Starting phenix.real_space_refine
on Tue Aug  4 16:42:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9vcv_64969/08_2026/9vcv_64969.map"
  }
  resolution = 3.63
  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=   0.032
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
     P       4      5.49       5
     S      28      5.16       5
     C    3119      2.51       5
     N     831      2.21       5
     O     909      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4891
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4811
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 601, 4811
          Classifications: {'peptide': 601}
          Link IDs: {'PTRANS': 32, 'TRANS': 568}
    Chain: "C"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 80
          Classifications: {'RNA': 4}
          Modifications used: {'rna3p_pyr': 4}
          Link IDs: {'rna3p': 3}
  Time building chain proxies: 0.94, per 1000 atoms: 0.19
  Number of scatterers: 4891
  At special positions: 0
  Unit cell: (79.68, 73.04, 112.05, 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      28     16.00
     P       4     15.00
     O     909      8.00
     N     831      7.00
     C    3119      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 111.6 milliseconds
  

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1146

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 3 sheets defined
      57.7% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 89 through 103
    Processing helix  chain 'A' and resid 103 through 113
      removed outlier: 3.656A  pdb=" N   TYR A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 134
    Processing helix  chain 'A' and resid 138 through 150
    Processing helix  chain 'A' and resid 154 through 157
    Processing helix  chain 'A' and resid 158 through 170
    Processing helix  chain 'A' and resid 171 through 183
      removed outlier: 5.480A  pdb=" N   ASP A 177 " --> pdb=" O   LEU A 173 " (cutoff:3.500A)
      removed outlier: 5.276A  pdb=" N   ASP A 178 " --> pdb=" O   ASP A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 191
    Processing helix  chain 'A' and resid 192 through 198
      removed outlier: 3.526A  pdb=" N   ARG A 196 " --> pdb=" O   TYR A 192 " (cutoff:3.500A)
      removed outlier: 4.380A  pdb=" N   MET A 198 " --> pdb=" O   ASP A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 224
      removed outlier: 3.553A  pdb=" N   HIS A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 247
    Processing helix  chain 'A' and resid 292 through 298
    Processing helix  chain 'A' and resid 301 through 312
      removed outlier: 3.994A  pdb=" N   TRP A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 322 through 324
      No H-bonds generated for 'chain 'A' and resid 322 through 324'
    Processing helix  chain 'A' and resid 325 through 337
    Processing helix  chain 'A' and resid 374 through 389
    Processing helix  chain 'A' and resid 400 through 412
    Processing helix  chain 'A' and resid 426 through 429
    Processing helix  chain 'A' and resid 460 through 470
    Processing helix  chain 'A' and resid 487 through 498
      removed outlier: 3.633A  pdb=" N   LEU A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 528 through 539
    Processing helix  chain 'A' and resid 551 through 561
    Processing helix  chain 'A' and resid 567 through 576
    Processing helix  chain 'A' and resid 583 through 600
      removed outlier: 4.087A  pdb=" N   CYS A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 612
      removed outlier: 3.648A  pdb=" N   LEU A 608 " --> pdb=" O   THR A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 643
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 4.175A  pdb=" N   ASN A 672 " --> pdb=" O   ASP A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 683
      removed outlier: 3.758A  pdb=" N   LEU A 676 " --> pdb=" O   ASN A 672 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 274 through 275
      removed outlier: 6.727A  pdb=" N   GLU A 286 " --> pdb=" O   ALA A 314 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 288 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS A 318 " --> pdb=" O   ALA A 288 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   LYS A 201 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   LEU A 319 " --> pdb=" O   LYS A 201 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   ILE A 203 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
      removed outlier: 8.434A  pdb=" N   GLY A 321 " --> pdb=" O   ILE A 203 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   HIS A 205 " --> pdb=" O   GLY A 321 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   PHE A 204 " --> pdb=" O   GLU A 341 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353
      removed outlier: 7.376A  pdb=" N   SER A 352 " --> pdb=" O   VAL A 483 " (cutoff:3.500A)
      removed outlier: 9.742A  pdb=" N   THR A 485 " --> pdb=" O   SER A 352 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   ILE A 438 " --> pdb=" O   THR A 484 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ALA A 423 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR A 424 " --> pdb=" O   ILE A 395 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 444 through 447

