Starting phenix.real_space_refine
on Tue Mar  3 13:35:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t32_25648/03_2026/7t32_25648.map"
  }
  resolution = 3.4
  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=   0.002 sd=   0.048
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2829 atoms to isotropic.
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      19      5.16       5
     C    1874      2.51       5
     N     473      2.21       5
     O     495      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2861
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2836
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 375, 2830
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 10, 'TRANS': 364}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 66
      Conformer: "B"
        Number of residues, atoms: 375, 2830
          Classifications: {'peptide': 375}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 10, 'TRANS': 364}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 103
          Unresolved non-hydrogen angles: 123
          Unresolved non-hydrogen dihedrals: 87
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 7, 'GLN:plan1': 1, 'GLU:plan': 3, 'PHE:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 66
          bond proxies already assigned to first conformer: 2883
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'ZMA': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ASER A  35 " occ=0.60
      ... (10 atoms not shown)
      pdb=" OG BSER A  35 " occ=0.40
  Time building chain proxies: 1.14, per 1000 atoms: 0.40
  Number of scatterers: 2861
  At special positions: 0
  Unit cell: (55.945, 78.49, 109.385, 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      19     16.00
     O     495      8.00
     N     473      7.00
     C    1874      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  74 " - pdb=" SG  CYS A 146 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  77 " - pdb=" SG  CYS A 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 355 " - pdb=" SG  CYS A 358 " 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: 0.23
  Conformation dependent library (CDL) restraints added in 173.8 milliseconds
  

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  714

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 0 sheets defined
      90.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.05
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.556A  pdb=" N   LEU A  19 " --> pdb=" O   ALA A  15 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LEU A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   VAL A  27 " --> pdb=" O   GLY A  23 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   TRP A  32 " --> pdb=" O   CYS A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 39 through 69
      removed outlier: 4.551A  pdb=" N   ILE A  60 " --> pdb=" O   GLY A  56 " (cutoff:3.500A)
      Proline residue:  A  61  - end of helix
      removed outlier: 4.007A  pdb=" N   THR A  68 " --> pdb=" O   ILE A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 108
      removed outlier: 4.849A  pdb=" N   VAL A  84 " --> pdb=" O   ILE A  80 " (cutoff:3.500A)
      removed outlier: 4.368A  pdb=" N   LEU A  85 " --> pdb=" O   ALA A  81 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A  91 " --> pdb=" O   LEU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 116
      removed outlier: 4.722A  pdb=" N   ASN A 113 " --> pdb=" O   PRO A 109 " (cutoff:3.500A)
      removed outlier: 5.141A  pdb=" N   GLY A 114 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 142
      Proline residue:  A 139  - end of helix
      removed outlier: 4.265A  pdb=" N   GLY A 142 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 157
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 173 through 181
    Processing helix  chain 'A' and resid 182 through 227
      Proline residue:  A 189  - end of helix
      removed outlier: 4.096A  pdb=" N   LEU A 222 " --> pdb=" O   LEU A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 232 through 250
    Processing helix  chain 'A' and resid 268 through 289
      removed outlier: 3.952A  pdb=" N   GLU A 289 " --> pdb=" O   LYS A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 355
      removed outlier: 3.987A  pdb=" N   THR A 304 " --> pdb=" O   GLU A 300 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   THR A 305 " --> pdb=" O   GLN A 301 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 319 " --> pdb=" O   GLU A 315 " (cutoff:3.500A)
