Starting phenix.real_space_refine
on Fri Aug 22 14:16:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8v3s_42952/08_2025/8v3s_42952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8v3s_42952/08_2025/8v3s_42952.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/8v3s_42952/08_2025/8v3s_42952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8v3s_42952/08_2025/8v3s_42952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8v3s_42952/08_2025/8v3s_42952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8v3s_42952/08_2025/8v3s_42952.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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      21      5.16       5
     C    2492      2.51       5
     N     697      2.21       5
     O     698      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 40 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: 3909
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 3870
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 499, 3870
          Classifications: {'peptide': 499}
          Incomplete info: {'truncation_to_alanine': 39}
          Link IDs: {'PTRANS': 35, 'TRANS': 463}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 166
          Unresolved non-hydrogen angles: 199
          Unresolved non-hydrogen dihedrals: 137
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 13, 'ARG:plan': 7, 'ASP:plan': 2, 'GLN:plan1': 4, 'ASN:plan1': 1, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 122
    Chain: "M"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 28
          Classifications: {'peptide': 5}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 4}
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'UNK:plan-1': 4, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "M"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Classifications: {'peptide': 1}
          Modifications used: {'COO': 1}
  Time building chain proxies: 1.01, per 1000 atoms: 0.26
  Number of scatterers: 3909
  At special positions: 0
  Unit cell: (80.925, 73.455, 69.72, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      21     16.00
     O     698      8.00
     N     697      7.00
     C    2492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.21
  Conformation dependent library (CDL) restraints added in 97.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 701 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 434 "
        pdb="ZN    ZN A 701 " - pdb=" ND1 HIS A 252 "


  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  948

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 5 sheets defined
      31.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 98 through 104
    Processing helix  chain 'A' and resid 160 through 175
    Processing helix  chain 'A' and resid 256 through 270
      removed outlier: 3.865A  pdb=" N   PHE A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 310 through 314
    Processing helix  chain 'A' and resid 323 through 340
    Processing helix  chain 'A' and resid 451 through 467
      removed outlier: 4.362A  pdb=" N   TYR A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      Proline residue:  A 462  - end of helix
    Processing helix  chain 'A' and resid 481 through 486
      removed outlier: 3.844A  pdb=" N   TYR A 485 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 497
      removed outlier: 3.659A  pdb=" N   GLY A 497 " --> pdb=" O   SER A 494 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 494 through 497'
    Processing helix  chain 'A' and resid 498 through 508
    Processing helix  chain 'A' and resid 551 through 570
      removed outlier: 3.976A  pdb=" N   ALA A 570 " --> pdb=" O   ALA A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 581
    Processing helix  chain 'A' and resid 585 through 601
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5
      removed outlier: 5.232A  pdb=" N   THR A 112 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
      removed outlier: 5.902A  pdb=" N   ARG A 118 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.733A  pdb=" N   TYR A  52 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   ASN A  91 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
      removed outlier: 6.387A  pdb=" N   PHE A  54 " --> pdb=" O   ASN A  91 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 128
    Processing sheet with id=AA4, first strand: chain 'A' and resid 189 through 198
      removed outlier: 7.153A  pdb=" N   VAL A 205 " --> pdb=" O   LEU A 196 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   PHE A 245 " --> pdb=" O   LYS A 287 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   ILE A 289 " --> pdb=" O   PHE A 245 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A 247 " --> pdb=" O   ILE A 289 " (cutoff:3.500A)
      removed outlier: 6.705A  pdb=" N   ILE A 244 " --> pdb=" O   TYR A 429 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   VAL A 431 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   PHE A 246 " --> pdb=" O   VAL A 431 " (cutoff:3.500A)
      removed outlier: 8.046A  pdb=" N   LEU A 433 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 7.064A  pdb=" N   SER A 248 " --> pdb=" O   LEU A 433 " (cutoff:3.500A)
      removed outlier: 9.218A  pdb=" N   GLY A 435 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 216 through 220
      removed outlier: 5.843A  pdb=" N   ASP A 219 " --> pdb=" O   ARG A 238 " (cutoff:3.500A)

    145 hydrogen bonds defined for protein.
    408 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: 0.48

