Starting phenix.real_space_refine
on Fri Aug 22 15:41:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ehx_28154/08_2025/8ehx_28154.cif"
  }
  resolution = 3.6
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    3408      2.51       5
     N     840      2.21       5
     O     869      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5153
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5153
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 631, 5153
          Classifications: {'peptide': 631}
          Link IDs: {'PTRANS': 23, 'TRANS': 607}
          Chain breaks: 3
  Time building chain proxies: 1.27, per 1000 atoms: 0.25
  Number of scatterers: 5153
  At special positions: 0
  Unit cell: (104.775, 83.325, 84.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O     869      8.00
     N     840      7.00
     C    3408      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A 559 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 130.6 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1210

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 1 sheets defined
      71.9% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 31 through 35
      removed outlier: 3.773A  pdb=" N   GLY A  35 " --> pdb=" O   VAL A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 39
    Processing helix  chain 'A' and resid 40 through 67
      removed outlier: 3.512A  pdb=" N   VAL A  44 " --> pdb=" O   GLY A  40 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ASP A  48 " --> pdb=" O   VAL A  44 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   PHE A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 4.718A  pdb=" N   PHE A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   VAL A  65 " --> pdb=" O   ILE A  61 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ALA A  66 " --> pdb=" O   LEU A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 134
      removed outlier: 3.855A  pdb=" N   PHE A 133 " --> pdb=" O   LEU A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 172
      removed outlier: 3.595A  pdb=" N   ILE A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   GLY A 146 " --> pdb=" O   ASP A 142 " (cutoff:3.500A)
      removed outlier: 8.711A  pdb=" N   ASP A 147 " --> pdb=" O   LYS A 143 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   ALA A 148 " --> pdb=" O   CYS A 144 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL A 149 " --> pdb=" O   GLY A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 179
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.726A  pdb=" N   ARG A 192 " --> pdb=" O   SER A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
    Processing helix  chain 'A' and resid 204 through 228
      removed outlier: 3.978A  pdb=" N   HIS A 208 " --> pdb=" O   LEU A 204 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA A 212 " --> pdb=" O   HIS A 208 " (cutoff:3.500A)
      removed outlier: 4.602A  pdb=" N   PHE A 213 " --> pdb=" O   THR A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 264
      removed outlier: 3.578A  pdb=" N   ILE A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   TYR A 264 " --> pdb=" O   PHE A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 306
      removed outlier: 3.717A  pdb=" N   MET A 282 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 352
    Processing helix  chain 'A' and resid 368 through 380
      removed outlier: 3.987A  pdb=" N   THR A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 403
    Processing helix  chain 'A' and resid 404 through 407
    Processing helix  chain 'A' and resid 427 through 458
      removed outlier: 3.854A  pdb=" N   TRP A 431 " --> pdb=" O   GLY A 427 " (cutoff:3.500A)
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 472 through 478
    Processing helix  chain 'A' and resid 478 through 501
      Proline residue:  A 492  - end of helix
      removed outlier: 3.967A  pdb=" N   PHE A 500 " --> pdb=" O   TYR A 496 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   PHE A 501 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 527
    Processing helix  chain 'A' and resid 527 through 544
      removed outlier: 5.095A  pdb=" N   PHE A 541 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 566 through 578
      removed outlier: 3.614A  pdb=" N   VAL A 570 " --> pdb=" O   GLY A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 587
    Processing helix  chain 'A' and resid 595 through 600
      removed outlier: 3.747A  pdb=" N   LEU A 600 " --> pdb=" O   ILE A 596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 612
      removed outlier: 4.209A  pdb=" N   ARG A 607 " --> pdb=" O   SER A 603 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ARG A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASN A 609 " --> pdb=" O   ALA A 605 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 610 " --> pdb=" O   GLU A 606 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 637
      removed outlier: 3.758A  pdb=" N   ALA A 623 " --> pdb=" O   GLN A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 667
      removed outlier: 4.289A  pdb=" N   PHE A 647 " --> pdb=" O   ILE A 643 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   MET A 650 " --> pdb=" O   PRO A 646 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   TYR A 651 " --> pdb=" O   PHE A 647 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   TYR A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 703
      removed outlier: 3.601A  pdb=" N   SER A 678 " --> pdb=" O   LYS A 674 " (cutoff:3.500A)
      Proline residue:  A 688  - end of helix
    Processing helix  chain 'A' and resid 707 through 726
    Processing helix  chain 'A' and resid 727 through 729
      No H-bonds generated for 'chain 'A' and resid 727 through 729'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 276
      removed outlier: 3.611A  pdb=" N   GLU A 271 " --> pdb=" O   THR A 365 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   MET A 361 " --> pdb=" O   CYS A 275 " (cutoff:3.500A)

    307 hydrogen bonds defined for protein.