      Proline residue:  A 344  - end of helix
    Processing helix  chain 'A' and resid 362 through 387
      removed outlier: 3.661A  pdb=" N   ASN A 376 " --> pdb=" O   LEU A 372 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   SER A 377 " --> pdb=" O   SER A 373 " (cutoff:3.500A)
      removed outlier: 4.534A  pdb=" N   VAL A 378 " --> pdb=" O   HIS A 374 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   VAL A 379 " --> pdb=" O   THR A 375 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN A 380 " --> pdb=" O   ASN A 376 " (cutoff:3.500A)
      Proline residue:  A 381  - end of helix
    Processing helix  chain 'A' and resid 388 through 398
      removed outlier: 3.856A  pdb=" N   THR A 394 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    735 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: 0.34

  Time building geometry restraints manager: 0.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 886
        1.34 -     1.46: 408
        1.46 -     1.57: 1606
        1.57 -     1.69: 0
        1.69 -     1.81: 25
  Bond restraints: 2925
  Sorted by residual:
  bond pdb=" C14 ZMA A1201 "
       pdb=" N15 ZMA A1201 "
    ideal  model  delta    sigma   weight residual
    1.321  1.450 -0.129 2.00e-02 2.50e+03 4.16e+01
  bond pdb=" C11 ZMA A1201 "
       pdb=" N10 ZMA A1201 "
    ideal  model  delta    sigma   weight residual
    1.334  1.453 -0.119 2.00e-02 2.50e+03 3.52e+01
  bond pdb=" C20 ZMA A1201 "
       pdb=" C21 ZMA A1201 "
    ideal  model  delta    sigma   weight residual
    1.442  1.526 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C18 ZMA A1201 "
       pdb=" N16 ZMA A1201 "
    ideal  model  delta    sigma   weight residual
    1.372  1.294  0.078 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" C18 ZMA A1201 "
       pdb=" N19 ZMA A1201 "
    ideal  model  delta    sigma   weight residual
    1.320  1.388 -0.068 2.00e-02 2.50e+03 1.14e+01
  ... (remaining 2920 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.72: 3855
        1.72 -     3.43: 104
        3.43 -     5.15: 25
        5.15 -     6.87: 8
        6.87 -     8.58: 4
  Bond angle restraints: 3996
  Sorted by residual:
  angle pdb=" N   VAL A 171 "
        pdb=" CA  VAL A 171 "
        pdb=" C   VAL A 171 "
      ideal   model   delta    sigma   weight residual
     113.53  109.69    3.84 9.80e-01 1.04e+00 1.54e+01
  angle pdb=" N   GLU A 226 "
        pdb=" CA  GLU A 226 "
        pdb=" CB  GLU A 226 "
      ideal   model   delta    sigma   weight residual
     110.28  116.02   -5.74 1.55e+00 4.16e-01 1.37e+01
  angle pdb=" N   VAL A  31 "
        pdb=" CA  VAL A  31 "
        pdb=" C   VAL A  31 "
      ideal   model   delta    sigma   weight residual
     113.00  108.85    4.15 1.30e+00 5.92e-01 1.02e+01
  angle pdb=" CA  GLU A 226 "
        pdb=" CB  GLU A 226 "
        pdb=" CG  GLU A 226 "
      ideal   model   delta    sigma   weight residual
     114.10  120.49   -6.39 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" C   ASP A 229 "
        pdb=" N   ASN A 230 "
        pdb=" CA  ASN A 230 "
      ideal   model   delta    sigma   weight residual
     121.54  127.48   -5.94 1.91e+00 2.74e-01 9.68e+00
  ... (remaining 3991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.31: 1523
       16.31 -    32.61: 136
       32.61 -    48.92: 32
       48.92 -    65.23: 12
       65.23 -    81.54: 2
  Dihedral angle restraints: 1705
    sinusoidal: 604
      harmonic: 1101
  Sorted by residual:
  dihedral pdb=" CB  CYS A  77 "
           pdb=" SG  CYS A  77 "
           pdb=" SG  CYS A 166 "
           pdb=" CB  CYS A 166 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  160.63  -67.63     1      1.00e+01 1.00e-02 5.95e+01
  dihedral pdb=" CA  PHE A 182 "
           pdb=" C   PHE A 182 "
           pdb=" N   PHE A 183 "
           pdb=" CA  PHE A 183 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.03  -19.97     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  CYS A 185 "
           pdb=" C   CYS A 185 "
           pdb=" N   VAL A 186 "
           pdb=" CA  VAL A 186 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.99   16.01     0      5.00e+00 4.00e-02 1.03e+01
  ... (remaining 1702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 315
       0.030 -    0.060: 106
       0.060 -    0.090: 40
       0.090 -    0.120: 16
       0.120 -    0.150: 3
  Chirality restraints: 480
  Sorted by residual:
  chirality pdb=" CA  GLU A 226 "
            pdb=" N   GLU A 226 "
            pdb=" C   GLU A 226 "