  Time building geometry restraints manager: 0.28 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 713
        1.31 -     1.44: 1089
        1.44 -     1.57: 2182
        1.57 -     1.69: 4
        1.69 -     1.82: 31
  Bond restraints: 4019
  Sorted by residual:
  bond pdb=" N   GLU M1001 "
       pdb=" CA  GLU M1001 "
    ideal  model  delta    sigma   weight residual
    1.458  1.525 -0.067 1.90e-02 2.77e+03 1.23e+01
  bond pdb=" CZ  ARG A 276 "
       pdb=" NH2 ARG A 276 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.10e+00
  bond pdb=" CA  GLU M1001 "
       pdb=" C   GLU M1001 "
    ideal  model  delta    sigma   weight residual
    1.525  1.588 -0.063 2.10e-02 2.27e+03 9.04e+00
  bond pdb=" CZ  ARG A 250 "
       pdb=" NH2 ARG A 250 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 8.96e+00
  bond pdb=" CZ  ARG A 238 "
       pdb=" NH2 ARG A 238 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.40e+00
  ... (remaining 4014 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.50: 3959
        1.50 -     2.99: 1199
        2.99 -     4.48: 242
        4.48 -     5.98: 48
        5.98 -     7.47: 16
  Bond angle restraints: 5464
  Sorted by residual:
  angle pdb=" N   ILE A 578 "
        pdb=" CA  ILE A 578 "
        pdb=" C   ILE A 578 "
      ideal   model   delta    sigma   weight residual
     110.62  116.35   -5.73 1.02e+00 9.61e-01 3.16e+01
  angle pdb=" C   SER A 539 "
        pdb=" N   PRO A 540 "
        pdb=" CA  PRO A 540 "
      ideal   model   delta    sigma   weight residual
     119.66  115.66    4.00 7.20e-01 1.93e+00 3.09e+01
  angle pdb=" C   ALA A 545 "
        pdb=" CA  ALA A 545 "
        pdb=" CB  ALA A 545 "
      ideal   model   delta    sigma   weight residual
     116.54  110.26    6.28 1.15e+00 7.56e-01 2.98e+01
  angle pdb=" C   SER A 548 "
        pdb=" CA  SER A 548 "
        pdb=" CB  SER A 548 "
      ideal   model   delta    sigma   weight residual
     117.23  110.47    6.76 1.36e+00 5.41e-01 2.47e+01
  angle pdb=" OE1 GLN A 475 "
        pdb=" CD  GLN A 475 "
        pdb=" NE2 GLN A 475 "
      ideal   model   delta    sigma   weight residual
     122.60  117.71    4.89 1.00e+00 1.00e+00 2.39e+01
  ... (remaining 5459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 2194
       17.82 -    35.65: 145
       35.65 -    53.47: 25
       53.47 -    71.30: 5
       71.30 -    89.12: 3
  Dihedral angle restraints: 2372
    sinusoidal: 904
      harmonic: 1468
  Sorted by residual:
  dihedral pdb=" CA  TYR A 519 "
           pdb=" C   TYR A 519 "
           pdb=" N   ASN A 520 "
           pdb=" CA  ASN A 520 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.40  -19.60     0      5.00e+00 4.00e-02 1.54e+01
  dihedral pdb=" CA  HIS A 583 "
           pdb=" C   HIS A 583 "
           pdb=" N   SER A 584 "
           pdb=" CA  SER A 584 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ARG A  72 "
           pdb=" C   ARG A  72 "
           pdb=" N   SER A  73 "
           pdb=" CA  SER A  73 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.51  -18.49     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 2369 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 375
       0.067 -    0.133: 130
       0.133 -    0.200: 60
       0.200 -    0.266: 14
       0.266 -    0.333: 6
  Chirality restraints: 585
  Sorted by residual:
  chirality pdb=" CA  SER A  16 "
            pdb=" N   SER A  16 "
            pdb=" C   SER A  16 "
            pdb=" CB  SER A  16 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.77e+00
  chirality pdb=" CA  GLU M1001 "
            pdb=" N   GLU M1001 "
            pdb=" C   GLU M1001 "
            pdb=" CB  GLU M1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.83   -0.32 2.00e-01 2.50e+01 2.60e+00
  chirality pdb=" CA  GLU M   3 "
            pdb=" N   GLU M   3 "
            pdb=" C   GLU M   3 "
            pdb=" CB  GLU M   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.82   -0.31 2.00e-01 2.50e+01 2.35e+00
  ... (remaining 582 not shown)