    894 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: 0.83

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1169
        1.33 -     1.45: 1189
        1.45 -     1.57: 2884
        1.57 -     1.69: 0
        1.69 -     1.81: 54
  Bond restraints: 5296
  Sorted by residual:
  bond pdb=" CG  TYR A 616 "
       pdb=" CD2 TYR A 616 "
    ideal  model  delta    sigma   weight residual
    1.389  1.306  0.083 2.10e-02 2.27e+03 1.58e+01
  bond pdb=" CE2 TYR A 616 "
       pdb=" CZ  TYR A 616 "
    ideal  model  delta    sigma   weight residual
    1.378  1.287  0.091 2.40e-02 1.74e+03 1.45e+01
  bond pdb=" N   HIS A 422 "
       pdb=" CA  HIS A 422 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.26e-02 6.30e+03 8.36e+00
  bond pdb=" CZ  ARG A 607 "
       pdb=" NH1 ARG A 607 "
    ideal  model  delta    sigma   weight residual
    1.323  1.284  0.039 1.40e-02 5.10e+03 7.59e+00
  bond pdb=" CZ  ARG A  29 "
       pdb=" NH2 ARG A  29 "
    ideal  model  delta    sigma   weight residual
    1.330  1.295  0.035 1.30e-02 5.92e+03 7.38e+00
  ... (remaining 5291 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 6869
        1.84 -     3.68: 258
        3.68 -     5.53: 40
        5.53 -     7.37: 11
        7.37 -     9.21: 2
  Bond angle restraints: 7180
  Sorted by residual:
  angle pdb=" N   LEU A 591 "
        pdb=" CA  LEU A 591 "
        pdb=" C   LEU A 591 "
      ideal   model   delta    sigma   weight residual
     113.97  104.76    9.21 1.28e+00 6.10e-01 5.18e+01
  angle pdb=" N   ALA A  54 "
        pdb=" CA  ALA A  54 "
        pdb=" C   ALA A  54 "
      ideal   model   delta    sigma   weight residual
     113.43  106.62    6.81 1.26e+00 6.30e-01 2.92e+01
  angle pdb=" N   LEU A 592 "
        pdb=" CA  LEU A 592 "
        pdb=" C   LEU A 592 "
      ideal   model   delta    sigma   weight residual
     113.19  107.66    5.53 1.19e+00 7.06e-01 2.16e+01
  angle pdb=" N   LEU A  53 "
        pdb=" CA  LEU A  53 "
        pdb=" C   LEU A  53 "
      ideal   model   delta    sigma   weight residual
     113.21  107.88    5.33 1.15e+00 7.56e-01 2.15e+01
  angle pdb=" N   PHE A  59 "
        pdb=" CA  PHE A  59 "
        pdb=" C   PHE A  59 "
      ideal   model   delta    sigma   weight residual
     111.33  106.52    4.81 1.21e+00 6.83e-01 1.58e+01
  ... (remaining 7175 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 2644
       17.93 -    35.87: 352
       35.87 -    53.80: 93
       53.80 -    71.73: 12
       71.73 -    89.66: 3
  Dihedral angle restraints: 3104
    sinusoidal: 1235
      harmonic: 1869
  Sorted by residual:
  dihedral pdb=" CB  CYS A  23 "
           pdb=" SG  CYS A  23 "
           pdb=" SG  CYS A 559 "
           pdb=" CB  CYS A 559 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -157.70   71.70     1      1.00e+01 1.00e-02 6.59e+01
  dihedral pdb=" CA  LEU A 537 "
           pdb=" C   LEU A 537 "
           pdb=" N   ASP A 538 "
           pdb=" CA  ASP A 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.08   26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  VAL A 278 "
           pdb=" C   VAL A 278 "
           pdb=" N   ALA A 279 "
           pdb=" CA  ALA A 279 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.02  -18.98     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 3101 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 645
       0.055 -    0.110: 139
       0.110 -    0.165: 19
       0.165 -    0.221: 0
       0.221 -    0.276: 5
  Chirality restraints: 808
  Sorted by residual:
  chirality pdb=" CA  ILE A  61 "
            pdb=" N   ILE A  61 "
            pdb=" C   ILE A  61 "
            pdb=" CB  ILE A  61 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.71   -0.28 2.00e-01 2.50e+01 1.90e+00
  chirality pdb=" CA  ALA A 604 "
            pdb=" N   ALA A 604 "
            pdb=" C   ALA A 604 "
            pdb=" CB  ALA A 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.24    0.25 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" CA  LEU A  58 "
            pdb=" N   LEU A  58 "
            pdb=" C   LEU A  58 "
            pdb=" CB  LEU A  58 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 805 not shown)

  Planarity restraints: 877
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 616 "   -0.016 2.00e-02 2.50e+03   3.66e-02 2.68e+01
        pdb=" CG  TYR A 616 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 616 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 616 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 616 "    0.042 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 616 "    0.058 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 616 "   -0.035 2.00e-02 2.50e+03
        pdb=" OH  TYR A 616 "   -0.038 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 645 "    0.061 5.00e-02 4.00e+02   9.10e-02 1.33e+01
        pdb=" N   PRO A 646 "   -0.157 5.00e-02 4.00e+02
        pdb=" CA  PRO A 646 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 646 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 229 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.76e+00
        pdb=" C   LYS A 229 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS A 229 "    0.017 2.00e-02 2.50e+03
        pdb=" N   MET A 230 "    0.015 2.00e-02 2.50e+03
  ... (remaining 874 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 804
