Starting phenix.real_space_refine
on Sun Apr 27 07:20:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.09
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjp_39345/04_2025/8yjp_39345.cif"
  }
  resolution = 3.09
  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=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      34      5.16       5
     C    3359      2.51       5
     N     726      2.21       5
     O     823      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4946
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2241
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 287}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 298, 2241
          Classifications: {'peptide': 298}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 10, 'TRANS': 287}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 246
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 246
          Unusual residues: {'CLR': 5, 'MW9': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
    Chain: "B"
      Number of atoms: 218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 218
          Unusual residues: {'CLR': 4, 'MW9': 2}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Time building chain proxies: 3.70, per 1000 atoms: 0.75
  Number of scatterers: 4946
  At special positions: 0
  Unit cell: (66.96, 79.98, 95.79, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       4     15.00
     O     823      8.00
     N     726      7.00
     C    3359      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 191 " - pdb=" SG  CYS A 216 " distance=2.44

  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: 1.59
  Conformation dependent library (CDL) restraints added in 562.5 milliseconds
  

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1112

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 1 sheets defined
      77.0% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 34
      removed outlier: 3.610A  pdb=" N   LYS A  29 " --> pdb=" O   HIS A  25 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   SER A  34 " --> pdb=" O   THR A  30 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 74
    Processing helix  chain 'A' and resid 77 through 83
    Processing helix  chain 'A' and resid 84 through 106
      removed outlier: 3.676A  pdb=" N   GLY A 106 " --> pdb=" O   ALA A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 114 through 150
      removed outlier: 4.011A  pdb=" N   THR A 118 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
      Proline residue:  A 137  - end of helix
    Processing helix  chain 'A' and resid 161 through 187
      removed outlier: 3.966A  pdb=" N   LEU A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 246
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.857A  pdb=" N   GLN A 256 " --> pdb=" O   PRO A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 281
    Processing helix  chain 'A' and resid 284 through 319
      Proline residue:  A 310  - end of helix
    Processing helix  chain 'B' and resid 23 through 34
      removed outlier: 3.934A  pdb=" N   LEU B  27 " --> pdb=" O   PRO B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 48 through 74
    Processing helix  chain 'B' and resid 77 through 83
    Processing helix  chain 'B' and resid 84 through 106
      removed outlier: 3.804A  pdb=" N   GLY B 106 " --> pdb=" O   ALA B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 151
      removed outlier: 3.862A  pdb=" N   THR B 118 " --> pdb=" O   SER B 114 " (cutoff:3.500A)
      Proline residue:  B 137  - end of helix
    Processing helix  chain 'B' and resid 161 through 187
      removed outlier: 3.880A  pdb=" N   LEU B 165 " --> pdb=" O   LYS B 161 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 246
    Processing helix  chain 'B' and resid 251 through 256
      removed outlier: 3.860A  pdb=" N   GLN B 256 " --> pdb=" O   PRO B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 281
    Processing helix  chain 'B' and resid 284 through 319
      Proline residue:  B 310  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 209 through 216
      removed outlier: 3.556A  pdb=" N   PHE A 215 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU A 192 " --> pdb=" O   PHE A 215 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 195 " --> pdb=" O   MET B 199 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   VAL A 197 " --> pdb=" O   VAL B 197 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   VAL B 197 " --> pdb=" O   VAL A 197 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   MET A 199 " --> pdb=" O   LEU B 195 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU B 195 " --> pdb=" O   MET A 199 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLN B 193 " --> pdb=" O   VAL A 201 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA B 217 " --> pdb=" O   GLN B 190 " (cutoff:3.500A)

    376 hydrogen bonds defined for protein.
    1122 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: 1.25