            pdb=" CB  GLU A 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.62e-01
  chirality pdb=" CA  ASN A 230 "
            pdb=" N   ASN A 230 "
            pdb=" C   ASN A 230 "
            pdb=" CB  ASN A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  GLN A 157 "
            pdb=" N   GLN A 157 "
            pdb=" C   GLN A 157 "
            pdb=" CB  GLN A 157 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.39    0.12 2.00e-01 2.50e+01 3.88e-01
  ... (remaining 477 not shown)

  Planarity restraints: 496
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 188 "   -0.049 5.00e-02 4.00e+02   7.44e-02 8.86e+00
        pdb=" N   PRO A 189 "    0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO A 189 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 189 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 148 "   -0.034 5.00e-02 4.00e+02   5.19e-02 4.31e+00
        pdb=" N   PRO A 149 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 149 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 149 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 307 "    0.010 2.00e-02 2.50e+03   1.96e-02 3.82e+00
        pdb=" C   ASN A 307 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   ASN A 307 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A 308 "    0.011 2.00e-02 2.50e+03
  ... (remaining 493 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 873
        2.83 -     3.35: 3113
        3.35 -     3.87: 4780
        3.87 -     4.38: 4854
        4.38 -     4.90: 8637
  Nonbonded interactions: 22257
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 242 "
            pdb=" OD1 ASP A 281 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   ALA A 231 "
            pdb=" N   GLN A 233 "
     model   vdw
     2.321 3.120
  nonbonded pdb=" O   LEU A 222 "
            pdb=" OE1 GLU A 226 "
     model   vdw
     2.341 3.040
  nonbonded pdb=" N   GLU A 294 "
            pdb=" OE1 GLU A 294 "
     model   vdw
     2.359 3.120
  nonbonded pdb=" O   ALA A 134 "
            pdb=" OG1 THR A 138 "
     model   vdw
     2.363 3.040
  ... (remaining 22252 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.40 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     4.990
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
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      :  0.006   0.129   2928  Z= 0.279
  Angle     :  0.774   8.585   4002  Z= 0.419
  Chirality :  0.039   0.150    480
  Planarity :  0.005   0.074    496
  Dihedral  : 14.073  81.537    982
  Min Nonbonded Distance : 2.313

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.12 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.86 (0.45), residues: 374
  helix:  1.56 (0.30), residues: 314
  sheet:  None (None), residues: 0
  loop : -0.32 (0.88), residues: 60

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 306 
 TYR   0.008   0.001   TYR A 384 
 PHE   0.018   0.001   PHE A 395 
 TRP   0.021   0.001   TRP A 364 
 HIS   0.002   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00553 ( 2925)
  covalent geometry    : angle       0.77423 ( 3996)
  SS BOND              : bond        0.00153 (    3)
  SS BOND              : angle       0.50009 (    6)
  hydrogen bonds       : bond        0.14883 (  245)
  hydrogen bonds       : angle       5.52284 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.097 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0400
  time to fit residues: 2.8413
Evaluate side-chains
  49 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.2980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 349 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.159472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.124669 restraints weight = 22025.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3840 rms_B_bonded: 8.76
r_work: 0.3553 rms_B_bonded: 8.09 restraints_weight: 2.0000
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3588
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3588 r_free = 0.3588    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3588
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.1413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   2928  Z= 0.152
  Angle     :  0.653   7.392   4002  Z= 0.337
  Chirality :  0.041   0.165    480
  Planarity :  0.005   0.060    496
  Dihedral  :  5.725  71.439    399
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 10.92 %
    Favored  : 88.38 %
  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 are not related in a simple way.