        2.75 -     3.29: 5331
        3.29 -     3.83: 8552
        3.83 -     4.36: 9629
        4.36 -     4.90: 16399
  Nonbonded interactions: 40715
  Sorted by model distance:
  nonbonded pdb=" O   ASN A 177 "
            pdb=" ND2 ASN A 197 "
     model   vdw
     2.214 3.120
  nonbonded pdb=" O   MET A 628 "
            pdb=" OG1 THR A 632 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" ND2 ASN A 177 "
            pdb=" O   THR A 193 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" O   SER A 603 "
            pdb=" OG  SER A 603 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   SER A  60 "
            pdb=" N   ARG A  63 "
     model   vdw
     2.299 3.120
  ... (remaining 40710 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.060
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091   5297  Z= 0.283
  Angle     :  0.796   9.211   7182  Z= 0.480
  Chirality :  0.049   0.276    808
  Planarity :  0.006   0.091    877
  Dihedral  : 17.023  89.662   1891
  Min Nonbonded Distance : 2.214

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.51 %
    Favored  : 91.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 29.23 %
    Favored  : 70.77 %
  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:  0.14 (0.36), residues: 623
  helix:  0.88 (0.27), residues: 402
  sheet:  1.80 (1.76), residues: 10
  loop : -1.50 (0.48), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A  29 
 TYR   0.058   0.002   TYR A 616 
 PHE   0.014   0.001   PHE A  59 
 TRP   0.012   0.002   TRP A 485 
 HIS   0.007   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 ( 5296)
  covalent geometry    : angle       0.79616 ( 7180)
  SS BOND              : bond        0.00265 (    1)
  SS BOND              : angle       0.85830 (    2)
  hydrogen bonds       : bond        0.17740 (  307)
  hydrogen bonds       : angle       7.50956 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  287 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8135 (mt-10)
REVERT: A  348 LYS cc_start: 0.8768 (mttt) cc_final: 0.8454 (pttt)
REVERT: A  571 ASN cc_start: 0.8675 (m-40) cc_final: 0.8443 (m110)
REVERT: A  592 LEU cc_start: 0.7870 (mt) cc_final: 0.7409 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0626
  time to fit residues: 8.3149
Evaluate side-chains
  92 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 16 optimal weight:    8.9990
   chunk 61 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0980
   chunk 25 optimal weight:    4.9990
   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 = 0.4149 r_free = 0.4149 target = 0.180354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.130326 restraints weight = 7731.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.134553 restraints weight = 3880.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.137006 restraints weight = 2687.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.138355 restraints weight = 2242.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.139149 restraints weight = 2050.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5297  Z= 0.138
  Angle     :  0.579   6.622   7182  Z= 0.307
  Chirality :  0.041   0.125    808
  Planarity :  0.005   0.070    877
  Dihedral  :  4.530  26.685    690
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.26 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 26.56 %
    Favored  : 68.09 %
  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:  0.61 (0.36), residues: 623
  helix:  1.35 (0.26), residues: 415
  sheet:  2.15 (1.66), residues: 10
  loop : -1.77 (0.49), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 607 
 TYR   0.031   0.002   TYR A 215 
 PHE   0.011   0.001   PHE A 213 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.003   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 5296)
  covalent geometry    : angle       0.57895 ( 7180)
  SS BOND              : bond        0.00063 (    1)
  SS BOND              : angle       0.52638 (    2)
  hydrogen bonds       : bond        0.04357 (  307)
  hydrogen bonds       : angle       4.77953 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 102
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.5891 (mtt)
REVERT: A  225 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6684 (ttt180)
REVERT: A  258 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8938 (ttpp)
REVERT: A  348 LYS cc_start: 0.8763 (mttt) cc_final: 0.8428 (pttt)
REVERT: A  584 ASP cc_start: 0.8571 (t0) cc_final: 0.8187 (t0)
REVERT: A  592 LEU cc_start: 0.7685 (mt) cc_final: 0.7125 (tt)
REVERT: A  613 HIS cc_start: 0.5290 (t-90) cc_final: 0.4951 (m170)
REVERT: A  614 GLN cc_start: 0.7319 (pt0) cc_final: 0.6856 (mm-40)
REVERT: A  683 GLN cc_start: 0.8546 (mt0) cc_final: 0.7992 (mt0)
  outliers start: 30
  outliers final: 18
  residues processed: 123
  average time/residue: 0.0591
  time to fit residues: 9.7652
Evaluate side-chains
  117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   50 MET
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  258 LYS
Chi-restraints excluded: chain A residue  267 CYS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  442 PHE
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  458 MET
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  628 MET