    246 hydrogen bonds defined for protein.
    699 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: 0.67

  Time building geometry restraints manager: 0.35 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: 1556
        1.34 -     1.46: 741
        1.46 -     1.58: 2663
        1.58 -     1.70: 7
        1.70 -     1.82: 42
  Bond restraints: 5009
  Sorted by residual:
  bond pdb=" C   TRP A 614 "
       pdb=" N   PRO A 615 "
    ideal  model  delta    sigma   weight residual
    1.335  1.365 -0.030 8.70e-03 1.32e+04 1.22e+01
  bond pdb=" N1    U C   3 "
       pdb=" C2    U C   3 "
    ideal  model  delta    sigma   weight residual
    1.381  1.402 -0.021 9.00e-03 1.23e+04 5.54e+00
  bond pdb=" C   PRO A 188 "
       pdb=" N   PRO A 189 "
    ideal  model  delta    sigma   weight residual
    1.334  1.369 -0.035 2.34e-02 1.83e+03 2.22e+00
  bond pdb=" CG  MET A 330 "
       pdb=" SD  MET A 330 "
    ideal  model  delta    sigma   weight residual
    1.803  1.769  0.034 2.50e-02 1.60e+03 1.88e+00
  bond pdb=" CA  GLU A 453 "
       pdb=" CB  GLU A 453 "
    ideal  model  delta    sigma   weight residual
    1.533  1.552 -0.019 1.90e-02 2.77e+03 1.02e+00
  ... (remaining 5004 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.12: 6656
        2.12 -     4.25: 111
        4.25 -     6.37: 18
        6.37 -     8.50: 8
        8.50 -    10.62: 5
  Bond angle restraints: 6798
  Sorted by residual:
  angle pdb=" C1'   U C   3 "
        pdb=" N1    U C   3 "
        pdb=" C2    U C   3 "
      ideal   model   delta    sigma   weight residual
     117.70  126.96   -9.26 1.20e+00 6.94e-01 5.95e+01
  angle pdb=" N1    U C   3 "
        pdb=" C2    U C   3 "
        pdb=" O2    U C   3 "
      ideal   model   delta    sigma   weight residual
     122.80  128.00   -5.20 7.00e-01 2.04e+00 5.51e+01
  angle pdb=" O2    U C   3 "
        pdb=" C2    U C   3 "
        pdb=" N3    U C   3 "
      ideal   model   delta    sigma   weight residual
     122.20  117.34    4.86 7.00e-01 2.04e+00 4.81e+01
  angle pdb=" CA  MET A 330 "
        pdb=" CB  MET A 330 "
        pdb=" CG  MET A 330 "
      ideal   model   delta    sigma   weight residual
     114.10  124.40  -10.30 2.00e+00 2.50e-01 2.65e+01
  angle pdb=" C1'   U C   3 "
        pdb=" N1    U C   3 "
        pdb=" C6    U C   3 "
      ideal   model   delta    sigma   weight residual
     121.20  114.18    7.02 1.40e+00 5.10e-01 2.52e+01
  ... (remaining 6793 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.26: 2882
       30.26 -    60.52: 163
       60.52 -    90.79: 12
       90.79 -   121.05: 0
      121.05 -   151.31: 2
  Dihedral angle restraints: 3059
    sinusoidal: 1293
      harmonic: 1766
  Sorted by residual:
  dihedral pdb=" O4'   U C   4 "
           pdb=" C1'   U C   4 "
           pdb=" N1    U C   4 "
           pdb=" C2    U C   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   48.69  151.31     1      1.50e+01 4.44e-03 8.01e+01
  dihedral pdb=" O4'   U C   2 "
           pdb=" C1'   U C   2 "
           pdb=" N1    U C   2 "
           pdb=" C2    U C   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   53.14  146.86     1      1.50e+01 4.44e-03 7.84e+01
  dihedral pdb=" O4'   U C   3 "
           pdb=" C1'   U C   3 "
           pdb=" N1    U C   3 "
           pdb=" C2    U C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  117.31   82.69     1      1.50e+01 4.44e-03 3.72e+01
  ... (remaining 3056 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 521
       0.033 -    0.067: 155
       0.067 -    0.100: 54
       0.100 -    0.134: 27
       0.134 -    0.167: 6
  Chirality restraints: 763
  Sorted by residual:
  chirality pdb=" CA  MET A 330 "
            pdb=" N   MET A 330 "
            pdb=" C   MET A 330 "
            pdb=" CB  MET A 330 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.97e-01
  chirality pdb=" CB  ILE A 187 "
            pdb=" CA  ILE A 187 "
            pdb=" CG1 ILE A 187 "
            pdb=" CG2 ILE A 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.56e-01
  chirality pdb=" CB  ILE A 444 "
            pdb=" CA  ILE A 444 "
            pdb=" CG1 ILE A 444 "
            pdb=" CG2 ILE A 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.15 2.00e-01 2.50e+01 5.30e-01
  ... (remaining 760 not shown)