  Planarity restraints: 718
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 519 "    0.050 2.00e-02 2.50e+03   2.65e-02 1.40e+01
        pdb=" CG  TYR A 519 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 519 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 519 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 519 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 519 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 519 "   -0.007 2.00e-02 2.50e+03
        pdb=" OH  TYR A 519 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A 192 "    0.037 2.00e-02 2.50e+03   2.90e-02 1.26e+01
        pdb=" CG  HIS A 192 "   -0.046 2.00e-02 2.50e+03
        pdb=" ND1 HIS A 192 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 HIS A 192 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 HIS A 192 "    0.005 2.00e-02 2.50e+03
        pdb=" NE2 HIS A 192 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 335 "   -0.039 2.00e-02 2.50e+03   2.49e-02 1.24e+01
        pdb=" CG  TYR A 335 "    0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 335 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 335 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 335 "    0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 335 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 335 "    0.013 2.00e-02 2.50e+03
        pdb=" OH  TYR A 335 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 715 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 5
        2.56 -     3.15: 3042
        3.15 -     3.73: 6284
        3.73 -     4.32: 8769
        4.32 -     4.90: 14492
  Nonbonded interactions: 32592
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     1.978 2.230
  nonbonded pdb=" OE2 GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.097 2.230
  nonbonded pdb=" CD  GLU A 255 "
            pdb="ZN    ZN A 701 "
     model   vdw
     2.263 2.460
  nonbonded pdb=" OG1 THR A 521 "
            pdb=" O   SER A 548 "
     model   vdw
     2.480 3.040
  nonbonded pdb=" O   ASN A 458 "
            pdb=" OH  TYR A 513 "
     model   vdw
     2.555 3.040
  ... (remaining 32587 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.120
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.980
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
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      :  0.013   0.257   4022  Z= 0.726
  Angle     :  1.522   7.475   5464  Z= 1.003
  Chirality :  0.086   0.333    585
  Planarity :  0.011   0.067    718
  Dihedral  : 12.860  89.124   1424
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.44 %
    Favored  : 91.56 %
  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: -1.14 (0.33), residues: 491
  helix: -0.47 (0.35), residues: 143
  sheet: -0.15 (0.58), residues: 72
  loop : -1.05 (0.34), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.002   ARG A  13 
 TYR   0.050   0.012   TYR A 519 
 PHE   0.036   0.006   PHE A 265 
 TRP   0.022   0.008   TRP A 575 
 HIS   0.018   0.006   HIS A 436 

Details of bonding type rmsd
  covalent geometry    : bond        0.01142 ( 4019)
  covalent geometry    : angle       1.52219 ( 5464)
  hydrogen bonds       : bond        0.17478 (  145)
  hydrogen bonds       : angle       7.73599 (  408)
  metal coordination   : bond        0.24871 (    2)
  Misc. bond           : bond        0.04527 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A    3 LEU cc_start: 0.8260 (mt) cc_final: 0.8056 (mm)
REVERT: A   52 TYR cc_start: 0.7967 (m-80) cc_final: 0.7673 (m-10)
REVERT: A   69 ASN cc_start: 0.7676 (t0) cc_final: 0.7414 (t0)
REVERT: A  307 ARG cc_start: 0.7254 (ttp80) cc_final: 0.6802 (ttp-170)
REVERT: A  521 THR cc_start: 0.8097 (t) cc_final: 0.7822 (m)
REVERT: A  557 GLN cc_start: 0.7552 (tp-100) cc_final: 0.6999 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 70
  average time/residue: 0.0681
  time to fit residues: 5.8329
Evaluate side-chains
  38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 48 optimal weight:    0.0770
   chunk 26 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0980
   chunk 16 optimal weight:    0.1980
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    0.2980
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0870
   overall best weight:    0.0910