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  700 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0070
   chunk 29 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 581 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.179680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.129802 restraints weight = 7607.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.133931 restraints weight = 3839.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.136087 restraints weight = 2662.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.137817 restraints weight = 2241.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138317 restraints weight = 2029.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5297  Z= 0.135
  Angle     :  0.556   6.069   7182  Z= 0.292
  Chirality :  0.040   0.124    808
  Planarity :  0.005   0.063    877
  Dihedral  :  4.394  26.735    690
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  6.74 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  6.77 %
    Allowed  : 26.56 %
    Favored  : 66.67 %
  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:  0.84 (0.36), residues: 623
  helix:  1.61 (0.26), residues: 416
  sheet:  2.72 (1.68), residues: 10
  loop : -1.95 (0.48), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 607 
 TYR   0.036   0.001   TYR A 215 
 PHE   0.011   0.001   PHE A  59 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.007   0.001   HIS A 259 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 5296)
  covalent geometry    : angle       0.55556 ( 7180)
  SS BOND              : bond        0.00128 (    1)
  SS BOND              : angle       0.46190 (    2)
  hydrogen bonds       : bond        0.04033 (  307)
  hydrogen bonds       : angle       4.52501 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 97
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6577 (tmm) cc_final: 0.5869 (mtt)
REVERT: A  283 PHE cc_start: 0.7168 (m-80) cc_final: 0.6946 (m-80)
REVERT: A  348 LYS cc_start: 0.8759 (mttt) cc_final: 0.8418 (pttt)
REVERT: A  523 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8047 (tp)
REVERT: A  542 ARG cc_start: 0.6849 (OUTLIER) cc_final: 0.6364 (mmm160)
REVERT: A  592 LEU cc_start: 0.7337 (mt) cc_final: 0.6893 (tt)
REVERT: A  607 ARG cc_start: 0.5045 (ptt-90) cc_final: 0.4448 (ptt-90)
REVERT: A  613 HIS cc_start: 0.5401 (t-90) cc_final: 0.5189 (m170)
REVERT: A  672 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8062 (pt)
REVERT: A  725 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7637 (mm)
REVERT: A  730 PHE cc_start: 0.6894 (t80) cc_final: 0.6501 (t80)
  outliers start: 38
  outliers final: 21
  residues processed: 125
  average time/residue: 0.0514
  time to fit residues: 8.8394
Evaluate side-chains
  122 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  458 MET
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  542 ARG
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  725 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 16 optimal weight:   20.0000
   chunk 54 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   chunk 28 optimal weight:    4.9990
   chunk 18 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 477 GLN
** A 613 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.177087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126794 restraints weight = 7642.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.130808 restraints weight = 3882.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.133242 restraints weight = 2711.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.134644 restraints weight = 2269.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.134909 restraints weight = 2071.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5297  Z= 0.176
  Angle     :  0.594   6.904   7182  Z= 0.308
  Chirality :  0.042   0.161    808
  Planarity :  0.005   0.063    877
  Dihedral  :  4.430  26.714    690
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.06 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  7.84 %
    Allowed  : 24.42 %
    Favored  : 67.74 %
  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:  0.74 (0.36), residues: 623
  helix:  1.53 (0.26), residues: 417
  sheet:  2.50 (1.61), residues: 10
  loop : -1.97 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.033   0.001   TYR A 215 
 PHE   0.009   0.001   PHE A 712 
 TRP   0.011   0.001   TRP A 485 
 HIS   0.006   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 ( 5296)
  covalent geometry    : angle       0.59443 ( 7180)
  SS BOND              : bond        0.00090 (    1)
  SS BOND              : angle       0.53190 (    2)
  hydrogen bonds       : bond        0.04135 (  307)
  hydrogen bonds       : angle       4.52891 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 96
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6701 (tmm) cc_final: 0.5937 (mtt)
REVERT: A   59 PHE cc_start: 0.8976 (t80) cc_final: 0.8670 (t80)
REVERT: A  225 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7064 (ttp-170)
REVERT: A  283 PHE cc_start: 0.7160 (m-80) cc_final: 0.6921 (m-80)
REVERT: A  348 LYS cc_start: 0.8804 (mttt) cc_final: 0.8445 (pttt)
REVERT: A  477 GLN cc_start: 0.7576 (mt0) cc_final: 0.7221 (mt0)
REVERT: A  523 ILE cc_start: 0.8368 (OUTLIER) cc_final: 0.8017 (tp)
REVERT: A  592 LEU cc_start: 0.7337 (mt) cc_final: 0.6812 (tt)
