.007   0.001   TYR A 284 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A  93 
 HIS   0.002   0.000   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 2413)
  covalent geometry    : angle       0.58389 ( 3284)
  SS BOND              : bond        0.00285 (    2)
  SS BOND              : angle       0.15710 (    4)
  hydrogen bonds       : bond        0.04120 (  165)
  hydrogen bonds       : angle       4.05415 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 67
  time to evaluate  : 0.054 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3870 (OUTLIER) cc_final: 0.3644 (m-10)
REVERT: A   63 ARG cc_start: 0.8456 (ttp-110) cc_final: 0.8175 (ttm-80)
  outliers start: 21
  outliers final: 17
  residues processed: 77
  average time/residue: 0.0441
  time to fit residues: 4.2147
Evaluate side-chains
  82 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 64
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  282 PHE
Chi-restraints excluded: chain A residue  285 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.152000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.134619 restraints weight = 3876.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137704 restraints weight = 2335.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.139936 restraints weight = 1618.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141308 restraints weight = 1227.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.142502 restraints weight = 1009.259|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.1364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   2415  Z= 0.154
  Angle     :  0.633   8.750   3288  Z= 0.320
  Chirality :  0.042   0.154    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.208 142.794    317
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.88 %
    Favored  : 94.12 %
  Rotamer:
    Outliers : 10.12 %
    Allowed  : 30.36 %
    Favored  : 59.51 %
  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 aren not related in a simple way.
  whole:  0.56 (0.51), residues: 289
  helix:  1.37 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.67 (0.68), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 251 
 TYR   0.008   0.001   TYR A 126 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A 152 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 2413)
  covalent geometry    : angle       0.63334 ( 3284)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.20093 (    4)
  hydrogen bonds       : bond        0.04242 (  165)
  hydrogen bonds       : angle       4.06877 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 66
  time to evaluate  : 0.092 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3894 (OUTLIER) cc_final: 0.3680 (m-10)
REVERT: A  282 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.8146 (t80)
REVERT: A  290 ASP cc_start: 0.8557 (m-30) cc_final: 0.8058 (m-30)
  outliers start: 25
  outliers final: 19
  residues processed: 80
  average time/residue: 0.0411
  time to fit residues: 4.1481
Evaluate side-chains
  87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 66
  time to evaluate  : 0.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  280 LEU
Chi-restraints excluded: chain A residue  281 SER
Chi-restraints excluded: chain A residue  282 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0980
   chunk 5 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 26 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.153121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.135429 restraints weight = 3901.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138614 restraints weight = 2338.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.140737 restraints weight = 1611.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.142088 restraints weight = 1227.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.143396 restraints weight = 1013.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2415  Z= 0.139
  Angle     :  0.608   8.158   3288  Z= 0.308
  Chirality :  0.041   0.138    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.143 141.774    317
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  8.91 %
    Allowed  : 33.20 %
    Favored  : 57.89 %
  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 aren not related in a simple way.
  whole:  0.64 (0.51), residues: 289
  helix:  1.45 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.71 (0.67), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.007   0.001   TYR A 284 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A  91 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2413)
  covalent geometry    : angle       0.60801 ( 3284)
  SS BOND              : bond        0.00263 (    2)
  SS BOND              : angle       0.26829 (    4)
  hydrogen bonds       : bond        0.04107 (  165)
  hydrogen bonds       : angle       4.01302 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 66
  time to evaluate  : 0.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3868 (OUTLIER) cc_final: 0.3638 (m-10)
REVERT: A   63 ARG cc_start: 0.8421 (ttp-110) cc_final: 0.8151 (ttm-80)
REVERT: A  290 ASP cc_start: 0.8544 (m-30) cc_final: 0.7951 (m-30)
  outliers start: 22
  outliers final: 17
  residues processed: 77
  average time/residue: 0.0462
  time to fit residues: 4.4529
Evaluate side-chains
  84 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 66
  time to evaluate  : 0.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  280 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 8 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 21 optimal weight:    0.2980
   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 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134597 restraints weight = 3901.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137803 restraints weight = 2327.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.139714 restraints weight = 1608.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.141413 restraints weight = 1245.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.142579 restraints weight = 1017.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2415  Z= 0.144
  Angle     :  0.607   7.798   3288  Z= 0.311
  Chirality :  0.041   0.157    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.105 140.833    317
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  9.31 %
    Allowed  : 31.98 %
    Favored  : 58.70 %
  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 aren not related in a simple way.
  whole:  0.59 (0.51), residues: 289
  helix:  1.37 (0.36), residues: 215
  sheet:  None (None), residues: 0
  loop : -2.64 (0.68), residues: 74

