Starting phenix.real_space_refine
on Wed Sep 17 05:52:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fkq_50525/09_2025/9fkq_50525.map"
  }
  resolution = 2.45
  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=   0.035
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       6      5.16       5
     C    1816      2.51       5
     N     456      2.21       5
     O     540      1.98       5
     H    2784      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5602
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5602
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 362, 5577
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 21, 'TRANS': 340}
      Conformer: "B"
        Number of residues, atoms: 362, 5577
          Classifications: {'peptide': 362}
          Link IDs: {'PTRANS': 21, 'TRANS': 340}
          bond proxies already assigned to first conformer: 5618
  Time building chain proxies: 2.40, per 1000 atoms: 0.43
  Number of scatterers: 5602
  At special positions: 0
  Unit cell: (81.03, 59.13, 67.16, 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)
     S       6     16.00
     O     540      8.00
     N     456      7.00
     C    1816      6.00
     H    2784      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 249.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  672

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 5 sheets defined
      52.8% alpha, 17.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 32
    Processing helix  chain 'A' and resid 42 through 52
      Proline residue:  A  48  - end of helix
    Processing helix  chain 'A' and resid 64 through 73
      removed outlier: 3.554A  pdb=" N   GLY A  68 " --> pdb=" O   HIS A  64 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   GLY A  69 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 87
    Processing helix  chain 'A' and resid 90 through 97
      removed outlier: 3.713A  pdb=" N   VAL A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 142
      removed outlier: 4.680A  pdb=" N   ALA A 134 " --> pdb=" O   GLU A 130 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   LYS A 137 " --> pdb=" O   PRO A 133 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LYS A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 162
      removed outlier: 3.564A  pdb=" N   THR A 157 " --> pdb=" O   GLU A 153 " (cutoff:3.500A)
      Proline residue:  A 159  - end of helix
    Processing helix  chain 'A' and resid 185 through 201
    Processing helix  chain 'A' and resid 209 through 219
    Processing helix  chain 'A' and resid 228 through 230
      No H-bonds generated for 'chain 'A' and resid 228 through 230'
    Processing helix  chain 'A' and resid 231 through 239
    Processing helix  chain 'A' and resid 272 through 283
    Processing helix  chain 'A' and resid 286 through 297
      removed outlier: 3.650A  pdb=" N   ASP A 296 " --> pdb=" O   ALA A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 312
      removed outlier: 3.685A  pdb=" N   GLU A 310 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 327
    Processing helix  chain 'A' and resid 335 through 352
      removed outlier: 3.529A  pdb=" N   ARG A 344 " --> pdb=" O   TRP A 340 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   THR A 345 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 366
      removed outlier: 3.772A  pdb=" N   THR A 366 " --> pdb=" O   LYS A 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38
      removed outlier: 6.753A  pdb=" N   GLY A 260 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   VAL A 110 " --> pdb=" O   GLY A 260 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU A 262 " --> pdb=" O   ILE A 108 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA A 301 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38
    Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 99
    Processing sheet with id=AA4, first strand: chain 'A' and resid 145 through 147
      removed outlier: 8.264A  pdb=" N   SER A 145 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   THR A 225 " --> pdb=" O   SER A 145 " (cutoff:3.500A)
      removed outlier: 8.038A  pdb=" N   LEU A 147 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 11.384A  pdb=" N   ASN A 227 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 6.748A  pdb=" N   ALA A 223 " --> pdb=" O   ASN A 118 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 170 through 172
      removed outlier: 4.074A  pdb=" N   LYS A 170 " --> pdb=" O   ASP A 177 " (cutoff:3.500A)

    145 hydrogen bonds defined for protein.