  Planarity restraints: 862
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 188 "    0.035 5.00e-02 4.00e+02   5.37e-02 4.61e+00
        pdb=" N   PRO A 189 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 363 "    0.011 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   ASN A 363 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 363 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A 364 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 365 "    0.029 5.00e-02 4.00e+02   4.44e-02 3.15e+00
        pdb=" N   PRO A 366 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 366 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 366 "    0.025 5.00e-02 4.00e+02
  ... (remaining 859 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 495
        2.74 -     3.28: 5338
        3.28 -     3.82: 8882
        3.82 -     4.36: 9783
        4.36 -     4.90: 16031
  Nonbonded interactions: 40529
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 374 "
            pdb=" OD1 ASN A 376 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" OG  SER A 374 "
            pdb=" OD2 ASP A 377 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ILE A 564 "
            pdb=" NH2 ARG A 571 "
     model   vdw
     2.266 3.120
  nonbonded pdb=" OG1 THR A 209 "
            pdb=" OE1 GLN A 466 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" N   GLN A 545 "
            pdb=" OE1 GLN A 545 "
     model   vdw
     2.300 3.120
  ... (remaining 40524 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             1.050
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.610
  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:0.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
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      :  0.003   0.035   5009  Z= 0.149
  Angle     :  0.738  10.624   6798  Z= 0.429
  Chirality :  0.043   0.167    763
  Planarity :  0.004   0.054    862
  Dihedral  : 17.942 151.309   1913
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.67 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.57 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.36), residues: 599
  helix:  1.39 (0.30), residues: 326
  sheet: -1.33 (0.74), residues: 60
  loop : -0.57 (0.43), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 383 
 TYR   0.009   0.001   TYR A 379 
 PHE   0.008   0.001   PHE A 593 
 TRP   0.022   0.002   TRP A 614 
 HIS   0.002   0.000   HIS A 271 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00288 /  0.15 ( 5009)
  covalent geometry    : angle       0.73788 /  0.43 ( 6798)
  hydrogen bonds       : bond        0.15342 /  9.76 (  246)
  hydrogen bonds       : angle       5.39607 /  4.11 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.0315
  time to fit residues: 2.6429
Evaluate side-chains
  51 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0040
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   overall best weight:    1.4598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 199 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.152340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.111315 restraints weight = 12563.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.114977 restraints weight = 7491.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.117280 restraints weight = 5430.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.119444 restraints weight = 4430.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.120511 restraints weight = 3798.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.4016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7128
moved from start:          0.0860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5009  Z= 0.169
  Angle     :  0.650   9.714   6798  Z= 0.340
  Chirality :  0.043   0.161    763
  Planarity :  0.005   0.060    862
  Dihedral  : 11.110 153.894    714
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.17 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 26.55 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.36), residues: 599
  helix:  1.32 (0.29), residues: 328
  sheet: -1.78 (0.84), residues: 45
  loop : -0.61 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 301 
 TYR   0.012   0.001   TYR A 229 
 PHE   0.008   0.001   PHE A 574 
 TRP   0.006   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A 271 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00370 /  0.17 ( 5009)
  covalent geometry    : angle       0.65019 /  0.34 ( 6798)
  hydrogen bonds       : bond        0.04122 /  2.63 (  246)
  hydrogen bonds       : angle       4.55833 /  3.45 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  316 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.6911 (mp0)
REVERT: A  482 GLU cc_start: 0.7681 (pm20) cc_final: 0.7435 (pm20)
REVERT: A  621 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.7911 (p0)
  outliers start: 18
  outliers final: 8
  residues processed: 72
  average time/residue: 0.0376
  time to fit residues: 3.9944
Evaluate side-chains
  66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  316 GLU
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 8 optimal weight:    6.9990
   chunk 21 optimal weight:    0.2980
   chunk 36 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    0.2980
   chunk 14 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 363 ASN
A 511 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.159614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.118003 restraints weight = 12131.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.121883 restraints weight = 7321.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.124350 restraints weight = 5306.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.125776 restraints weight = 4336.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 71)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.127445 restraints weight = 3824.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5009  Z= 0.126
  Angle     :  0.617   9.858   6798  Z= 0.321
  Chirality :  0.042   0.169    763
  Planarity :  0.005   0.063    862
  Dihedral  : 11.092 154.272    714
  Min Nonbonded Distance : 2.275