REVERT: A  607 ARG cc_start: 0.4930 (ptt-90) cc_final: 0.4504 (ptt-90)
REVERT: A  613 HIS cc_start: 0.5512 (t-90) cc_final: 0.5268 (m170)
REVERT: A  672 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8100 (pt)
REVERT: A  725 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7608 (mm)
REVERT: A  730 PHE cc_start: 0.6770 (t80) cc_final: 0.6451 (t80)
  outliers start: 44
  outliers final: 32
  residues processed: 128
  average time/residue: 0.0530
  time to fit residues: 9.2582
Evaluate side-chains
  128 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  193 THR
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  225 ARG
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  700 THR
Chi-restraints excluded: chain A residue  701 MET
Chi-restraints excluded: chain A residue  725 LEU
Chi-restraints excluded: chain A residue  732 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 37 optimal weight:    0.0570
   chunk 10 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0060
   chunk 19 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 44 optimal weight:    7.9990
   chunk 49 optimal weight:    9.9990
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.3314

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

Flipped N/Q/H residues before XYZ refinement:
A 516 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.180478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.131248 restraints weight = 7754.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.135496 restraints weight = 3845.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.138145 restraints weight = 2634.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.139186 restraints weight = 2161.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.140255 restraints weight = 1982.834|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7545
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5297  Z= 0.110
  Angle     :  0.562   9.186   7182  Z= 0.284
  Chirality :  0.039   0.229    808
  Planarity :  0.004   0.061    877
  Dihedral  :  4.292  26.848    690
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.94 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  : 27.27 %
    Favored  : 67.74 %
  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:  0.97 (0.36), residues: 623
  helix:  1.73 (0.26), residues: 416
  sheet:  2.79 (1.67), residues: 10
  loop : -1.96 (0.48), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 556 
 TYR   0.033   0.001   TYR A 215 
 PHE   0.010   0.001   PHE A 569 
 TRP   0.008   0.001   TRP A 485 
 HIS   0.006   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5296)
  covalent geometry    : angle       0.56201 ( 7180)
  SS BOND              : bond        0.00044 (    1)
  SS BOND              : angle       0.32787 (    2)
  hydrogen bonds       : bond        0.03554 (  307)
  hydrogen bonds       : angle       4.25921 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 103
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6650 (tmm) cc_final: 0.5919 (mtt)
REVERT: A   59 PHE cc_start: 0.8919 (t80) cc_final: 0.8630 (t80)
REVERT: A  348 LYS cc_start: 0.8766 (mttt) cc_final: 0.8426 (pttt)
REVERT: A  447 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.7983 (t80)
REVERT: A  469 TYR cc_start: 0.8275 (t80) cc_final: 0.7980 (t80)
REVERT: A  477 GLN cc_start: 0.7556 (mt0) cc_final: 0.7203 (mt0)
REVERT: A  496 TYR cc_start: 0.8001 (m-80) cc_final: 0.7577 (m-80)
REVERT: A  523 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7727 (tp)
REVERT: A  592 LEU cc_start: 0.7236 (mt) cc_final: 0.6743 (tt)
REVERT: A  607 ARG cc_start: 0.4939 (ptt-90) cc_final: 0.4692 (ptt-90)
REVERT: A  614 GLN cc_start: 0.7448 (pt0) cc_final: 0.6952 (mm-40)
REVERT: A  619 GLN cc_start: 0.8076 (pt0) cc_final: 0.7345 (pm20)
REVERT: A  730 PHE cc_start: 0.6886 (t80) cc_final: 0.6630 (t80)
  outliers start: 28
  outliers final: 17
  residues processed: 124
  average time/residue: 0.0562
  time to fit residues: 9.2151
Evaluate side-chains
  116 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  558 GLU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  732 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 29 optimal weight:   10.0000
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.178519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.128431 restraints weight = 7826.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.132530 restraints weight = 3949.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.134754 restraints weight = 2736.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.136425 restraints weight = 2290.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.136686 restraints weight = 2070.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5297  Z= 0.130
  Angle     :  0.570   6.847   7182  Z= 0.289
  Chirality :  0.040   0.160    808
  Planarity :  0.005   0.062    877
  Dihedral  :  4.259  26.767    690
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.94 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  5.35 %
    Allowed  : 27.27 %
    Favored  : 67.38 %
  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:  1.00 (0.36), residues: 623
  helix:  1.73 (0.26), residues: 417
  sheet:  2.57 (1.61), residues: 10
  loop : -1.91 (0.48), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 556 