    419 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: 1.14

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2784
        1.03 -     1.23: 0
        1.23 -     1.42: 1194
        1.42 -     1.61: 1684
        1.61 -     1.81: 12
  Bond restraints: 5674
  Sorted by residual:
  bond pdb=" C   GLY A 252 "
       pdb=" N   GLN A 253 "
    ideal  model  delta    sigma   weight residual
    1.331  1.358 -0.027 2.07e-02 2.33e+03 1.65e+00
  bond pdb=" CA  ILE A 132 "
       pdb=" CB  ILE A 132 "
    ideal  model  delta    sigma   weight residual
    1.539  1.534  0.005 5.40e-03 3.43e+04 9.27e-01
  bond pdb=" CA  ASN A 100 "
       pdb=" CB  ASN A 100 "
    ideal  model  delta    sigma   weight residual
    1.529  1.541 -0.012 1.62e-02 3.81e+03 5.09e-01
  bond pdb=" CB  ASN A 100 "
       pdb=" CG  ASN A 100 "
    ideal  model  delta    sigma   weight residual
    1.516  1.533 -0.017 2.50e-02 1.60e+03 4.40e-01
  bond pdb=" CA  GLY A 260 "
       pdb=" C   GLY A 260 "
    ideal  model  delta    sigma   weight residual
    1.514  1.520 -0.005 8.20e-03 1.49e+04 4.24e-01
  ... (remaining 5669 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.75: 8906
        0.75 -     1.50: 1245
        1.50 -     2.25: 129
        2.25 -     3.00: 13
        3.00 -     3.75: 17
  Bond angle restraints: 10310
  Sorted by residual:
  angle pdb=" N   ASN A 100 "
        pdb=" CA  ASN A 100 "
        pdb=" C   ASN A 100 "
      ideal   model   delta    sigma   weight residual
     111.54  109.32    2.22 1.36e+00 5.41e-01 2.66e+00
  angle pdb=" CA  ASN A 100 "
        pdb=" CB  ASN A 100 "
        pdb=" CG  ASN A 100 "
      ideal   model   delta    sigma   weight residual
     112.60  114.07   -1.47 1.00e+00 1.00e+00 2.15e+00
  angle pdb=" CA  GLU A 309 "
        pdb=" CB  GLU A 309 "
        pdb=" CG  GLU A 309 "
      ideal   model   delta    sigma   weight residual
     114.10  116.97   -2.87 2.00e+00 2.50e-01 2.06e+00
  angle pdb=" C   PHE A  61 "
        pdb=" N   TRP A  62 "
        pdb=" CA  TRP A  62 "
      ideal   model   delta    sigma   weight residual
     122.09  119.56    2.53 1.86e+00 2.89e-01 1.85e+00
  angle pdb=" C   MET A 224 "
        pdb=" N   THR A 225 "
        pdb=" CA  THR A 225 "
      ideal   model   delta    sigma   weight residual
     121.87  124.02   -2.15 1.64e+00 3.72e-01 1.72e+00
  ... (remaining 10305 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.09: 2481
       17.09 -    34.17: 141
       34.17 -    51.26: 41
       51.26 -    68.34: 19
       68.34 -    85.43: 3
  Dihedral angle restraints: 2685
    sinusoidal: 1439
      harmonic: 1246
  Sorted by residual:
  dihedral pdb=" CB  GLU A 131 "
           pdb=" CG  GLU A 131 "
           pdb=" CD  GLU A 131 "
           pdb=" OE1 GLU A 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -85.43   85.43     1      3.00e+01 1.11e-03 9.82e+00
  dihedral pdb=" CG  LYS A  34 "
           pdb=" CD  LYS A  34 "
           pdb=" CE  LYS A  34 "
           pdb=" NZ  LYS A  34 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  110.88  -50.88     3      1.50e+01 4.44e-03 8.95e+00
  dihedral pdb=" CA  ASP A  58 "
           pdb=" CB  ASP A  58 "
           pdb=" CG  ASP A  58 "
           pdb=" OD1 ASP A  58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -80.92   50.92     1      2.00e+01 2.50e-03 8.87e+00
  ... (remaining 2682 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 256
       0.026 -    0.051: 115
       0.051 -    0.077: 22
       0.077 -    0.102: 15
       0.102 -    0.128: 18
  Chirality restraints: 426
  Sorted by residual:
  chirality pdb=" CA  ILE A 116 "
            pdb=" N   ILE A 116 "
            pdb=" C   ILE A 116 "
            pdb=" CB  ILE A 116 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.08e-01
  chirality pdb=" CA  VAL A  35 "
            pdb=" N   VAL A  35 "
            pdb=" C   VAL A  35 "
            pdb=" CB  VAL A  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.92e-01
  chirality pdb=" CA  VAL A   8 "
            pdb=" N   VAL A   8 "
            pdb=" C   VAL A   8 "
            pdb=" CB  VAL A   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.85e-01
  ... (remaining 423 not shown)

  Planarity restraints: 854
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 270 "    0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 271 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 271 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 271 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  47 "    0.025 5.00e-02 4.00e+02   3.71e-02 2.20e+00