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 680
        1.31 -     1.44: 1267
        1.44 -     1.56: 3060
        1.56 -     1.69: 8
        1.69 -     1.82: 48
  Bond restraints: 5063
  Sorted by residual:
  bond pdb=" C8  MW9 A 402 "
       pdb=" C9  MW9 A 402 "
    ideal  model  delta    sigma   weight residual
    1.548  1.332  0.216 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C8  MW9 B 404 "
       pdb=" C9  MW9 B 404 "
    ideal  model  delta    sigma   weight residual
    1.548  1.333  0.215 2.00e-02 2.50e+03 1.16e+02
  bond pdb=" C8  MW9 B 403 "
       pdb=" C9  MW9 B 403 "
    ideal  model  delta    sigma   weight residual
    1.548  1.335  0.213 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C8  MW9 A 401 "
       pdb=" C9  MW9 A 401 "
    ideal  model  delta    sigma   weight residual
    1.548  1.336  0.212 2.00e-02 2.50e+03 1.13e+02
  bond pdb=" C24 MW9 A 402 "
       pdb=" O8  MW9 A 402 "
    ideal  model  delta    sigma   weight residual
    1.342  1.417 -0.075 2.00e-02 2.50e+03 1.41e+01
  ... (remaining 5058 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.73: 6831
        5.73 -    11.47: 63
       11.47 -    17.20: 12
       17.20 -    22.94: 0
       22.94 -    28.67: 4
  Bond angle restraints: 6910
  Sorted by residual:
  angle pdb=" C32 MW9 B 403 "
        pdb=" C33 MW9 B 403 "
        pdb=" C34 MW9 B 403 "
      ideal   model   delta    sigma   weight residual
     125.32  153.99  -28.67 3.00e+00 1.11e-01 9.13e+01
  angle pdb=" C32 MW9 A 402 "
        pdb=" C33 MW9 A 402 "
        pdb=" C34 MW9 A 402 "
      ideal   model   delta    sigma   weight residual
     125.32  153.33  -28.01 3.00e+00 1.11e-01 8.72e+01
  angle pdb=" C32 MW9 B 404 "
        pdb=" C33 MW9 B 404 "
        pdb=" C34 MW9 B 404 "
      ideal   model   delta    sigma   weight residual
     125.32  153.03  -27.71 3.00e+00 1.11e-01 8.53e+01
  angle pdb=" C32 MW9 A 401 "
        pdb=" C33 MW9 A 401 "
        pdb=" C34 MW9 A 401 "
      ideal   model   delta    sigma   weight residual
     125.32  152.94  -27.62 3.00e+00 1.11e-01 8.48e+01
  angle pdb=" C   SER B 251 "
        pdb=" N   PRO B 252 "
        pdb=" CA  PRO B 252 "
      ideal   model   delta    sigma   weight residual
     120.38  113.44    6.94 1.03e+00 9.43e-01 4.53e+01
  ... (remaining 6905 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.62: 3319
       35.62 -    71.24: 121
       71.24 -   106.86: 27
      106.86 -   142.48: 10
      142.48 -   178.09: 9
  Dihedral angle restraints: 3486
    sinusoidal: 1766
      harmonic: 1720
  Sorted by residual:
  dihedral pdb=" C20 MW9 A 402 "
           pdb=" O2  MW9 A 402 "
           pdb=" P   MW9 A 402 "
           pdb=" O5  MW9 A 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.77  123.68  178.09     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C11 MW9 B 403 "
           pdb=" C10 MW9 B 403 "
           pdb=" C9  MW9 B 403 "
           pdb=" C8  MW9 B 403 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -59.86  114.41 -174.27     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" O   MW9 A 401 "
           pdb=" C16 MW9 A 401 "
           pdb=" C17 MW9 A 401 "
           pdb=" C15 MW9 A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     102.59  -90.28 -167.13     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 3483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.105: 792
       0.105 -    0.210: 56
       0.210 -    0.315: 9
       0.315 -    0.420: 11
       0.420 -    0.525: 4
  Chirality restraints: 872
  Sorted by residual:
  chirality pdb=" C14 CLR B 405 "
            pdb=" C13 CLR B 405 "
            pdb=" C15 CLR B 405 "
            pdb=" C8  CLR B 405 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.84    0.52 2.00e-01 2.50e+01 6.88e+00
  chirality pdb=" C14 CLR B 406 "
            pdb=" C13 CLR B 406 "
            pdb=" C15 CLR B 406 "
            pdb=" C8  CLR B 406 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.84    0.52 2.00e-01 2.50e+01 6.87e+00
  chirality pdb=" C14 CLR A 407 "
            pdb=" C13 CLR A 407 "
            pdb=" C15 CLR A 407 "
            pdb=" C8  CLR A 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.84    0.52 2.00e-01 2.50e+01 6.84e+00
  ... (remaining 869 not shown)