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.34 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 25.99 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.44 (0.35), residues: 599
  helix:  1.27 (0.29), residues: 328
  sheet: -1.76 (0.83), residues: 45
  loop : -0.64 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 383 
 TYR   0.010   0.001   TYR A 229 
 PHE   0.014   0.001   PHE A 593 
 TRP   0.008   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.13 ( 5009)
  covalent geometry    : angle       0.61672 /  0.32 ( 6798)
  hydrogen bonds       : bond        0.03583 /  2.31 (  246)
  hydrogen bonds       : angle       4.36514 /  3.30 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6998 (tt0)
REVERT: A  279 CYS cc_start: 0.8087 (t) cc_final: 0.7875 (p)
REVERT: A  421 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5774 (pp)
REVERT: A  621 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8074 (p0)
REVERT: A  651 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6216 (m-30)
  outliers start: 20
  outliers final: 7
  residues processed: 76
  average time/residue: 0.0490
  time to fit residues: 5.5232
Evaluate side-chains
  66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  651 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 54 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 56 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0040
   overall best weight:    0.6192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.160551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.118760 restraints weight = 11937.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.122937 restraints weight = 6682.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.126040 restraints weight = 4714.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.127751 restraints weight = 3750.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.128598 restraints weight = 3237.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5009  Z= 0.121
  Angle     :  0.622   9.803   6798  Z= 0.317
  Chirality :  0.042   0.169    763
  Planarity :  0.004   0.064    862
  Dihedral  : 11.065 154.972    714
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.17 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 24.86 %
    Favored  : 70.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.36), residues: 599
  helix:  1.26 (0.29), residues: 330
  sheet: -1.67 (0.83), residues: 45
  loop : -0.54 (0.43), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 383 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.015   0.001   PHE A 593 
 TRP   0.007   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 ( 5009)
  covalent geometry    : angle       0.62229 /  0.32 ( 6798)
  hydrogen bonds       : bond        0.03221 /  2.06 (  246)
  hydrogen bonds       : angle       4.27291 /  3.23 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  263 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6948 (tt0)
REVERT: A  279 CYS cc_start: 0.8097 (t) cc_final: 0.7824 (p)
REVERT: A  421 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5609 (pp)
REVERT: A  621 ASN cc_start: 0.8780 (OUTLIER) cc_final: 0.8150 (p0)
REVERT: A  623 LYS cc_start: 0.9094 (OUTLIER) cc_final: 0.8852 (mmmt)
  outliers start: 23
  outliers final: 10
  residues processed: 80
  average time/residue: 0.0598
  time to fit residues: 6.7680
Evaluate side-chains
  71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 57
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  662 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 12 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    1.3184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 511 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.154469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.112711 restraints weight = 12469.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.116826 restraints weight = 7208.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 68)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.119577 restraints weight = 5127.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.121155 restraints weight = 4108.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.122317 restraints weight = 3571.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7082
moved from start:          0.1345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5009  Z= 0.153
  Angle     :  0.631   9.489   6798  Z= 0.327
  Chirality :  0.042   0.164    763
  Planarity :  0.005   0.062    862
  Dihedral  : 11.114 155.745    714
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.67 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 24.48 %
    Favored  : 70.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.36), residues: 599
  helix:  1.27 (0.29), residues: 330
  sheet: -1.57 (0.93), residues: 40
  loop : -0.58 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 436 
 TYR   0.011   0.001   TYR A 229 
 PHE   0.013   0.001   PHE A 593 
 TRP   0.009   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A 511 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00338 /  0.15 ( 5009)
  covalent geometry    : angle       0.63141 /  0.33 ( 6798)
  hydrogen bonds       : bond        0.03370 /  2.16 (  246)
  hydrogen bonds       : angle       4.34112 /  3.28 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 57
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8333 (mm)
REVERT: A  243 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8705 (mttp)
REVERT: A  263 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6913 (tt0)
REVERT: A  421 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5725 (pp)
REVERT: A  621 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8150 (p0)
REVERT: A  623 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8883 (mmmt)
REVERT: A  651 ASP cc_start: 0.7155 (OUTLIER) cc_final: 0.6544 (m-30)
  outliers start: 29
  outliers final: 13
  residues processed: 80
  average time/residue: 0.0517
  time to fit residues: 5.6785
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 56
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  477 ARG
Chi-restraints excluded: chain A residue  542 VAL
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  651 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 38 optimal weight:    5.9990
   chunk 3 optimal weight:    7.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    6.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.8784