        pdb=" N   PRO A  48 "   -0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO A  48 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A  48 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 132 "    0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 133 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 133 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 133 "    0.018 5.00e-02 4.00e+02
  ... (remaining 851 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 591
        2.25 -     2.84: 13058
        2.84 -     3.42: 15231
        3.42 -     4.01: 20833
        4.01 -     4.60: 32303
  Nonbonded interactions: 82016
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  90 "
            pdb=" HG1 THR A  93 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" H   VAL A 302 "
            pdb=" OE1 GLU A 308 "
     model   vdw
     1.662 2.450
  nonbonded pdb=" O   SER A 145 "
            pdb=" H   ALA A 223 "
     model   vdw
     1.784 2.450
  nonbonded pdb=" OD1 ASP A  65 "
            pdb=" H   ARG A  66 "
     model   vdw
     1.790 2.450
  nonbonded pdb=" O   PRO A  81 "
            pdb="HE21 GLN A  86 "
     model   vdw
     1.791 2.450
  ... (remaining 82011 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=0.00 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:             5.710
  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:             0.060
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.080
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6199
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      :  0.002   0.027   2890  Z= 0.106
  Angle     :  0.486   3.747   3930  Z= 0.274
  Chirality :  0.039   0.128    426
  Planarity :  0.004   0.039    511
  Dihedral  : 11.962  85.429   1059
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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:  0.71 (0.45), residues: 363
  helix:  0.36 (0.40), residues: 169
  sheet:  0.78 (0.95), residues: 23
  loop :  0.79 (0.52), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 354 
 TYR   0.005   0.001   TYR A 283 
 PHE   0.005   0.001   PHE A  92 
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.001   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 2890)
  covalent geometry    : angle       0.48629 ( 3930)
  hydrogen bonds       : bond        0.16819 (  135)
  hydrogen bonds       : angle       7.49337 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.9740
  time to fit residues: 50.3137
Evaluate side-chains
  35 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4680 r_free = 0.4680 target = 0.241057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.228501 restraints weight = 17320.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4542 rms_B_bonded: 2.27
r_work: 0.4463 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.4463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4473
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4473 r_free = 0.4473    target_work(ls_wunit_k1) = 0.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4473 r_free = 0.4473    target_work(ls_wunit_k1) = 0.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4473
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6313
moved from start:          0.1602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   2890  Z= 0.171
  Angle     :  0.557   3.953   3930  Z= 0.301
  Chirality :  0.042   0.131    426
  Planarity :  0.005   0.039    511
  Dihedral  :  4.085  15.132    387
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  9.93 %
    Favored  : 90.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.44), residues: 363
  helix:  0.33 (0.37), residues: 174
  sheet:  0.76 (1.01), residues: 23
  loop :  0.78 (0.52), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 354 
 TYR   0.010   0.001   TYR A  99 
 PHE   0.011   0.001   PHE A  92 
 TRP   0.007   0.001   TRP A  62 
 HIS   0.004   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 2890)
  covalent geometry    : angle       0.55662 ( 3930)
  hydrogen bonds       : bond        0.05581 (  135)
  hydrogen bonds       : angle       5.69957 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 LEU cc_start: 0.5939 (tp) cc_final: 0.5586 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 45
  average time/residue: 0.8981
  time to fit residues: 41.8639
Evaluate side-chains
  38 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 4 optimal weight:    0.0980
   chunk 27 optimal weight:    0.8980
   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  72 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.236058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4542 r_free = 0.4542 target = 0.224910 restraints weight = 12717.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.4518 rms_B_bonded: 1.80