  whole:  2.19 (0.45), residues: 374
  helix:  1.80 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.49 (0.93), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.029   0.002   TYR A   9 
 PHE   0.015   0.001   PHE A  62 
 TRP   0.017   0.001   TRP A 364 
 HIS   0.002   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 2925)
  covalent geometry    : angle       0.65275 ( 3996)
  SS BOND              : bond        0.00107 (    3)
  SS BOND              : angle       0.48778 (    6)
  hydrogen bonds       : bond        0.05231 (  245)
  hydrogen bonds       : angle       4.70745 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.068 
Fit side-chains
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7855 (mp0)
REVERT: A  291 LYS cc_start: 0.7208 (mttt) cc_final: 0.6994 (mttt)
REVERT: A  368 LEU cc_start: 0.8291 (tp) cc_final: 0.7999 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.0432
  time to fit residues: 3.3279
Evaluate side-chains
  54 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   11 THR
Chi-restraints excluded: chain A residue  224 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 9 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 = 0.4126 r_free = 0.4126 target = 0.158825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.124201 restraints weight = 18941.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3685 rms_B_bonded: 7.98
r_work: 0.3417 rms_B_bonded: 7.62 restraints_weight: 2.0000
r_work (final): 0.3417
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3404
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3404 r_free = 0.3404    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3404
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.1753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2928  Z= 0.153
  Angle     :  0.643   6.628   4002  Z= 0.329
  Chirality :  0.041   0.219    480
  Planarity :  0.005   0.051    496
  Dihedral  :  5.498  65.501    399
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 13.73 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.33 (0.45), residues: 374
  helix:  1.89 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.48 (0.94), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 306 
 TYR   0.021   0.002   TYR A   9 
 PHE   0.020   0.001   PHE A 182 
 TRP   0.021   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 2925)
  covalent geometry    : angle       0.64338 ( 3996)
  SS BOND              : bond        0.00070 (    3)
  SS BOND              : angle       0.49894 (    6)
  hydrogen bonds       : bond        0.04985 (  245)
  hydrogen bonds       : angle       4.53705 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7679 (mp)
REVERT: A  219 ASN cc_start: 0.8797 (t0) cc_final: 0.8565 (m-40)
REVERT: A  368 LEU cc_start: 0.8161 (tp) cc_final: 0.7934 (tt)
REVERT: A  384 TYR cc_start: 0.8503 (m-10) cc_final: 0.8138 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 61
  average time/residue: 0.0392
  time to fit residues: 3.2202
Evaluate side-chains
  54 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 48
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 11 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 25 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 163 GLN

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 = 0.157030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.121728 restraints weight = 16293.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3698 rms_B_bonded: 7.78
r_work: 0.3432 rms_B_bonded: 7.24 restraints_weight: 2.0000
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2928  Z= 0.148
  Angle     :  0.636   6.825   4002  Z= 0.322
  Chirality :  0.041   0.196    480
  Planarity :  0.004   0.046    496
  Dihedral  :  5.314  59.574    399
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 13.03 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.45), residues: 374
  helix:  1.89 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.52 (0.93), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 306 
 TYR   0.018   0.001   TYR A   9 
 PHE   0.013   0.001   PHE A  62 
 TRP   0.024   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 2925)
  covalent geometry    : angle       0.63637 ( 3996)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       0.46422 (    6)
  hydrogen bonds       : bond        0.04853 (  245)
  hydrogen bonds       : angle       4.48499 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.061 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7455 (mp)
REVERT: A  219 ASN cc_start: 0.8755 (t0) cc_final: 0.8535 (m-40)
REVERT: A  294 GLU cc_start: 0.7652 (mp0) cc_final: 0.7379 (mp0)
REVERT: A  340 LEU cc_start: 0.8216 (tt) cc_final: 0.7974 (tp)
REVERT: A  368 LEU cc_start: 0.8175 (tp) cc_final: 0.7915 (tt)
REVERT: A  384 TYR cc_start: 0.8516 (m-80) cc_final: 0.8234 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 61
  average time/residue: 0.0404
  time to fit residues: 3.2107
Evaluate side-chains
  58 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 13 optimal weight:    0.0870
