Starting phenix.real_space_refine
on Thu Jun  5 05:34:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_25648.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_25648.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_25648.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_25648.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t32_25648/06_2025/7t32_25648.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7}
          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: {'GLN:plan1': 1, 'ASP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 7}
          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: 3.94, per 1000 atoms: 1.38
  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: 0.76
  Conformation dependent library (CDL) restraints added in 641.9 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: 0.26
  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: 0.73

  Time building geometry restraints manager: 0.87 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     14.010
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:3.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.930
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.021   0.001   TRP A 364 
 HIS   0.002   0.001   HIS A 155 
 PHE   0.018   0.001   PHE A 395 
 TYR   0.008   0.001   TYR A 384 
 ARG   0.002   0.000   ARG A 306 

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

*********************** 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  : 0.278 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.1149
  time to fit residues: 8.0971
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  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 14 optimal weight:   20.0000
   chunk 29 optimal weight:    0.9990
   chunk 11 optimal weight:    0.3980
   chunk 17 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    6.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.156212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.127384 restraints weight = 14872.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3765 rms_B_bonded: 9.36
r_work: 0.3400 rms_B_bonded: 8.10 restraints_weight: 2.0000
r_work: 0.3556 rms_B_bonded: 5.05 restraints_weight: 4.0000
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   2928  Z= 0.160
  Angle     :  0.662   7.943   4002  Z= 0.340
  Chirality :  0.041   0.173    480
  Planarity :  0.005   0.061    496
  Dihedral  :  5.766  72.611    399
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  : 11.62 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.45), residues: 374
  helix:  1.76 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.48 (0.94), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 364 
 HIS   0.002   0.001   HIS A 374 
 PHE   0.015   0.001   PHE A  62 
 TYR   0.029   0.002   TYR A   9 
 ARG   0.001   0.000   ARG A 392 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05432 (  245)
  hydrogen bonds       : angle       4.73249 (  735)
  SS BOND              : bond        0.00097 (    3)
  SS BOND              : angle       0.49240 (    6)
  covalent geometry    : bond        0.00353 ( 2925)
  covalent geometry    : angle       0.66180 ( 3996)

*********************** 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  : 0.307 
Fit side-chains
   revert: symmetry clash
REVERT: A  289 GLU cc_start: 0.8045 (mm-30) cc_final: 0.7745 (mp0)
REVERT: A  291 LYS cc_start: 0.7280 (mttt) cc_final: 0.7035 (mttt)
REVERT: A  368 LEU cc_start: 0.8172 (tp) cc_final: 0.7891 (tt)
  outliers start: 2
  outliers final: 2
  residues processed: 58
  average time/residue: 0.1086
  time to fit residues: 8.1161
Evaluate side-chains
  53 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 51
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
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 28 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 9 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.4078 r_free = 0.4078 target = 0.154998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.120446 restraints weight = 15922.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 7.69
r_work: 0.3414 rms_B_bonded: 7.30 restraints_weight: 2.0000
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3425
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3425 r_free = 0.3425    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3425
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.1798

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= 0.157
  Angle     :  0.652   6.842   4002  Z= 0.335
  Chirality :  0.041   0.181    480
  Planarity :  0.005   0.051    496
  Dihedral  :  5.485  64.816    399
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.08 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.45), residues: 374
  helix:  1.87 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.42 (0.96), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.022   0.001   PHE A 182 
 TYR   0.020   0.002   TYR A   9 
 ARG   0.005   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05116 (  245)
  hydrogen bonds       : angle       4.55944 (  735)
  SS BOND              : bond        0.00077 (    3)
  SS BOND              : angle       0.51087 (    6)
  covalent geometry    : bond        0.00353 ( 2925)
  covalent geometry    : angle       0.65213 ( 3996)

*********************** 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
  63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 55
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  135 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7628 (mp)
REVERT: A  219 ASN cc_start: 0.8763 (t0) cc_final: 0.8536 (m-40)
REVERT: A  368 LEU cc_start: 0.8211 (tp) cc_final: 0.7981 (tt)
REVERT: A  384 TYR cc_start: 0.8577 (m-80) cc_final: 0.8362 (m-10)
  outliers start: 8
  outliers final: 4
  residues processed: 62
  average time/residue: 0.1063
  time to fit residues: 8.4997
Evaluate side-chains
  56 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 51
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 27 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 35 optimal weight:    3.9990
   chunk 16 optimal weight:    0.0370
   chunk 19 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.4101 r_free = 0.4101 target = 0.157228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.122562 restraints weight = 15253.610|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 7.25
r_work: 0.3442 rms_B_bonded: 7.16 restraints_weight: 2.0000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7779
moved from start:          0.2040