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

Flipped N/Q/H residues before XYZ refinement:
A 599 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.131920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.120386 restraints weight = 5981.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.123321 restraints weight = 3379.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.125270 restraints weight = 2232.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126633 restraints weight = 1616.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.127510 restraints weight = 1231.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4022  Z= 0.115
  Angle     :  0.603  12.636   5464  Z= 0.303
  Chirality :  0.042   0.142    585
  Planarity :  0.005   0.042    718
  Dihedral  :  4.900  48.763    557
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 11.17 %
    Favored  : 87.10 %
  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: -0.17 (0.36), residues: 491
  helix:  0.85 (0.40), residues: 143
  sheet:  0.06 (0.57), residues: 74
  loop : -0.66 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 220 
 TYR   0.018   0.002   TYR A 461 
 PHE   0.015   0.001   PHE A 265 
 TRP   0.003   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 596 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 4019)
  covalent geometry    : angle       0.60329 ( 5464)
  hydrogen bonds       : bond        0.04284 (  145)
  hydrogen bonds       : angle       5.65468 (  408)
  metal coordination   : bond        0.00336 (    2)
  Misc. bond           : bond        0.00025 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.163 
Fit side-chains
REVERT: A  557 GLN cc_start: 0.8135 (tp-100) cc_final: 0.7880 (tp-100)
REVERT: A  586 LEU cc_start: 0.8303 (tp) cc_final: 0.8009 (tp)
  outliers start: 7
  outliers final: 6
  residues processed: 52
  average time/residue: 0.0760
  time to fit residues: 5.0406
Evaluate side-chains
  42 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  578 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.0970
   chunk 29 optimal weight:    0.0050
   chunk 16 optimal weight:    0.0060
   chunk 34 optimal weight:    0.0970
   chunk 10 optimal weight:    0.3980
   chunk 28 optimal weight:    0.2980
   chunk 25 optimal weight:    0.0980
   chunk 0 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0010
   chunk 21 optimal weight:    0.4980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.0412

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.132166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.120655 restraints weight = 5936.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.123585 restraints weight = 3385.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.125460 restraints weight = 2234.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.126638 restraints weight = 1629.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.127672 restraints weight = 1273.736|
|-----------------------------------------------------------------------------|
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   4022  Z= 0.100
  Angle     :  0.561  10.564   5464  Z= 0.280
  Chirality :  0.041   0.160    585
  Planarity :  0.004   0.047    718
  Dihedral  :  4.678  46.948    557
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 13.90 %
    Favored  : 84.37 %
  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:  0.08 (0.37), residues: 491
  helix:  1.34 (0.42), residues: 143
  sheet:  0.15 (0.59), residues: 75
  loop : -0.66 (0.36), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 598 
 TYR   0.023   0.001   TYR A 161 
 PHE   0.012   0.001   PHE A 265 
 TRP   0.003   0.000   TRP A 119 
 HIS   0.003   0.001   HIS A 192 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 4019)
  covalent geometry    : angle       0.56109 ( 5464)
  hydrogen bonds       : bond        0.03598 (  145)
  hydrogen bonds       : angle       5.24100 (  408)
  metal coordination   : bond        0.00120 (    2)
  Misc. bond           : bond        0.00017 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 0.145 
Fit side-chains
REVERT: A  586 LEU cc_start: 0.8297 (tp) cc_final: 0.8050 (tp)
  outliers start: 7
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0603
  time to fit residues: 3.5355
Evaluate side-chains
  38 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 32
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  578 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 35 optimal weight:    0.0970
   chunk 11 optimal weight:    0.5980
   chunk 44 optimal weight:    0.5980
   chunk 7 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0980
   chunk 4 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.3578

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.119486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.107351 restraints weight = 6125.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.110151 restraints weight = 3556.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112017 restraints weight = 2403.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.113224 restraints weight = 1787.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114155 restraints weight = 1426.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.3080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4022  Z= 0.226
  Angle     :  0.677  10.372   5464  Z= 0.345
  Chirality :  0.046   0.151    585
  Planarity :  0.005   0.042    718
  Dihedral  :  5.196  51.183    557
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 11.41 %
    Favored  : 84.12 %
  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: -0.02 (0.37), residues: 491
  helix:  1.12 (0.42), residues: 138
  sheet:  0.44 (0.55), residues: 88
  loop : -0.77 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 598 
 TYR   0.019   0.002   TYR A 461 
 PHE   0.015   0.002   PHE A 268 
 TRP   0.007   0.002   TRP A 592 
 HIS   0.004   0.001   HIS A 511 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 4019)
  covalent geometry    : angle       0.67699 ( 5464)
  hydrogen bonds       : bond        0.04777 (  145)
  hydrogen bonds       : angle       5.27258 (  408)
  metal coordination   : bond        0.00530 (    2)
  Misc. bond           : bond        0.00129 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 43
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A  191 TYR cc_start: 0.7534 (t80) cc_final: 0.7318 (t80)
REVERT: A  287 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7736 (mmtm)
REVERT: A  551 THR cc_start: 0.8445 (OUTLIER) cc_final: 0.8205 (m)
REVERT: A  595 LYS cc_start: 0.8767 (mtpp) cc_final: 0.8330 (mtmm)
  outliers start: 18
  outliers final: 13
  residues processed: 58
  average time/residue: 0.0686
  time to fit residues: 5.0951
Evaluate side-chains
  51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 37
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  551 THR
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    0.0670
   chunk 3 optimal weight:    0.1980
   chunk 42 optimal weight:    0.0970
   chunk 9 optimal weight:    0.0980
   chunk 25 optimal weight:    0.0970
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0770
   chunk 24 optimal weight:    0.0870
   chunk 19 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.0850