r_work: 0.4454 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4373 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.4373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4372 r_free = 0.4372    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4372 r_free = 0.4372    target_work(ls_wunit_k1) = 0.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
r_final: 0.4372
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6516
moved from start:          0.2548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2890  Z= 0.152
  Angle     :  0.546   4.969   3930  Z= 0.290
  Chirality :  0.041   0.136    426
  Planarity :  0.004   0.034    511
  Dihedral  :  4.245  16.435    387
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 10.27 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.38 (0.44), residues: 363
  helix:  0.20 (0.36), residues: 176
  sheet:  0.83 (1.06), residues: 23
  loop :  0.47 (0.53), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 354 
 TYR   0.016   0.002   TYR A  99 
 PHE   0.015   0.002   PHE A  85 
 TRP   0.008   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 2890)
  covalent geometry    : angle       0.54634 ( 3930)
  hydrogen bonds       : bond        0.04898 (  135)
  hydrogen bonds       : angle       5.44754 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.151 
Fit side-chains
REVERT: A   73 SER cc_start: 0.6803 (m) cc_final: 0.6581 (p)
REVERT: A  135 LEU cc_start: 0.6001 (tp) cc_final: 0.5735 (mt)
REVERT: A  144 LYS cc_start: 0.7067 (mmtt) cc_final: 0.6656 (mmpt)
REVERT: A  205 ASN cc_start: 0.7798 (m-40) cc_final: 0.7525 (m-40)
  outliers start: 2
  outliers final: 2
  residues processed: 48
  average time/residue: 1.0656
  time to fit residues: 52.7048
Evaluate side-chains
  40 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  234 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0570
   chunk 8 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.6898

-------------------------------------------------------------------------------
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 = 0.4620 r_free = 0.4620 target = 0.233085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.220815 restraints weight = 17089.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.4486 rms_B_bonded: 2.18
r_work: 0.4413 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work (final): 0.4413
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4416 r_free = 0.4416    target_work(ls_wunit_k1) = 0.213         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6486
moved from start:          0.3189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2890  Z= 0.154
  Angle     :  0.535   4.160   3930  Z= 0.285
  Chirality :  0.041   0.134    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.212  16.929    387
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 12.67 %
    Favored  : 86.99 %
  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 (0.44), residues: 363
  helix:  0.15 (0.37), residues: 177
  sheet:  0.63 (1.04), residues: 23
  loop :  0.51 (0.53), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 354 
 TYR   0.012   0.001   TYR A  99 
 PHE   0.011   0.002   PHE A  47 
 TRP   0.006   0.001   TRP A 129 
 HIS   0.003   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2890)
  covalent geometry    : angle       0.53484 ( 3930)
  hydrogen bonds       : bond        0.04542 (  135)
  hydrogen bonds       : angle       5.38288 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 41
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.6750 (m) cc_final: 0.6508 (p)
REVERT: A  135 LEU cc_start: 0.5881 (tp) cc_final: 0.5618 (mp)
REVERT: A  140 LYS cc_start: 0.6292 (mmtp) cc_final: 0.5838 (mmmt)
REVERT: A  144 LYS cc_start: 0.6923 (mmtt) cc_final: 0.6505 (mmpt)
REVERT: A  205 ASN cc_start: 0.7731 (m-40) cc_final: 0.7460 (m-40)
REVERT: A  328 GLU cc_start: 0.7601 (tt0) cc_final: 0.7371 (tt0)
  outliers start: 1
  outliers final: 1
  residues processed: 42
  average time/residue: 0.8998
  time to fit residues: 39.0490
Evaluate side-chains
  40 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    0.4980
   chunk 7 optimal weight:    0.5980
   chunk 10 optimal weight:    0.3980
   chunk 2 optimal weight:    0.3980
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.4780

-------------------------------------------------------------------------------
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 = 0.4628 r_free = 0.4628 target = 0.233467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.220899 restraints weight = 18061.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.4490 rms_B_bonded: 2.28
r_work: 0.4408 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.4408
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4413