 TYR   0.033   0.001   TYR A 215 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.010   0.001   TRP A 485 
 HIS   0.006   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5296)
  covalent geometry    : angle       0.56975 ( 7180)
  SS BOND              : bond        0.00062 (    1)
  SS BOND              : angle       0.35066 (    2)
  hydrogen bonds       : bond        0.03687 (  307)
  hydrogen bonds       : angle       4.26192 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6690 (tmm) cc_final: 0.5975 (mtt)
REVERT: A   59 PHE cc_start: 0.8955 (t80) cc_final: 0.8685 (t80)
REVERT: A  199 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7216 (mmtt)
REVERT: A  206 TRP cc_start: 0.7819 (OUTLIER) cc_final: 0.7507 (m-10)
REVERT: A  348 LYS cc_start: 0.8774 (mttt) cc_final: 0.8407 (pttt)
REVERT: A  469 TYR cc_start: 0.8321 (t80) cc_final: 0.7985 (t80)
REVERT: A  477 GLN cc_start: 0.7568 (mt0) cc_final: 0.7199 (mt0)
REVERT: A  496 TYR cc_start: 0.8018 (m-80) cc_final: 0.7626 (m-80)
REVERT: A  523 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.7790 (tp)
REVERT: A  592 LEU cc_start: 0.7153 (mt) cc_final: 0.6653 (tt)
REVERT: A  607 ARG cc_start: 0.5016 (ptt-90) cc_final: 0.4794 (ptt-90)
REVERT: A  614 GLN cc_start: 0.7395 (pt0) cc_final: 0.6681 (mm110)
REVERT: A  619 GLN cc_start: 0.8113 (pt0) cc_final: 0.7393 (pm20)
REVERT: A  672 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8019 (pt)
  outliers start: 30
  outliers final: 21
  residues processed: 116
  average time/residue: 0.0584
  time to fit residues: 8.8574
Evaluate side-chains
  120 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 SER
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  542 ARG
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  672 LEU
Chi-restraints excluded: chain A residue  681 VAL
Chi-restraints excluded: chain A residue  685 VAL
Chi-restraints excluded: chain A residue  732 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    6.9990
   chunk 52 optimal weight:    0.4980
   chunk 32 optimal weight:    0.6980
   chunk 49 optimal weight:    0.3980
   chunk 36 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9990
   chunk 15 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4151 r_free = 0.4151 target = 0.180775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.131218 restraints weight = 7682.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.135396 restraints weight = 3865.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.137637 restraints weight = 2677.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.139370 restraints weight = 2243.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.139741 restraints weight = 2025.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5297  Z= 0.111
  Angle     :  0.585  14.830   7182  Z= 0.288
  Chirality :  0.039   0.153    808
  Planarity :  0.004   0.064    877
  Dihedral  :  4.226  26.796    690
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.42 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  5.53 %
    Allowed  : 27.81 %
    Favored  : 66.67 %
  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:  1.10 (0.36), residues: 623
  helix:  1.80 (0.26), residues: 418
  sheet:  2.66 (1.64), residues: 10
  loop : -1.86 (0.49), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 556 
 TYR   0.034   0.001   TYR A 215 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.009   0.001   TRP A 485 
 HIS   0.005   0.001   HIS A 150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5296)
  covalent geometry    : angle       0.58489 ( 7180)
  SS BOND              : bond        0.00058 (    1)
  SS BOND              : angle       0.23946 (    2)
  hydrogen bonds       : bond        0.03498 (  307)
  hydrogen bonds       : angle       4.17194 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 97
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6739 (tmm) cc_final: 0.5990 (mtt)
REVERT: A   59 PHE cc_start: 0.8906 (t80) cc_final: 0.8571 (t80)
REVERT: A  206 TRP cc_start: 0.7809 (OUTLIER) cc_final: 0.7553 (m-10)
REVERT: A  348 LYS cc_start: 0.8772 (mttt) cc_final: 0.8408 (pttt)
REVERT: A  447 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7939 (t80)
REVERT: A  469 TYR cc_start: 0.8294 (t80) cc_final: 0.7973 (t80)
REVERT: A  477 GLN cc_start: 0.7521 (mt0) cc_final: 0.7164 (mt0)
REVERT: A  496 TYR cc_start: 0.7978 (m-80) cc_final: 0.7570 (m-80)
REVERT: A  523 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7748 (tp)
REVERT: A  619 GLN cc_start: 0.8031 (pt0) cc_final: 0.7443 (pm20)
  outliers start: 31
  outliers final: 20
  residues processed: 119
  average time/residue: 0.0612
  time to fit residues: 9.5200
Evaluate side-chains
  118 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  685 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 44 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN
** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.175843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.128457 restraints weight = 7778.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.129665 restraints weight = 4491.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.131836 restraints weight = 3281.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.131856 restraints weight = 2571.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.132029 restraints weight = 2697.395|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5297  Z= 0.172
  Angle     :  0.633  11.543   7182  Z= 0.317