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.111546 restraints weight = 6070.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.114343 restraints weight = 3578.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.116202 restraints weight = 2445.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.117449 restraints weight = 1819.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.118460 restraints weight = 1442.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4022  Z= 0.106
  Angle     :  0.560   9.540   5464  Z= 0.282
  Chirality :  0.041   0.130    585
  Planarity :  0.004   0.045    718
  Dihedral  :  4.771  52.657    557
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 15.14 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.37), residues: 491
  helix:  1.18 (0.41), residues: 144
  sheet:  0.62 (0.56), residues: 85
  loop : -0.72 (0.37), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 598 
 TYR   0.019   0.001   TYR A 161 
 PHE   0.014   0.001   PHE A 286 
 TRP   0.004   0.000   TRP A 592 
 HIS   0.003   0.001   HIS A 323 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 4019)
  covalent geometry    : angle       0.55957 ( 5464)
  hydrogen bonds       : bond        0.03586 (  145)
  hydrogen bonds       : angle       5.02186 (  408)
  metal coordination   : bond        0.00152 (    2)
  Misc. bond           : bond        0.00022 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  150 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8193 (p)
REVERT: A  191 TYR cc_start: 0.7447 (t80) cc_final: 0.7182 (t80)
REVERT: A  440 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8146 (mtm180)
REVERT: A  459 MET cc_start: 0.8202 (mtt) cc_final: 0.7836 (mtp)
REVERT: A  593 MET cc_start: 0.8105 (tpp) cc_final: 0.7895 (tpp)
REVERT: A  595 LYS cc_start: 0.8713 (mtpp) cc_final: 0.8322 (mtmm)
  outliers start: 13
  outliers final: 9
  residues processed: 48
  average time/residue: 0.0721
  time to fit residues: 4.3645
Evaluate side-chains
  45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 34
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  440 ARG
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 30 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0980
   chunk 6 optimal weight:    0.4980
   chunk 12 optimal weight:    0.6980
   chunk 48 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0070
   chunk 14 optimal weight:    0.5980
   chunk 47 optimal weight:    0.0980
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.1998

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

Flipped N/Q/H residues before XYZ refinement:
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN
A 336 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.109510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.095730 restraints weight = 6408.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.098555 restraints weight = 3792.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.100536 restraints weight = 2613.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.101807 restraints weight = 1970.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.102824 restraints weight = 1592.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4022  Z= 0.145
  Angle     :  0.577   9.113   5464  Z= 0.291
  Chirality :  0.041   0.129    585
  Planarity :  0.004   0.046    718
  Dihedral  :  4.725  52.287    557
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 14.14 %
    Favored  : 81.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.18 (0.37), residues: 491
  helix:  1.36 (0.42), residues: 138
  sheet:  0.79 (0.57), residues: 85
  loop : -0.78 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 307 
 TYR   0.016   0.002   TYR A 161 
 PHE   0.013   0.001   PHE A 135 
 TRP   0.004   0.001   TRP A  57 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4019)
  covalent geometry    : angle       0.57736 ( 5464)
  hydrogen bonds       : bond        0.03674 (  145)
  hydrogen bonds       : angle       5.01283 (  408)
  metal coordination   : bond        0.00315 (    2)
  Misc. bond           : bond        0.00057 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 34
  time to evaluate  : 0.154 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.8761 (m) cc_final: 0.8496 (m)
REVERT: A  150 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8411 (p)
REVERT: A  191 TYR cc_start: 0.7769 (t80) cc_final: 0.7455 (t80)
REVERT: A  440 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7976 (mtm180)
REVERT: A  593 MET cc_start: 0.8108 (tpp) cc_final: 0.7885 (tpp)
  outliers start: 16
  outliers final: 12
  residues processed: 48
  average time/residue: 0.0732
  time to fit residues: 4.4932
Evaluate side-chains
  47 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 33
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  440 ARG
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 11 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 48 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 39 optimal weight:    0.3980
   chunk 12 optimal weight:    0.2980
   overall best weight:    0.2780