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4413 r_free = 0.4413    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4413 r_free = 0.4413    target_work(ls_wunit_k1) = 0.212         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.4413
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2890  Z= 0.119
  Angle     :  0.496   4.080   3930  Z= 0.258
  Chirality :  0.039   0.132    426
  Planarity :  0.004   0.031    511
  Dihedral  :  4.063  15.153    387
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  0.34 %
    Allowed  : 13.01 %
    Favored  : 86.64 %
  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:  0.48 (0.44), residues: 363
  helix:  0.32 (0.38), residues: 177
  sheet:  0.60 (1.00), residues: 23
  loop :  0.51 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 354 
 TYR   0.006   0.001   TYR A  99 
 PHE   0.009   0.001   PHE A  47 
 TRP   0.005   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 2890)
  covalent geometry    : angle       0.49621 ( 3930)
  hydrogen bonds       : bond        0.04086 (  135)
  hydrogen bonds       : angle       5.17915 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.6715 (m) cc_final: 0.6480 (p)
REVERT: A  135 LEU cc_start: 0.5927 (tp) cc_final: 0.5577 (mp)
REVERT: A  140 LYS cc_start: 0.6169 (mmtp) cc_final: 0.5706 (mmmt)
REVERT: A  144 LYS cc_start: 0.6912 (mmtt) cc_final: 0.6462 (mmpt)
REVERT: A  205 ASN cc_start: 0.7761 (m-40) cc_final: 0.7508 (m-40)
  outliers start: 1
  outliers final: 1
  residues processed: 43
  average time/residue: 0.7737
  time to fit residues: 34.6158
Evaluate side-chains
  43 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 42
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4603 r_free = 0.4603 target = 0.230731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.218440 restraints weight = 17558.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.4468 rms_B_bonded: 2.26
r_work: 0.4390 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work (final): 0.4390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4392 r_free = 0.4392    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4392 r_free = 0.4392    target_work(ls_wunit_k1) = 0.210         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6533
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2890  Z= 0.156
  Angle     :  0.527   4.085   3930  Z= 0.277
  Chirality :  0.041   0.132    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.189  16.676    387
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 3.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 12.67 %
    Favored  : 86.64 %
  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:  0.37 (0.44), residues: 363
  helix:  0.31 (0.38), residues: 177
  sheet:  0.40 (0.98), residues: 23
  loop :  0.36 (0.53), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 354 
 TYR   0.007   0.001   TYR A 167 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.007   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 2890)
  covalent geometry    : angle       0.52739 ( 3930)
  hydrogen bonds       : bond        0.04395 (  135)
  hydrogen bonds       : angle       5.30321 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 40
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.6789 (m) cc_final: 0.6548 (p)
REVERT: A  135 LEU cc_start: 0.6001 (tp) cc_final: 0.5657 (mp)
REVERT: A  140 LYS cc_start: 0.6214 (mmtp) cc_final: 0.5813 (mmmt)
REVERT: A  205 ASN cc_start: 0.7801 (m-40) cc_final: 0.7545 (m-40)
  outliers start: 2
  outliers final: 1
  residues processed: 42
  average time/residue: 0.8296
  time to fit residues: 36.3446
Evaluate side-chains
  40 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 39
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   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 = 0.4588 r_free = 0.4588 target = 0.228677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.216704 restraints weight = 16479.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.4458 rms_B_bonded: 2.16
r_work: 0.4389 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.4296 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.4296
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4290 r_free = 0.4290    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4290 r_free = 0.4290    target_work(ls_wunit_k1) = 0.198         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4290
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6679
moved from start:          0.4262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2890  Z= 0.164
  Angle     :  0.553   4.813   3930  Z= 0.290
  Chirality :  0.041   0.134    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.291  17.003    387
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.64 %
    Favored  : 86.99 %
  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:  0.20 (0.44), residues: 363