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= 0.145
  Angle     :  0.624   6.659   4002  Z= 0.318
  Chirality :  0.040   0.206    480
  Planarity :  0.004   0.046    496
  Dihedral  :  5.264  58.134    399
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 14.44 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.39 (0.45), residues: 374
  helix:  1.94 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.53 (0.94), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.012   0.001   PHE A  62 
 TYR   0.018   0.001   TYR A   9 
 ARG   0.001   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04749 (  245)
  hydrogen bonds       : angle       4.47716 (  735)
  SS BOND              : bond        0.00049 (    3)
  SS BOND              : angle       0.47538 (    6)
  covalent geometry    : bond        0.00320 ( 2925)
  covalent geometry    : angle       0.62376 ( 3996)

*********************** 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
  65 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7524 (t80)
REVERT: A  135 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7803 (mp)
REVERT: A  219 ASN cc_start: 0.8716 (t0) cc_final: 0.8495 (m-40)
REVERT: A  340 LEU cc_start: 0.8248 (tt) cc_final: 0.8001 (tp)
REVERT: A  368 LEU cc_start: 0.8195 (tp) cc_final: 0.7922 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1131
  time to fit residues: 9.2468
Evaluate side-chains
  59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
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  352 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 18 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    8.9990
   chunk 15 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4185 r_free = 0.4185 target = 0.159164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.131555 restraints weight = 13993.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3959 rms_B_bonded: 9.54
r_work: 0.3537 rms_B_bonded: 8.68 restraints_weight: 2.0000
r_work: 0.3706 rms_B_bonded: 5.34 restraints_weight: 4.0000
r_work (final): 0.3706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3691
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3691 r_free = 0.3691    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3691
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   2928  Z= 0.155
  Angle     :  0.647   6.779   4002  Z= 0.333
  Chirality :  0.042   0.209    480
  Planarity :  0.004   0.044    496
  Dihedral  :  5.247  56.098    399
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.20 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.45), residues: 374
  helix:  1.89 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.40 (0.96), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.010   0.001   PHE A  62 
 TYR   0.019   0.002   TYR A 384 
 ARG   0.001   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04843 (  245)
  hydrogen bonds       : angle       4.46716 (  735)
  SS BOND              : bond        0.00036 (    3)
  SS BOND              : angle       0.44827 (    6)
  covalent geometry    : bond        0.00352 ( 2925)
  covalent geometry    : angle       0.64711 ( 3996)

*********************** 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
  67 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8543 (OUTLIER) cc_final: 0.7661 (t80)
REVERT: A  135 ILE cc_start: 0.8461 (OUTLIER) cc_final: 0.8116 (mp)
REVERT: A  219 ASN cc_start: 0.8585 (t0) cc_final: 0.8357 (m-40)
REVERT: A  340 LEU cc_start: 0.8284 (tt) cc_final: 0.8017 (tp)
REVERT: A  368 LEU cc_start: 0.8192 (tp) cc_final: 0.7907 (tt)
  outliers start: 10
  outliers final: 7
  residues processed: 65
  average time/residue: 0.1031
  time to fit residues: 8.7533
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  : 0.310 
-------------------------------------------------------------------------------
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  226 GLU
Chi-restraints excluded: chain A residue  352 THR
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 18 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 10 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 30 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4181 r_free = 0.4181 target = 0.158767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.125196 restraints weight = 15821.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3851 rms_B_bonded: 7.46
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3838
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3838 r_free = 0.3838    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 = 0.3838 r_free = 0.3838    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3838
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7666
moved from start:          0.2375

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= 0.150
  Angle     :  0.635   9.914   4002  Z= 0.323
  Chirality :  0.041   0.194    480
  Planarity :  0.004   0.042    496
  Dihedral  :  5.110  52.398    399
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.55 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.45), residues: 374
  helix:  1.97 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.28 (0.97), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.012   0.001   PHE A 395 
 TYR   0.016   0.001   TYR A   9 
 ARG   0.001   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04734 (  245)
  hydrogen bonds       : angle       4.41542 (  735)
  SS BOND              : bond        0.00041 (    3)
  SS BOND              : angle       0.42540 (    6)
  covalent geometry    : bond        0.00339 ( 2925)
  covalent geometry    : angle       0.63550 ( 3996)