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.159686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.117742 restraints weight = 12197.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.121885 restraints weight = 7013.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.124862 restraints weight = 4985.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.126538 restraints weight = 3975.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.127870 restraints weight = 3441.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.4030
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.1411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5009  Z= 0.133
  Angle     :  0.657   9.756   6798  Z= 0.333
  Chirality :  0.043   0.183    763
  Planarity :  0.005   0.063    862
  Dihedral  : 11.139 155.949    714
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.84 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  5.27 %
    Allowed  : 25.24 %
    Favored  : 69.49 %
  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 are not related in a simple way.
  whole:  0.52 (0.36), residues: 599
  helix:  1.25 (0.29), residues: 330
  sheet: -1.53 (0.92), residues: 40
  loop : -0.55 (0.43), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 477 
 TYR   0.010   0.001   TYR A 229 
 PHE   0.016   0.001   PHE A 593 
 TRP   0.012   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 ( 5009)
  covalent geometry    : angle       0.65661 /  0.33 ( 6798)
  hydrogen bonds       : bond        0.03217 /  2.06 (  246)
  hydrogen bonds       : angle       4.26420 /  3.22 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 57
  time to evaluate  : 0.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8346 (mm)
REVERT: A  263 GLN cc_start: 0.7338 (OUTLIER) cc_final: 0.6969 (tt0)
REVERT: A  421 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5621 (pp)
REVERT: A  621 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8154 (p0)
REVERT: A  623 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8795 (mmmt)
  outliers start: 28
  outliers final: 15
  residues processed: 81
  average time/residue: 0.0449
  time to fit residues: 5.0222
Evaluate side-chains
  73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 53
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  427 ILE
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  477 ARG
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  623 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 27 optimal weight:    7.9990
   chunk 41 optimal weight:    0.0470
   chunk 7 optimal weight:    7.9990
   chunk 18 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 52 optimal weight:    0.2980
   overall best weight:    0.5078

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.161156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.119195 restraints weight = 12347.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.123362 restraints weight = 7116.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.125976 restraints weight = 5104.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.127507 restraints weight = 4170.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 68)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.129359 restraints weight = 3671.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.4046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5009  Z= 0.124
  Angle     :  0.667   9.899   6798  Z= 0.334
  Chirality :  0.042   0.176    763
  Planarity :  0.005   0.064    862
  Dihedral  : 11.192 156.263    714
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.84 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.80 %
    Favored  : 69.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.36), residues: 599
  helix:  1.25 (0.30), residues: 328
  sheet: -1.53 (0.92), residues: 40
  loop : -0.55 (0.43), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 383 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.015   0.001   PHE A 593 
 TRP   0.016   0.002   TRP A 614 
 HIS   0.002   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 5009)
  covalent geometry    : angle       0.66652 /  0.33 ( 6798)
  hydrogen bonds       : bond        0.03137 /  2.02 (  246)
  hydrogen bonds       : angle       4.20229 /  3.17 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8348 (mm)
REVERT: A  243 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8698 (mttp)
REVERT: A  263 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.6989 (tt0)
REVERT: A  421 LEU cc_start: 0.5963 (OUTLIER) cc_final: 0.5659 (pp)
REVERT: A  621 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8132 (p0)
REVERT: A  623 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8780 (mmmt)
REVERT: A  651 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.5614 (m-30)
  outliers start: 24
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0562
  time to fit residues: 5.9554
Evaluate side-chains
  71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 54
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  383 ARG
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  651 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0970
   chunk 31 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 8 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.5176