   chunk 16 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0770
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 18 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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 = 0.4274 r_free = 0.4274 target = 0.165407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.134275 restraints weight = 24618.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3899 rms_B_bonded: 8.70
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3902
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3902 r_free = 0.3902    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3902
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.2237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   2928  Z= 0.137
  Angle     :  0.623   9.695   4002  Z= 0.318
  Chirality :  0.040   0.220    480
  Planarity :  0.004   0.044    496
  Dihedral  :  5.172  55.051    399
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.49 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.48 (0.45), residues: 374
  helix:  2.00 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.54 (0.93), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 387 
 TYR   0.017   0.001   TYR A   9 
 PHE   0.016   0.001   PHE A 182 
 TRP   0.026   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 2925)
  covalent geometry    : angle       0.62350 ( 3996)
  SS BOND              : bond        0.00034 (    3)
  SS BOND              : angle       0.46801 (    6)
  hydrogen bonds       : bond        0.04400 (  245)
  hydrogen bonds       : angle       4.40922 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7647 (t80)
REVERT: A  135 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7844 (mp)
REVERT: A  219 ASN cc_start: 0.8054 (t0) cc_final: 0.7846 (m-40)
REVERT: A  291 LYS cc_start: 0.6933 (mtmt) cc_final: 0.6674 (mmtp)
REVERT: A  294 GLU cc_start: 0.7542 (mp0) cc_final: 0.7336 (mp0)
REVERT: A  368 LEU cc_start: 0.8314 (tp) cc_final: 0.8023 (tt)
  outliers start: 8
  outliers final: 5
  residues processed: 65
  average time/residue: 0.0410
  time to fit residues: 3.5199
Evaluate side-chains
  62 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    8.9990
   chunk 27 optimal weight:    0.0980
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   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 = 0.4252 r_free = 0.4252 target = 0.163770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.136897 restraints weight = 14156.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.3948 rms_B_bonded: 9.19
r_work: 0.3541 rms_B_bonded: 8.55 restraints_weight: 2.0000
r_work: 0.3706 rms_B_bonded: 5.24 restraints_weight: 4.0000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3720
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3720 r_free = 0.3720    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3720
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   2928  Z= 0.145
  Angle     :  0.632   9.195   4002  Z= 0.323
  Chirality :  0.040   0.189    480
  Planarity :  0.004   0.042    496
  Dihedral  :  5.082  52.196    399
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.25 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.59 (0.45), residues: 374
  helix:  2.06 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.34 (0.94), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 306 
 TYR   0.017   0.002   TYR A 384 
 PHE   0.016   0.001   PHE A 395 
 TRP   0.026   0.002   TRP A 364 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 2925)
  covalent geometry    : angle       0.63270 ( 3996)
  SS BOND              : bond        0.00046 (    3)
  SS BOND              : angle       0.40144 (    6)
  hydrogen bonds       : bond        0.04494 (  245)
  hydrogen bonds       : angle       4.35766 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.079 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.7573 (t80)
REVERT: A  135 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7982 (mp)
REVERT: A  167 LEU cc_start: 0.8988 (tp) cc_final: 0.8426 (tt)
REVERT: A  219 ASN cc_start: 0.8586 (t0) cc_final: 0.8378 (m-40)
REVERT: A  368 LEU cc_start: 0.8187 (tp) cc_final: 0.7913 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0381
  time to fit residues: 3.0013
Evaluate side-chains
  60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 THR
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 15 optimal weight:   10.0000
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4180 r_free = 0.4180 target = 0.158866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.124718 restraints weight = 17902.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 7.85
r_work (final): 0.3846
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   2928  Z= 0.154
  Angle     :  0.637   9.154   4002  Z= 0.327
  Chirality :  0.040   0.217    480
  Planarity :  0.004   0.042    496
  Dihedral  :  5.084  51.444    399
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.77 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 17.96 %
    Favored  : 78.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.58 (0.45), residues: 374