  Planarity restraints: 754
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 148 "    0.014 2.00e-02 2.50e+03   2.84e-02 8.04e+00
        pdb=" C   VAL A 148 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   VAL A 148 "    0.018 2.00e-02 2.50e+03
        pdb=" N   PHE A 149 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 229 "    0.017 2.00e-02 2.50e+03   1.76e-02 7.70e+00
        pdb=" CG  TRP A 229 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 229 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 229 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 229 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 229 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 229 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 229 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 229 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 147 "    0.013 2.00e-02 2.50e+03   2.60e-02 6.76e+00
        pdb=" C   LYS B 147 "   -0.045 2.00e-02 2.50e+03
        pdb=" O   LYS B 147 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 148 "    0.015 2.00e-02 2.50e+03
  ... (remaining 751 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 883
        2.77 -     3.30: 4956
        3.30 -     3.84: 8012
        3.84 -     4.37: 9033
        4.37 -     4.90: 15913
  Nonbonded interactions: 38797
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 132 "
            pdb=" OD2 ASP B 176 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   LYS A  76 "
            pdb=" NZ  LYS A  81 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" OG  SER A 218 "
            pdb=" O   MW9 A 402 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" O   VAL B 298 "
            pdb=" OG1 THR B 302 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" O   THR B  98 "
            pdb=" OG  SER B 101 "
     model   vdw
     2.292 3.040
  ... (remaining 38792 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 22 through 319 or resid 405 through 406))
  selection = (chain 'B' and (resid 22 through 319 or resid 405 through 406))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             20.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.940
  Find NCS groups from input model:        0.190
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6765
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      :  0.011   0.407   5064  Z= 0.560
  Angle     :  1.474  28.669   6912  Z= 0.575
  Chirality :  0.079   0.525    872
  Planarity :  0.005   0.042    754
  Dihedral  : 22.112 178.095   2371
  Min Nonbonded Distance : 2.240

Molprobity Statistics.
  All-atom Clashscore : 15.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  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:  1.56 (0.35), residues: 592
  helix:  2.09 (0.24), residues: 436
  sheet:  1.50 (0.83), residues: 36
  loop : -3.36 (0.50), residues: 120