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4473 r_free = 0.4473 target = 0.161643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.119587 restraints weight = 12449.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.123630 restraints weight = 7192.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.126671 restraints weight = 5170.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.128376 restraints weight = 4151.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.129402 restraints weight = 3581.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7026
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5009  Z= 0.124
  Angle     :  0.693  10.263   6798  Z= 0.341
  Chirality :  0.043   0.179    763
  Planarity :  0.005   0.065    862
  Dihedral  : 11.262 156.728    714
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 11.98
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.67 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 26.55 %
    Favored  : 69.11 %
  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 are not related in a simple way.
  whole:  0.45 (0.36), residues: 599
  helix:  1.23 (0.30), residues: 327
  sheet: -1.47 (0.79), residues: 50
  loop : -0.57 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 569 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.012   0.001   PHE A 593 
 TRP   0.029   0.002   TRP A 607 
 HIS   0.002   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.12 ( 5009)
  covalent geometry    : angle       0.69296 /  0.34 ( 6798)
  hydrogen bonds       : bond        0.03063 /  1.96 (  246)
  hydrogen bonds       : angle       4.20217 /  3.18 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 58
  time to evaluate  : 0.144 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8284 (mm)
REVERT: A  243 LYS cc_start: 0.9076 (mmtm) cc_final: 0.8699 (mttp)
REVERT: A  263 GLN cc_start: 0.7334 (OUTLIER) cc_final: 0.7026 (tt0)
REVERT: A  333 MET cc_start: 0.7087 (tpt) cc_final: 0.6883 (tpt)
REVERT: A  421 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5603 (pp)
REVERT: A  607 TRP cc_start: 0.7501 (t-100) cc_final: 0.7285 (t-100)
REVERT: A  621 ASN cc_start: 0.8801 (OUTLIER) cc_final: 0.8171 (p0)
  outliers start: 23
  outliers final: 14
  residues processed: 77
  average time/residue: 0.0440
  time to fit residues: 4.7242
Evaluate side-chains
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  383 ARG
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  670 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:   30.0000
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0470
   chunk 27 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0270
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.3936