  helix:  0.22 (0.38), residues: 177
  sheet:  0.26 (0.97), residues: 23
  loop :  0.22 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 354 
 TYR   0.013   0.002   TYR A 171 
 PHE   0.013   0.002   PHE A  47 
 TRP   0.007   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 2890)
  covalent geometry    : angle       0.55271 ( 3930)
  hydrogen bonds       : bond        0.04386 (  135)
  hydrogen bonds       : angle       5.35349 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 40
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.7058 (m) cc_final: 0.6830 (p)
REVERT: A  135 LEU cc_start: 0.6109 (tp) cc_final: 0.5734 (mp)
REVERT: A  140 LYS cc_start: 0.6414 (mmtp) cc_final: 0.6011 (mmmt)
REVERT: A  205 ASN cc_start: 0.7894 (m-40) cc_final: 0.7641 (m-40)
REVERT: A  365 GLN cc_start: 0.6723 (tp-100) cc_final: 0.6189 (tt0)
  outliers start: 4
  outliers final: 3
  residues processed: 42
  average time/residue: 0.7431
  time to fit residues: 32.5207
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  234 ASN
Chi-restraints excluded: chain A residue  330 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0670
   chunk 28 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   chunk 2 optimal weight:    0.9990
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.4598 r_free = 0.4598 target = 0.229836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.217966 restraints weight = 17028.972|
|-----------------------------------------------------------------------------|
r_work (start): 0.4464 rms_B_bonded: 2.19
r_work: 0.4394 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.4299 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.4299
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4299
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4299 r_free = 0.4299    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4299 r_free = 0.4299    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4299
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6646
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   2890  Z= 0.120
  Angle     :  0.510   4.024   3930  Z= 0.262
  Chirality :  0.040   0.133    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.109  15.298    387
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 12.67 %
    Favored  : 85.96 %
  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:  0.37 (0.44), residues: 363
  helix:  0.32 (0.38), residues: 177
  sheet:  0.38 (0.97), residues: 23
  loop :  0.35 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 354 
 TYR   0.010   0.001   TYR A 171 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.000   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2890)
  covalent geometry    : angle       0.51008 ( 3930)
  hydrogen bonds       : bond        0.03934 (  135)
  hydrogen bonds       : angle       5.20799 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.134 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.7030 (m) cc_final: 0.6820 (p)
REVERT: A  135 LEU cc_start: 0.6035 (tp) cc_final: 0.5683 (mp)
REVERT: A  140 LYS cc_start: 0.6343 (mmtp) cc_final: 0.5931 (mmmt)
REVERT: A  178 ILE cc_start: 0.7474 (mm) cc_final: 0.7120 (mp)
REVERT: A  205 ASN cc_start: 0.7867 (m-40) cc_final: 0.7627 (m-40)
REVERT: A  365 GLN cc_start: 0.6609 (tp-100) cc_final: 0.6104 (tt0)
  outliers start: 4
  outliers final: 2
  residues processed: 43
  average time/residue: 0.8154
  time to fit residues: 36.4534
Evaluate side-chains
  40 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 38
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  330 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 4 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   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 = 0.4536 r_free = 0.4536 target = 0.226249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.215224 restraints weight = 14450.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.4442 rms_B_bonded: 1.86
r_work: 0.4375 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.4292 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.4292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4291 r_free = 0.4291    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4291 r_free = 0.4291    target_work(ls_wunit_k1) = 0.199         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.4465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2890  Z= 0.150
  Angle     :  0.532   4.407   3930  Z= 0.277
  Chirality :  0.041   0.136    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.218  16.499    387
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  : 13.36 %
    Favored  : 85.62 %
  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 aren not related in a simple way.