  Chirality :  0.043   0.224    808
  Planarity :  0.005   0.065    877
  Dihedral  :  4.407  26.518    690
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.06 %
    Favored  : 92.78 %
  Rotamer:
    Outliers :  6.95 %
    Allowed  : 26.02 %
    Favored  : 67.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.36), residues: 623
  helix:  1.68 (0.26), residues: 418
  sheet:  2.08 (1.48), residues: 10
  loop : -1.74 (0.50), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 607 
 TYR   0.035   0.002   TYR A 215 
 PHE   0.010   0.001   PHE A 697 
 TRP   0.012   0.001   TRP A 485 
 HIS   0.012   0.002   HIS A 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 5296)
  covalent geometry    : angle       0.63262 ( 7180)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       1.17044 (    2)
  hydrogen bonds       : bond        0.03996 (  307)
  hydrogen bonds       : angle       4.37642 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 93
  time to evaluate  : 0.118 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6704 (tmm) cc_final: 0.5971 (mtt)
REVERT: A   59 PHE cc_start: 0.8984 (t80) cc_final: 0.8719 (t80)
REVERT: A  199 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7281 (mmtt)
REVERT: A  206 TRP cc_start: 0.7849 (OUTLIER) cc_final: 0.7543 (m-10)
REVERT: A  348 LYS cc_start: 0.8814 (mttt) cc_final: 0.8446 (pttt)
REVERT: A  469 TYR cc_start: 0.8334 (t80) cc_final: 0.8049 (t80)
REVERT: A  477 GLN cc_start: 0.7663 (mt0) cc_final: 0.7292 (mt0)
REVERT: A  496 TYR cc_start: 0.8085 (m-80) cc_final: 0.7691 (m-80)
REVERT: A  523 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8065 (tp)
REVERT: A  611 LYS cc_start: 0.5536 (tppt) cc_final: 0.5267 (tppt)
REVERT: A  619 GLN cc_start: 0.8077 (pt0) cc_final: 0.7426 (pm20)
  outliers start: 39
  outliers final: 25
  residues processed: 119
  average time/residue: 0.0599
  time to fit residues: 9.4089
Evaluate side-chains
  115 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 87
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  220 VAL
Chi-restraints excluded: chain A residue  241 THR
Chi-restraints excluded: chain A residue  247 ILE
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  347 TYR
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Chi-restraints excluded: chain A residue  700 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 36 optimal weight:    0.5980
   chunk 61 optimal weight:    0.3980
   chunk 3 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 732 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.177956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.128253 restraints weight = 7725.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.132209 restraints weight = 3935.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.134701 restraints weight = 2770.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.135880 restraints weight = 2301.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.136822 restraints weight = 2109.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5297  Z= 0.134
  Angle     :  0.625  11.743   7182  Z= 0.309
  Chirality :  0.041   0.195    808
  Planarity :  0.005   0.067    877
  Dihedral  :  4.460  26.584    690
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.90 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  4.63 %
    Allowed  : 28.88 %
    Favored  : 66.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.37), residues: 623
  helix:  1.73 (0.26), residues: 417
  sheet:  2.14 (1.46), residues: 10
  loop : -1.78 (0.51), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 607 
 TYR   0.036   0.001   TYR A 215 
 PHE   0.009   0.001   PHE A 569 
 TRP   0.012   0.001   TRP A 485 
 HIS   0.010   0.002   HIS A 732 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5296)
  covalent geometry    : angle       0.62517 ( 7180)
  SS BOND              : bond        0.00277 (    1)
  SS BOND              : angle       0.85180 (    2)
  hydrogen bonds       : bond        0.03723 (  307)
  hydrogen bonds       : angle       4.28739 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 92
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6725 (tmm) cc_final: 0.6010 (mtt)
REVERT: A   59 PHE cc_start: 0.8947 (t80) cc_final: 0.8690 (t80)
REVERT: A  199 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7760 (tttp)
REVERT: A  206 TRP cc_start: 0.7805 (OUTLIER) cc_final: 0.7532 (m-10)
REVERT: A  348 LYS cc_start: 0.8782 (mttt) cc_final: 0.8420 (pttt)
REVERT: A  469 TYR cc_start: 0.8344 (t80) cc_final: 0.8061 (t80)
REVERT: A  477 GLN cc_start: 0.7602 (mt0) cc_final: 0.7253 (mt0)
REVERT: A  496 TYR cc_start: 0.8011 (m-80) cc_final: 0.7614 (m-80)
REVERT: A  523 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7831 (tp)
REVERT: A  619 GLN cc_start: 0.8021 (pt0) cc_final: 0.7457 (pm20)
  outliers start: 26
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0646
  time to fit residues: 9.4994
Evaluate side-chains
  115 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  372 THR