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.094568 restraints weight = 6514.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.097303 restraints weight = 3862.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.099215 restraints weight = 2635.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.100600 restraints weight = 1979.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.101546 restraints weight = 1577.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.3651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4022  Z= 0.178
  Angle     :  0.596   8.556   5464  Z= 0.301
  Chirality :  0.043   0.129    585
  Planarity :  0.005   0.046    718
  Dihedral  :  4.797  51.569    557
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 7.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 13.90 %
    Favored  : 82.38 %
  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:  0.13 (0.37), residues: 491
  helix:  1.21 (0.42), residues: 138
  sheet:  0.85 (0.57), residues: 85
  loop : -0.77 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 307 
 TYR   0.016   0.002   TYR A 161 
 PHE   0.012   0.002   PHE A 286 
 TRP   0.005   0.001   TRP A  57 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 4019)
  covalent geometry    : angle       0.59567 ( 5464)
  hydrogen bonds       : bond        0.03992 (  145)
  hydrogen bonds       : angle       5.06015 (  408)
  metal coordination   : bond        0.00392 (    2)
  Misc. bond           : bond        0.00063 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 33
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.8728 (m) cc_final: 0.8484 (m)
REVERT: A  440 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8068 (mtm180)
  outliers start: 15
  outliers final: 12
  residues processed: 46
  average time/residue: 0.0699
  time to fit residues: 4.2361
Evaluate side-chains
  45 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 32
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  440 ARG
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0870
   chunk 14 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    0.1980
   chunk 31 optimal weight:    0.0670
   chunk 48 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 21 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.2296

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.109087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.095706 restraints weight = 6362.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.098484 restraints weight = 3769.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.100263 restraints weight = 2586.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.101709 restraints weight = 1968.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.102638 restraints weight = 1566.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.3747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4022  Z= 0.153
  Angle     :  0.580   8.415   5464  Z= 0.292
  Chirality :  0.042   0.127    585
  Planarity :  0.004   0.046    718
  Dihedral  :  4.694  48.808    557
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 6.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.40 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.37), residues: 491
  helix:  1.26 (0.42), residues: 138
  sheet:  0.95 (0.57), residues: 85
  loop : -0.76 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 307 
 TYR   0.016   0.002   TYR A 161 
 PHE   0.009   0.001   PHE A 286 
 TRP   0.004   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 4019)
  covalent geometry    : angle       0.58016 ( 5464)
  hydrogen bonds       : bond        0.03720 (  145)
  hydrogen bonds       : angle       5.00462 (  408)
  metal coordination   : bond        0.00317 (    2)
  Misc. bond           : bond        0.00054 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 33
  time to evaluate  : 0.156 
Fit side-chains
  outliers start: 16
  outliers final: 14
  residues processed: 47
  average time/residue: 0.0515
  time to fit residues: 3.3113
Evaluate side-chains
  44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 13 optimal weight:    0.2980
   chunk 41 optimal weight:    0.8980
   chunk 39 optimal weight:    0.3980
   chunk 30 optimal weight:    0.1980
   chunk 35 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.2780

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.107905 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.094789 restraints weight = 6455.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.097458 restraints weight = 3887.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.099358 restraints weight = 2691.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.100646 restraints weight = 2027.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.101651 restraints weight = 1629.764|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   4022  Z= 0.177
  Angle     :  0.597   8.174   5464  Z= 0.301
  Chirality :  0.043   0.128    585
  Planarity :  0.005   0.046    718
  Dihedral  :  4.712  46.792    557
  Min Nonbonded Distance : 1.979