*********************** 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
  66 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 56
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.7693 (t80)
REVERT: A  135 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.8103 (mp)
REVERT: A  219 ASN cc_start: 0.8115 (t0) cc_final: 0.7895 (m-40)
REVERT: A  368 LEU cc_start: 0.8336 (tp) cc_final: 0.8049 (tt)
  outliers start: 10
  outliers final: 8
  residues processed: 63
  average time/residue: 0.0982
  time to fit residues: 8.1244
Evaluate side-chains
  64 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 54
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
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  224 VAL
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    1.9990
   chunk 1 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4188 r_free = 0.4188 target = 0.159119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.125261 restraints weight = 21446.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 8.84
r_work: 0.3519 rms_B_bonded: 8.54 restraints_weight: 2.0000
r_work: 0.3684 rms_B_bonded: 5.25 restraints_weight: 4.0000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3686
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3686 r_free = 0.3686    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3686
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2476

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= 0.153
  Angle     :  0.638   9.540   4002  Z= 0.325
  Chirality :  0.040   0.212    480
  Planarity :  0.004   0.040    496
  Dihedral  :  5.074  50.672    399
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.23 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 16.90 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.45), residues: 374
  helix:  2.00 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.45 (0.92), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.010   0.001   PHE A  62 
 TYR   0.017   0.002   TYR A 384 
 ARG   0.001   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04773 (  245)
  hydrogen bonds       : angle       4.44246 (  735)
  SS BOND              : bond        0.00060 (    3)
  SS BOND              : angle       0.40901 (    6)
  covalent geometry    : bond        0.00344 ( 2925)
  covalent geometry    : angle       0.63851 ( 3996)

*********************** 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
  63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7663 (t80)
REVERT: A  135 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8268 (mp)
REVERT: A  219 ASN cc_start: 0.8593 (t0) cc_final: 0.8371 (m-40)
REVERT: A  368 LEU cc_start: 0.8182 (tp) cc_final: 0.7922 (tt)
REVERT: A  384 TYR cc_start: 0.8423 (m-10) cc_final: 0.8174 (m-10)
  outliers start: 10
  outliers final: 7
  residues processed: 60
  average time/residue: 0.0947
  time to fit residues: 7.5382
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  : 0.299 
-------------------------------------------------------------------------------
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  224 VAL
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 36 optimal weight:    0.6980
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0050
   chunk 10 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.6194

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.163439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.136451 restraints weight = 10861.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3938 rms_B_bonded: 7.39
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3930
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3930 r_free = 0.3930    target_work(ls_wunit_k1) = 0.135         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3930
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   2928  Z= 0.145
  Angle     :  0.644   9.839   4002  Z= 0.326
  Chirality :  0.040   0.224    480
  Planarity :  0.004   0.039    496
  Dihedral  :  5.017  48.557    399
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.55 (0.45), residues: 374
  helix:  2.06 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.57 (0.90), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 326 
 PHE   0.017   0.001   PHE A 182 
 TYR   0.017   0.002   TYR A 384 
 ARG   0.000   0.000   ARG A 270 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04589 (  245)
  hydrogen bonds       : angle       4.39820 (  735)
  SS BOND              : bond        0.00047 (    3)
  SS BOND              : angle       0.40572 (    6)
  covalent geometry    : bond        0.00321 ( 2925)
  covalent geometry    : angle       0.64459 ( 3996)

*********************** 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
  63 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8525 (OUTLIER) cc_final: 0.7729 (t80)
REVERT: A  135 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8276 (mp)
REVERT: A  167 LEU cc_start: 0.8855 (tp) cc_final: 0.8423 (tt)
REVERT: A  368 LEU cc_start: 0.8341 (tp) cc_final: 0.8047 (tt)
  outliers start: 9
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1186
  time to fit residues: 9.0266
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  : 0.319 
-------------------------------------------------------------------------------
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  224 VAL
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.2182

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.159733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.132271 restraints weight = 15077.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3887 rms_B_bonded: 9.42
r_work: 0.3452 rms_B_bonded: 8.92 restraints_weight: 2.0000
r_work: 0.3621 rms_B_bonded: 5.50 restraints_weight: 4.0000
r_work (final): 0.3621
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3636 r_free = 0.3636    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.2710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   2928  Z= 0.180
  Angle     :  0.683   9.543   4002  Z= 0.351
  Chirality :  0.043   0.250    480
  Planarity :  0.004   0.041    496
  Dihedral  :  5.111  49.628    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 :  2.82 %
    Allowed  : 17.96 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.45), residues: 374
  helix:  1.89 (0.30), residues: 321
  sheet:  None (None), residues: 0
  loop : -0.77 (0.85), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 364 
 HIS   0.001   0.001   HIS A 326 
 PHE   0.010   0.001   PHE A  62 
 TYR   0.020   0.002   TYR A 384 
 ARG   0.002   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05326 (  245)
  hydrogen bonds       : angle       4.52809 (  735)
  SS BOND              : bond        0.00094 (    3)
  SS BOND              : angle       0.44568 (    6)
  covalent geometry    : bond        0.00429 ( 2925)
  covalent geometry    : angle       0.68354 ( 3996)