  whole:  0.19 (0.44), residues: 363
  helix:  0.20 (0.38), residues: 177
  sheet:  0.25 (0.96), residues: 23
  loop :  0.25 (0.51), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 354 
 TYR   0.012   0.001   TYR A 171 
 PHE   0.011   0.001   PHE A  47 
 TRP   0.006   0.001   TRP A 129 
 HIS   0.002   0.001   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2890)
  covalent geometry    : angle       0.53160 ( 3930)
  hydrogen bonds       : bond        0.04250 (  135)
  hydrogen bonds       : angle       5.31501 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 39
  time to evaluate  : 0.177 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.6985 (m) cc_final: 0.6773 (p)
REVERT: A  135 LEU cc_start: 0.6053 (tp) cc_final: 0.5732 (mp)
REVERT: A  140 LYS cc_start: 0.6314 (mmtp) cc_final: 0.5922 (mmmt)
REVERT: A  178 ILE cc_start: 0.7558 (mm) cc_final: 0.7265 (mp)
REVERT: A  205 ASN cc_start: 0.7888 (m-40) cc_final: 0.7659 (m-40)
REVERT: A  365 GLN cc_start: 0.6600 (tp-100) cc_final: 0.6098 (tt0)
  outliers start: 3
  outliers final: 2
  residues processed: 41
  average time/residue: 0.8532
  time to fit residues: 36.4046
Evaluate side-chains
  41 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  330 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.4540 r_free = 0.4540 target = 0.226595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4442 r_free = 0.4442 target = 0.214383 restraints weight = 19283.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.4435 rms_B_bonded: 2.25
r_work: 0.4356 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4355 r_free = 0.4355    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4355 r_free = 0.4355    target_work(ls_wunit_k1) = 0.207         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   2890  Z= 0.136
  Angle     :  0.514   3.992   3930  Z= 0.268
  Chirality :  0.040   0.131    426
  Planarity :  0.004   0.033    511
  Dihedral  :  4.186  15.907    387
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 13.70 %
    Favored  : 85.62 %
  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 aren not related in a simple way.
  whole:  0.23 (0.44), residues: 363
  helix:  0.22 (0.38), residues: 177
  sheet:  0.27 (0.96), residues: 23
  loop :  0.28 (0.51), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 354 
 TYR   0.010   0.001   TYR A 171 
 PHE   0.010   0.001   PHE A  47 
 TRP   0.006   0.001   TRP A 129 
 HIS   0.001   0.000   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 2890)
  covalent geometry    : angle       0.51427 ( 3930)
  hydrogen bonds       : bond        0.04060 (  135)
  hydrogen bonds       : angle       5.26270 (  419)

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

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

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  726 Ramachandran restraints generated.
    363 Oldfield, 0 Emsley, 363 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 SER cc_start: 0.6782 (m) cc_final: 0.6576 (p)
REVERT: A  135 LEU cc_start: 0.6035 (tp) cc_final: 0.5730 (mp)
REVERT: A  140 LYS cc_start: 0.6185 (mmtp) cc_final: 0.5786 (mmmt)
REVERT: A  178 ILE cc_start: 0.7535 (mm) cc_final: 0.7296 (mp)
REVERT: A  205 ASN cc_start: 0.7817 (m-40) cc_final: 0.7613 (m-40)
REVERT: A  365 GLN cc_start: 0.6421 (tp-100) cc_final: 0.5981 (tt0)
  outliers start: 2
  outliers final: 2
  residues processed: 40
  average time/residue: 0.8469
  time to fit residues: 35.2543
Evaluate side-chains
  41 residues out of total 286 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 39
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 THR
Chi-restraints excluded: chain A residue  330 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 36
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 34 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0370
   chunk 8 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.4598 r_free = 0.4598 target = 0.230154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.219455 restraints weight = 13767.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.4470 rms_B_bonded: 1.86
r_work: 0.4405 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.4321 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.4321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4327
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4327 r_free = 0.4327    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4327 r_free = 0.4327    target_work(ls_wunit_k1) = 0.202         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4327
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.4574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.019   2890  Z= 0.112
  Angle     :  0.498   3.982   3930  Z= 0.255
  Chirality :  0.040   0.132    426
  Planarity :  0.004   0.032    511
  Dihedral  :  4.011  14.015    387
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 13.70 %
    Favored  : 85.62 %
  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 aren not related in a simple way.
  whole:  0.39 (0.44), residues: 363
  helix:  0.33 (0.38), residues: 177
  sheet:  0.43 (0.96), residues: 23
  loop :  0.38 (0.52), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 354 
 TYR   0.010   0.001   TYR A 171 
 PHE   0.008   0.001   PHE A  47 
 TRP   0.005   0.001   TRP A 129 
 HIS   0.001   0.000   HIS A  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 2890)
  covalent geometry    : angle       0.49814 ( 3930)
  hydrogen bonds       : bond        0.03765 (  135)
  hydrogen bonds       : angle       5.12171 (  419)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2853.16 seconds
wall clock time: 49 minutes 7.15 seconds (2947.15 seconds total)