  helix:  2.04 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.31 (0.96), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 306 
 TYR   0.017   0.001   TYR A   9 
 PHE   0.012   0.001   PHE A  62 
 TRP   0.025   0.002   TRP A 364 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 2925)
  covalent geometry    : angle       0.63751 ( 3996)
  SS BOND              : bond        0.00096 (    3)
  SS BOND              : angle       0.42948 (    6)
  hydrogen bonds       : bond        0.04716 (  245)
  hydrogen bonds       : angle       4.38484 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.099 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.7689 (t80)
REVERT: A  135 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (mp)
REVERT: A  167 LEU cc_start: 0.8930 (tp) cc_final: 0.8430 (tt)
REVERT: A  219 ASN cc_start: 0.8123 (t0) cc_final: 0.7921 (m-40)
REVERT: A  368 LEU cc_start: 0.8375 (tp) cc_final: 0.8095 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0348
  time to fit residues: 2.6993
Evaluate side-chains
  60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 28 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 15 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4225 r_free = 0.4225 target = 0.161616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.127321 restraints weight = 20024.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 8.40
r_work: 0.3525 rms_B_bonded: 8.07 restraints_weight: 2.0000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3531
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3531 r_free = 0.3531    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3531
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.2549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   2928  Z= 0.160
  Angle     :  0.644   9.090   4002  Z= 0.332
  Chirality :  0.041   0.232    480
  Planarity :  0.004   0.040    496
  Dihedral  :  5.089  49.660    399
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.96 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.01 %
    Favored  : 77.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.45), residues: 374
  helix:  2.05 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.50 (0.90), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 270 
 TYR   0.018   0.002   TYR A 384 
 PHE   0.011   0.001   PHE A  62 
 TRP   0.022   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 2925)
  covalent geometry    : angle       0.64433 ( 3996)
  SS BOND              : bond        0.00063 (    3)
  SS BOND              : angle       0.42807 (    6)
  hydrogen bonds       : bond        0.04841 (  245)
  hydrogen bonds       : angle       4.41083 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.066 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 TYR cc_start: 0.8284 (t80) cc_final: 0.8020 (t80)
REVERT: A  133 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: A  135 ILE cc_start: 0.8598 (OUTLIER) cc_final: 0.8244 (mp)
REVERT: A  167 LEU cc_start: 0.9031 (tp) cc_final: 0.8448 (tt)
REVERT: A  169 GLU cc_start: 0.9038 (pm20) cc_final: 0.8133 (mm-30)
REVERT: A  219 ASN cc_start: 0.8816 (t0) cc_final: 0.8604 (m-40)
REVERT: A  368 LEU cc_start: 0.8258 (tp) cc_final: 0.7976 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.0399
  time to fit residues: 2.8950
Evaluate side-chains
  58 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 4 optimal weight:    4.9990
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 326 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4235 r_free = 0.4235 target = 0.162386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.128601 restraints weight = 19036.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3841 rms_B_bonded: 7.95
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3840
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3840 r_free = 0.3840    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3840
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2928  Z= 0.154
  Angle     :  0.640   8.958   4002  Z= 0.329
  Chirality :  0.041   0.272    480
  Planarity :  0.004   0.039    496
  Dihedral  :  5.102  48.343    399
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.37 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.55 (0.45), residues: 374
  helix:  2.09 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.78 (0.88), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 270 
 TYR   0.016   0.002   TYR A 384 
 PHE   0.010   0.001   PHE A  62 
 TRP   0.022   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 346 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 2925)
  covalent geometry    : angle       0.63994 ( 3996)
  SS BOND              : bond        0.00052 (    3)
  SS BOND              : angle       0.44094 (    6)
  hydrogen bonds       : bond        0.04770 (  245)
  hydrogen bonds       : angle       4.38804 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 0.065 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7650 (t80)
REVERT: A  135 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: A  167 LEU cc_start: 0.8930 (tp) cc_final: 0.8465 (tt)