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 51 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 43 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.178674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132002 restraints weight = 7778.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.132937 restraints weight = 4368.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.134833 restraints weight = 3247.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.135519 restraints weight = 2563.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.135679 restraints weight = 2472.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5297  Z= 0.131
  Angle     :  0.637  11.574   7182  Z= 0.312
  Chirality :  0.041   0.193    808
  Planarity :  0.005   0.068    877
  Dihedral  :  4.424  26.621    690
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.58 %
    Favored  : 93.26 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 29.23 %
    Favored  : 66.31 %
  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:  1.06 (0.37), residues: 623
  helix:  1.75 (0.26), residues: 419
  sheet:  2.20 (1.45), residues: 10
  loop : -1.81 (0.51), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 134 
 TYR   0.035   0.001   TYR A 215 
 PHE   0.008   0.001   PHE A 618 
 TRP   0.034   0.001   TRP A 128 
 HIS   0.005   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5296)
  covalent geometry    : angle       0.63733 ( 7180)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       0.61908 (    2)
  hydrogen bonds       : bond        0.03653 (  307)
  hydrogen bonds       : angle       4.25840 (  894)

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

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

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1246 Ramachandran restraints generated.
    623 Oldfield, 0 Emsley, 623 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 MET cc_start: 0.6749 (tmm) cc_final: 0.6002 (mtt)
REVERT: A   59 PHE cc_start: 0.8911 (t80) cc_final: 0.8706 (t80)
REVERT: A  197 ASN cc_start: 0.8415 (t0) cc_final: 0.8094 (t0)
REVERT: A  199 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7741 (tttm)
REVERT: A  206 TRP cc_start: 0.7803 (OUTLIER) cc_final: 0.7558 (m-10)
REVERT: A  348 LYS cc_start: 0.8794 (mttt) cc_final: 0.8429 (pttt)
REVERT: A  469 TYR cc_start: 0.8312 (t80) cc_final: 0.8029 (t80)
REVERT: A  496 TYR cc_start: 0.7992 (m-80) cc_final: 0.7628 (m-80)
REVERT: A  523 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7849 (tp)
REVERT: A  619 GLN cc_start: 0.8030 (pt0) cc_final: 0.7414 (pm20)
REVERT: A  725 LEU cc_start: 0.8042 (mm) cc_final: 0.7820 (mm)
  outliers start: 25
  outliers final: 21
  residues processed: 112
  average time/residue: 0.0557
  time to fit residues: 8.3403
Evaluate side-chains
  117 residues out of total 561 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   51 CYS
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  158 ILE
Chi-restraints excluded: chain A residue  172 ILE
Chi-restraints excluded: chain A residue  199 LYS
Chi-restraints excluded: chain A residue  206 TRP
Chi-restraints excluded: chain A residue  218 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 HIS
Chi-restraints excluded: chain A residue  376 LEU
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  453 ILE
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  523 ILE
Chi-restraints excluded: chain A residue  526 VAL
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  539 LEU
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  579 ILE
Chi-restraints excluded: chain A residue  645 VAL
Chi-restraints excluded: chain A residue  657 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 63
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 416 GLN
** A 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.175638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.128540 restraints weight = 7876.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129106 restraints weight = 4460.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131121 restraints weight = 3150.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.131243 restraints weight = 2688.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.131523 restraints weight = 2624.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5297  Z= 0.168
  Angle     :  0.657  10.354   7182  Z= 0.327
  Chirality :  0.043   0.205    808
  Planarity :  0.005   0.069    877
  Dihedral  :  4.536  26.631    690
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  8.03 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 29.41 %
    Favored  : 66.31 %
  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:  0.95 (0.36), residues: 623
  helix:  1.67 (0.26), residues: 418
  sheet:  1.91 (1.41), residues: 10
  loop : -1.82 (0.51), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 607 
 TYR   0.037   0.002   TYR A 215 
 PHE   0.009   0.001   PHE A 631 
 TRP   0.031   0.002   TRP A 128 
 HIS   0.005   0.001   HIS A 613 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 5296)
  covalent geometry    : angle       0.65702 ( 7180)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.59347 (    2)
  hydrogen bonds       : bond        0.03947 (  307)
  hydrogen bonds       : angle       4.37503 (  894)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1057.85 seconds
wall clock time: 18 minutes 55.32 seconds (1135.32 seconds total)