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  22 
 TYR   0.007   0.001   TYR A 126 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A 152 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 2413)
  covalent geometry    : angle       0.60750 ( 3284)
  SS BOND              : bond        0.00233 (    2)
  SS BOND              : angle       0.18019 (    4)
  hydrogen bonds       : bond        0.04162 (  165)
  hydrogen bonds       : angle       3.98842 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 66
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3867 (OUTLIER) cc_final: 0.3635 (m-10)
REVERT: A   63 ARG cc_start: 0.8426 (ttp-110) cc_final: 0.8155 (ttm-80)
  outliers start: 23
  outliers final: 19
  residues processed: 77
  average time/residue: 0.0449
  time to fit residues: 4.3376
Evaluate side-chains
  86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  165 LYS
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  280 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0040
   chunk 17 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 14 optimal weight:    0.5980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.135745 restraints weight = 3957.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.138985 restraints weight = 2351.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.141082 restraints weight = 1617.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.142814 restraints weight = 1236.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.143938 restraints weight = 994.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   2415  Z= 0.129
  Angle     :  0.602   7.670   3288  Z= 0.307
  Chirality :  0.041   0.163    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.011 139.111    317
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  7.69 %
    Allowed  : 32.79 %
    Favored  : 59.51 %
  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 aren not related in a simple way.
  whole:  0.62 (0.51), residues: 289
  helix:  1.42 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.69 (0.67), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.006   0.001   TYR A 126 
 PHE   0.011   0.001   PHE A 197 
 TRP   0.003   0.001   TRP A 152 
 HIS   0.002   0.000   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 2413)
  covalent geometry    : angle       0.60240 ( 3284)
  SS BOND              : bond        0.00211 (    2)
  SS BOND              : angle       0.08276 (    4)
  hydrogen bonds       : bond        0.04086 (  165)
  hydrogen bonds       : angle       3.97771 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 68
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3862 (OUTLIER) cc_final: 0.3622 (m-10)
REVERT: A   63 ARG cc_start: 0.8398 (ttp-110) cc_final: 0.8109 (ttm110)
  outliers start: 19
  outliers final: 17
  residues processed: 79
  average time/residue: 0.0438
  time to fit residues: 4.3775
Evaluate side-chains
  83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  170 GLN
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  280 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 21 optimal weight:    0.4980
   chunk 12 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3734 r_free = 0.3734 target = 0.151269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133545 restraints weight = 4005.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.136550 restraints weight = 2394.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.138720 restraints weight = 1664.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.140285 restraints weight = 1262.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.141060 restraints weight = 1040.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2415  Z= 0.184
  Angle     :  0.647   9.344   3288  Z= 0.331
  Chirality :  0.043   0.181    378
  Planarity :  0.005   0.050    398
  Dihedral  :  9.132 140.846    317
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.57 %
    Favored  : 93.43 %
  Rotamer:
    Outliers :  8.10 %
    Allowed  : 33.20 %
    Favored  : 58.70 %
  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 aren not related in a simple way.
  whole:  0.43 (0.51), residues: 289
  helix:  1.46 (0.36), residues: 209
  sheet:  None (None), residues: 0
  loop : -3.05 (0.63), residues: 80

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 251 
 TYR   0.011   0.002   TYR A 126 
 PHE   0.009   0.001   PHE A 197 
 TRP   0.005   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 2413)
  covalent geometry    : angle       0.64785 ( 3284)
  SS BOND              : bond        0.00226 (    2)
  SS BOND              : angle       0.21409 (    4)
  hydrogen bonds       : bond        0.04374 (  165)
  hydrogen bonds       : angle       4.06706 (  483)

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

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

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  578 Ramachandran restraints generated.
    289 Oldfield, 0 Emsley, 289 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 66
  time to evaluate  : 0.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 TRP cc_start: 0.3886 (OUTLIER) cc_final: 0.3686 (m-10)
REVERT: A   63 ARG cc_start: 0.8440 (ttp-110) cc_final: 0.8169 (ttm-80)
REVERT: A  190 GLU cc_start: 0.9238 (mm-30) cc_final: 0.8928 (mm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 76
  average time/residue: 0.0466
  time to fit residues: 4.4624
Evaluate side-chains
  83 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.086 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 HIS
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   29 VAL
Chi-restraints excluded: chain A residue   30 LEU
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   59 TRP
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  100 CYS
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  149 CYS
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  255 PHE
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  274 LEU
Chi-restraints excluded: chain A residue  280 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 29
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 18 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 9 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   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 = 0.3743 r_free = 0.3743 target = 0.152121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.134684 restraints weight = 3902.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.137760 restraints weight = 2315.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.139810 restraints weight = 1602.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.141455 restraints weight = 1227.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.142357 restraints weight = 998.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.1577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   2415  Z= 0.154
  Angle     :  0.635   9.397   3288  Z= 0.323
  Chirality :  0.042   0.185    378
  Planarity :  0.005   0.049    398
  Dihedral  :  9.138 140.690    317
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  6.48 %
    Allowed  : 36.03 %
    Favored  : 57.49 %
  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 aren not related in a simple way.
  whole:  0.46 (0.51), residues: 289
  helix:  1.31 (0.36), residues: 214
  sheet:  None (None), residues: 0
  loop : -2.76 (0.66), residues: 75

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 251 
 TYR   0.008   0.001   TYR A 126 
 PHE   0.010   0.001   PHE A 197 
 TRP   0.004   0.001   TRP A 152 
 HIS   0.002   0.001   HIS A 161 

Details of bonding type rmsd
  covalent geometry    : bond        0.00362 ( 2413)
  covalent geometry    : angle       0.63505 ( 3284)
  SS BOND              : bond        0.00246 (    2)
  SS BOND              : angle       0.18357 (    4)
  hydrogen bonds       : bond        0.04289 (  165)
  hydrogen bonds       : angle       4.05119 (  483)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 572.86 seconds
wall clock time: 10 minutes 40.37 seconds (640.37 seconds total)