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.15 %
    Favored  : 82.88 %
  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:  0.16 (0.37), residues: 491
  helix:  1.15 (0.42), residues: 138
  sheet:  0.90 (0.55), residues: 90
  loop : -0.75 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 307 
 TYR   0.015   0.002   TYR A 161 
 PHE   0.015   0.001   PHE A 286 
 TRP   0.005   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 4019)
  covalent geometry    : angle       0.59681 ( 5464)
  hydrogen bonds       : bond        0.03945 (  145)
  hydrogen bonds       : angle       5.03149 (  408)
  metal coordination   : bond        0.00417 (    2)
  Misc. bond           : bond        0.00058 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 32
  time to evaluate  : 0.107 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.8800 (m) cc_final: 0.8545 (m)
  outliers start: 16
  outliers final: 14
  residues processed: 46
  average time/residue: 0.0592
  time to fit residues: 3.6712
Evaluate side-chains
  44 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 20 optimal weight:    0.1980
   chunk 29 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 9 optimal weight:    0.0970
   chunk 40 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 7 optimal weight:    0.3980
   chunk 37 optimal weight:    0.9980
   chunk 48 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0970
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.1976

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 104 GLN
A 314 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.109159 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.095991 restraints weight = 6392.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.098681 restraints weight = 3841.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.100528 restraints weight = 2664.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.101923 restraints weight = 2010.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.102811 restraints weight = 1602.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4022  Z= 0.141
  Angle     :  0.583   7.945   5464  Z= 0.291
  Chirality :  0.042   0.132    585
  Planarity :  0.004   0.046    718
  Dihedral  :  4.616  43.997    557
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 13.90 %
    Favored  : 82.38 %
  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:  0.21 (0.37), residues: 491
  helix:  1.25 (0.42), residues: 138
  sheet:  1.21 (0.57), residues: 83
  loop : -0.82 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 307 
 TYR   0.016   0.001   TYR A 161 
 PHE   0.011   0.001   PHE A 286 
 TRP   0.004   0.001   TRP A 119 
 HIS   0.003   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 4019)
  covalent geometry    : angle       0.58298 ( 5464)
  hydrogen bonds       : bond        0.03644 (  145)
  hydrogen bonds       : angle       4.98266 (  408)
  metal coordination   : bond        0.00287 (    2)
  Misc. bond           : bond        0.00041 (    1)

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

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

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  982 Ramachandran restraints generated.
    491 Oldfield, 0 Emsley, 491 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 34
  time to evaluate  : 0.153 
Fit side-chains
REVERT: A  110 VAL cc_start: 0.8804 (m) cc_final: 0.8547 (m)
  outliers start: 15
  outliers final: 14
  residues processed: 47
  average time/residue: 0.0498
  time to fit residues: 3.2200
Evaluate side-chains
  46 residues out of total 442 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    5 CYS
Chi-restraints excluded: chain A residue   22 VAL
Chi-restraints excluded: chain A residue   65 THR
Chi-restraints excluded: chain A residue  140 VAL
Chi-restraints excluded: chain A residue  144 VAL
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  151 THR
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  233 THR
Chi-restraints excluded: chain A residue  309 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  444 MET
Chi-restraints excluded: chain A residue  456 VAL
Chi-restraints excluded: chain A residue  583 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 43 optimal weight:    0.4980
   chunk 6 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0870
   chunk 36 optimal weight:    0.0980
   overall best weight:    0.3358

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 314 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.106155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.093007 restraints weight = 6495.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.095637 restraints weight = 3935.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.097454 restraints weight = 2744.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.098674 restraints weight = 2086.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.099699 restraints weight = 1695.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.4044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4022  Z= 0.205
  Angle     :  0.628   7.918   5464  Z= 0.317
  Chirality :  0.044   0.134    585
  Planarity :  0.005   0.048    718
  Dihedral  :  4.756  42.397    557
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.67 %
    Favored  : 96.33 %
  Rotamer:
    Outliers :  3.97 %
    Allowed  : 13.90 %
    Favored  : 82.13 %
  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:  0.02 (0.36), residues: 491
  helix:  1.04 (0.41), residues: 138
  sheet:  1.00 (0.55), residues: 88
  loop : -0.90 (0.37), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 307 
 TYR   0.015   0.002   TYR A 161 
 PHE   0.016   0.002   PHE A 286 
 TRP   0.006   0.001   TRP A 119 
 HIS   0.004   0.001   HIS A 336 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 4019)
  covalent geometry    : angle       0.62843 ( 5464)
  hydrogen bonds       : bond        0.04177 (  145)
  hydrogen bonds       : angle       5.11475 (  408)
  metal coordination   : bond        0.00499 (    2)
  Misc. bond           : bond        0.00065 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 930.53 seconds
wall clock time: 16 minutes 43.21 seconds (1003.21 seconds total)