REVERT: A  219 ASN cc_start: 0.8066 (t0) cc_final: 0.7854 (m-40)
REVERT: A  368 LEU cc_start: 0.8342 (tp) cc_final: 0.8043 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 59
  average time/residue: 0.0371
  time to fit residues: 2.9192
Evaluate side-chains
  60 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    8.9990
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 2 optimal weight:    0.0470
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6478

-------------------------------------------------------------------------------
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 = 0.4198 r_free = 0.4198 target = 0.160152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.132331 restraints weight = 12308.044|
|-----------------------------------------------------------------------------|
r_work (start): 0.3934 rms_B_bonded: 8.11
r_work: 0.3564 rms_B_bonded: 7.74 restraints_weight: 2.0000
r_work (final): 0.3564
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3574
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3574 r_free = 0.3574    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3574
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   2928  Z= 0.151
  Angle     :  0.644   9.018   4002  Z= 0.332
  Chirality :  0.041   0.251    480
  Planarity :  0.004   0.039    496
  Dihedral  :  5.064  47.745    399
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.96 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 19.37 %
    Favored  : 77.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.45), residues: 374
  helix:  2.08 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.74 (0.89), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.017   0.002   TYR A 103 
 PHE   0.019   0.001   PHE A 182 
 TRP   0.022   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 2925)
  covalent geometry    : angle       0.64467 ( 3996)
  SS BOND              : bond        0.00039 (    3)
  SS BOND              : angle       0.40283 (    6)
  hydrogen bonds       : bond        0.04642 (  245)
  hydrogen bonds       : angle       4.45807 (  735)

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

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

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  748 Ramachandran restraints generated.
    374 Oldfield, 0 Emsley, 374 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.065 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.7407 (p) cc_final: 0.7201 (p)
REVERT: A  103 TYR cc_start: 0.8277 (t80) cc_final: 0.8057 (t80)
REVERT: A  133 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.7656 (t80)
REVERT: A  135 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8334 (mp)
REVERT: A  167 LEU cc_start: 0.9003 (tp) cc_final: 0.8473 (tt)
REVERT: A  219 ASN cc_start: 0.8750 (t0) cc_final: 0.8538 (m-40)
REVERT: A  226 GLU cc_start: 0.6719 (OUTLIER) cc_final: 0.6474 (mp0)
REVERT: A  368 LEU cc_start: 0.8194 (tp) cc_final: 0.7907 (tt)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.0464
  time to fit residues: 3.4860
Evaluate side-chains
  59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  135 ILE
Chi-restraints excluded: chain A residue  193 MET
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  365 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 22 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 3 optimal weight:    0.3980
   chunk 4 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9980
   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 = 0.4193 r_free = 0.4193 target = 0.160076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.132184 restraints weight = 17033.472|
|-----------------------------------------------------------------------------|
r_work (start): 0.3942 rms_B_bonded: 10.35
r_work: 0.3490 rms_B_bonded: 9.50 restraints_weight: 2.0000
r_work: 0.3663 rms_B_bonded: 5.81 restraints_weight: 4.0000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3683 r_free = 0.3683    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2805

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   2928  Z= 0.149
  Angle     :  0.642   8.978   4002  Z= 0.330
  Chirality :  0.041   0.268    480
  Planarity :  0.004   0.039    496
  Dihedral  :  5.004  46.514    399
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 20.07 %
    Favored  : 76.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.45), residues: 374
  helix:  2.08 (0.29), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.79 (0.88), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.016   0.002   TYR A 103 
 PHE   0.005   0.001   PHE A 351 
 TRP   0.021   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 2925)
  covalent geometry    : angle       0.64268 ( 3996)
  SS BOND              : bond        0.00026 (    3)
  SS BOND              : angle       0.40802 (    6)
  hydrogen bonds       : bond        0.04560 (  245)
  hydrogen bonds       : angle       4.42934 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 951.33 seconds
wall clock time: 16 minutes 52.00 seconds (1012.00 seconds total)