*********************** 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
  57 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8570 (OUTLIER) cc_final: 0.7633 (t80)
REVERT: A  135 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8403 (mp)
REVERT: A  167 LEU cc_start: 0.9025 (tp) cc_final: 0.8502 (tt)
REVERT: A  368 LEU cc_start: 0.8150 (tp) cc_final: 0.7859 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 54
  average time/residue: 0.1143
  time to fit residues: 8.0823
Evaluate side-chains
  57 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 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  224 VAL
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 17 optimal weight:    0.7980
   chunk 33 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   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 = 0.4189 r_free = 0.4189 target = 0.159399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.131476 restraints weight = 15660.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3943 rms_B_bonded: 9.95
r_work: 0.3499 rms_B_bonded: 9.14 restraints_weight: 2.0000
r_work: 0.3673 rms_B_bonded: 5.61 restraints_weight: 4.0000
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3652
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3652 r_free = 0.3652    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3652
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2928  Z= 0.149
  Angle     :  0.650   9.595   4002  Z= 0.333
  Chirality :  0.041   0.225    480
  Planarity :  0.004   0.038    496
  Dihedral  :  5.004  46.691    399
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.96 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.96 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.45), residues: 374
  helix:  2.03 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.88 (0.84), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A 374 
 PHE   0.010   0.001   PHE A  62 
 TYR   0.017   0.002   TYR A 384 
 ARG   0.002   0.000   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04732 (  245)
  hydrogen bonds       : angle       4.46669 (  735)
  SS BOND              : bond        0.00037 (    3)
  SS BOND              : angle       0.41376 (    6)
  covalent geometry    : bond        0.00332 ( 2925)
  covalent geometry    : angle       0.65005 ( 3996)

********************** 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
  59 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7624 (t80)
REVERT: A  135 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8397 (mp)
REVERT: A  167 LEU cc_start: 0.9057 (tp) cc_final: 0.8530 (tt)
REVERT: A  368 LEU cc_start: 0.8110 (tp) cc_final: 0.7820 (tt)
  outliers start: 8
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1196
  time to fit residues: 8.5592
Evaluate side-chains
  56 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 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  224 VAL
Chi-restraints excluded: chain A residue  226 GLU
Chi-restraints excluded: chain A residue  352 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 37
   random chunks:
   chunk 27 optimal weight:    0.0020
   chunk 0 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0070
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 11 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 16 optimal weight:    0.0970
   chunk 4 optimal weight:    0.8980
   overall best weight:    0.2604

-------------------------------------------------------------------------------
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 = 0.4277 r_free = 0.4277 target = 0.166140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.139677 restraints weight = 12434.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.3953 rms_B_bonded: 8.42
r_work: 0.3566 rms_B_bonded: 7.99 restraints_weight: 2.0000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3580
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3580 r_free = 0.3580    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 = 0.3580 r_free = 0.3580    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3580
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   2928  Z= 0.140
  Angle     :  0.638   9.962   4002  Z= 0.326
  Chirality :  0.041   0.286    480
  Planarity :  0.004   0.037    496
  Dihedral  :  4.935  44.012    399
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.50 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.66 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.45), residues: 374
  helix:  2.09 (0.30), residues: 320
  sheet:  None (None), residues: 0
  loop : -0.88 (0.86), residues: 54

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 364 
 HIS   0.001   0.000   HIS A  75 
 PHE   0.018   0.001   PHE A 182 
 TYR   0.016   0.002   TYR A 103 
 ARG   0.002   0.000   ARG A 387 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04204 (  245)
  hydrogen bonds       : angle       4.46368 (  735)
  SS BOND              : bond        0.00020 (    3)
  SS BOND              : angle       0.39949 (    6)
  covalent geometry    : bond        0.00298 ( 2925)
  covalent geometry    : angle       0.63851 ( 3996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2293.56 seconds
wall clock time: 39 minutes 47.68 seconds (2387.68 seconds total)