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.157120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.115434 restraints weight = 12570.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.119538 restraints weight = 7093.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 70)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.122647 restraints weight = 5025.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.124349 restraints weight = 3993.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.125335 restraints weight = 3434.379|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5009  Z= 0.120
  Angle     :  0.690  13.420   6798  Z= 0.340
  Chirality :  0.042   0.184    763
  Planarity :  0.005   0.066    862
  Dihedral  : 11.362 156.920    714
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.67 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 26.93 %
    Favored  : 69.11 %
  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 are not related in a simple way.
  whole:  0.51 (0.36), residues: 599
  helix:  1.29 (0.30), residues: 328
  sheet: -1.46 (0.79), residues: 50
  loop : -0.58 (0.44), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 569 
 TYR   0.012   0.001   TYR A 379 
 PHE   0.011   0.001   PHE A 593 
 TRP   0.018   0.002   TRP A 607 
 HIS   0.002   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 5009)
  covalent geometry    : angle       0.69000 /  0.34 ( 6798)
  hydrogen bonds       : bond        0.03014 /  1.93 (  246)
  hydrogen bonds       : angle       4.18184 /  3.16 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 57
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8278 (mm)
REVERT: A  243 LYS cc_start: 0.9130 (mmtm) cc_final: 0.8762 (mttp)
REVERT: A  263 GLN cc_start: 0.7293 (OUTLIER) cc_final: 0.6992 (tt0)
REVERT: A  421 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5639 (pp)
REVERT: A  621 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8145 (p0)
  outliers start: 21
  outliers final: 15
  residues processed: 75
  average time/residue: 0.0508
  time to fit residues: 5.3854
Evaluate side-chains
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 55
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  383 ARG
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    2.1186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 205 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.152849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.110637 restraints weight = 12549.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.114568 restraints weight = 7303.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 69)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.117413 restraints weight = 5237.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.118787 restraints weight = 4203.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.120060 restraints weight = 3697.567|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5009  Z= 0.210
  Angle     :  0.752  11.666   6798  Z= 0.379
  Chirality :  0.045   0.191    763
  Planarity :  0.006   0.061    862
  Dihedral  : 11.602 158.719    714
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.87
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.67 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 27.50 %
    Favored  : 68.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.36), residues: 599
  helix:  1.18 (0.30), residues: 327
  sheet: -1.59 (0.80), residues: 50
  loop : -0.67 (0.44), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 569 
 TYR   0.012   0.002   TYR A 229 
 PHE   0.012   0.001   PHE A 554 
 TRP   0.052   0.004   TRP A 607 
 HIS   0.005   0.001   HIS A 271 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.21 ( 5009)
  covalent geometry    : angle       0.75181 /  0.38 ( 6798)
  hydrogen bonds       : bond        0.03701 /  2.33 (  246)
  hydrogen bonds       : angle       4.61170 /  3.51 (  699)

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

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

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1198 Ramachandran restraints generated.
    599 Oldfield, 0 Emsley, 599 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  236 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8410 (mm)
REVERT: A  263 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.6943 (tt0)
REVERT: A  421 LEU cc_start: 0.6154 (OUTLIER) cc_final: 0.5858 (pp)
REVERT: A  621 ASN cc_start: 0.8755 (OUTLIER) cc_final: 0.8117 (p0)
REVERT: A  623 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8784 (mmmt)
REVERT: A  651 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6278 (m-30)
  outliers start: 21
  outliers final: 15
  residues processed: 76
  average time/residue: 0.0583
  time to fit residues: 6.2143
Evaluate side-chains
  76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 55
  time to evaluate  : 0.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  173 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  263 GLN
Chi-restraints excluded: chain A residue  278 MET
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 ILE
Chi-restraints excluded: chain A residue  383 ARG
Chi-restraints excluded: chain A residue  398 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 ASP
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  460 THR
Chi-restraints excluded: chain A residue  560 LEU
Chi-restraints excluded: chain A residue  587 CYS
Chi-restraints excluded: chain A residue  621 ASN
Chi-restraints excluded: chain A residue  623 LYS
Chi-restraints excluded: chain A residue  651 ASP
Chi-restraints excluded: chain A residue  670 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 53 optimal weight:    0.2980
   chunk 0 optimal weight:   50.0000
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 13 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.6380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.156210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.114424 restraints weight = 12579.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.118561 restraints weight = 7082.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.121669 restraints weight = 5006.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.123368 restraints weight = 3957.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.124776 restraints weight = 3410.648|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7027
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5009  Z= 0.133
  Angle     :  0.727  14.487   6798  Z= 0.360
  Chirality :  0.043   0.187    763
  Planarity :  0.005   0.062    862
  Dihedral  : 11.682 158.201    714
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.17 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 28.06 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.36), residues: 599
  helix:  1.15 (0.30), residues: 327
  sheet: -1.57 (0.79), residues: 50
  loop : -0.57 (0.45), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 569 
 TYR   0.007   0.001   TYR A 379 
 PHE   0.010   0.001   PHE A 593 
 TRP   0.042   0.003   TRP A 607 
 HIS   0.003   0.000   HIS A 523 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.13 ( 5009)
  covalent geometry    : angle       0.72698 /  0.36 ( 6798)
  hydrogen bonds       : bond        0.03304 /  2.11 (  246)
  hydrogen bonds       : angle       4.41053 /  3.35 (  699)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1164.37 seconds
wall clock time: 20 minutes 38.15 seconds (1238.15 seconds total)