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 229 
 HIS   0.001   0.000   HIS B  73 
 PHE   0.008   0.002   PHE B 105 
 TYR   0.015   0.002   TYR A 241 
 ARG   0.003   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10925 (  376)
  hydrogen bonds       : angle       5.36663 ( 1122)
  SS BOND              : bond        0.40680 (    1)
  SS BOND              : angle      10.01902 (    2)
  covalent geometry    : bond        0.00940 ( 5063)
  covalent geometry    : angle       1.46454 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.537 
Fit side-chains
REVERT: A  265 ASN cc_start: 0.7159 (m-40) cc_final: 0.6933 (m110)
REVERT: B  194 ILE cc_start: 0.7669 (pt) cc_final: 0.7456 (pt)
REVERT: B  265 ASN cc_start: 0.7141 (m-40) cc_final: 0.6823 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.2028
  time to fit residues: 29.0904
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 255 ASN
A 304 ASN
B 121 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.172999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.147155 restraints weight = 6458.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.03
r_work: 0.3802 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3631 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   5064  Z= 0.182
  Angle     :  0.687   8.856   6912  Z= 0.320
  Chirality :  0.044   0.155    872
  Planarity :  0.005   0.042    754
  Dihedral  : 22.845 179.177   1433
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.61 %
    Favored  : 88.78 %
  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:  1.91 (0.34), residues: 592
  helix:  2.38 (0.23), residues: 438
  sheet:  1.43 (0.85), residues: 32
  loop : -3.25 (0.46), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 229 
 HIS   0.001   0.000   HIS B  73 
 PHE   0.011   0.002   PHE B 105 
 TYR   0.014   0.002   TYR A 241 
 ARG   0.001   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04601 (  376)
  hydrogen bonds       : angle       4.55788 ( 1122)
  SS BOND              : bond        0.00299 (    1)
  SS BOND              : angle       0.80777 (    2)
  covalent geometry    : bond        0.00409 ( 5063)
  covalent geometry    : angle       0.68675 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 99
  time to evaluate  : 0.527 
Fit side-chains
REVERT: A  265 ASN cc_start: 0.7991 (m-40) cc_final: 0.7776 (m110)
REVERT: B   82 MET cc_start: 0.7792 (mmm) cc_final: 0.7480 (mmm)
REVERT: B  194 ILE cc_start: 0.7971 (pt) cc_final: 0.7753 (pt)
REVERT: B  265 ASN cc_start: 0.8084 (m-40) cc_final: 0.7770 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 100
  average time/residue: 0.1554
  time to fit residues: 20.2836
Evaluate side-chains
  96 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 94
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain B residue  166 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0030
   chunk 1 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 55 optimal weight:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.3308

-------------------------------------------------------------------------------
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 = 0.4271 r_free = 0.4271 target = 0.174073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.148153 restraints weight = 6435.569|
|-----------------------------------------------------------------------------|
r_work (start): 0.3951 rms_B_bonded: 2.08
r_work: 0.3820 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3645 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.1582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5064  Z= 0.132
  Angle     :  0.594  11.349   6912  Z= 0.282
  Chirality :  0.040   0.135    872
  Planarity :  0.004   0.042    754
  Dihedral  : 20.305 179.701   1433
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.27 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.32 (0.34), residues: 592
  helix:  2.66 (0.23), residues: 438
  sheet:  1.91 (0.87), residues: 32
  loop : -3.14 (0.46), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 284 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.021   0.001   PHE B 275 
 TYR   0.023   0.002   TYR A 241 
 ARG   0.002   0.000   ARG B 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04226 (  376)
  hydrogen bonds       : angle       4.28957 ( 1122)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.58914 (    2)
  covalent geometry    : bond        0.00274 ( 5063)
  covalent geometry    : angle       0.59437 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.475 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7461 (m-80) cc_final: 0.7111 (m-80)
REVERT: A  265 ASN cc_start: 0.7947 (m-40) cc_final: 0.7725 (m110)
REVERT: B   82 MET cc_start: 0.7873 (mmm) cc_final: 0.7540 (mmm)
REVERT: B  265 ASN cc_start: 0.8034 (m-40) cc_final: 0.7731 (m110)
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 0.1521
  time to fit residues: 21.0637
Evaluate side-chains
  105 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue  174 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.5980
   chunk 13 optimal weight:    0.4980
   chunk 31 optimal weight:    0.0030
   chunk 9 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.172710 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.146742 restraints weight = 6523.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.12
r_work: 0.3791 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5064  Z= 0.157
  Angle     :  0.614  10.537   6912  Z= 0.289
  Chirality :  0.041   0.138    872
  Planarity :  0.005   0.042    754
  Dihedral  : 18.681 175.245   1433
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.08 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.29 (0.34), residues: 592
  helix:  2.63 (0.23), residues: 438
  sheet:  2.21 (0.88), residues: 32
  loop : -3.23 (0.47), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 229 
 HIS   0.002   0.000   HIS B  73 
 PHE   0.026   0.002   PHE B 275 
 TYR   0.017   0.002   TYR A 241 
 ARG   0.001   0.000   ARG B 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  376)
  hydrogen bonds       : angle       4.31678 ( 1122)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.47626 (    2)
  covalent geometry    : bond        0.00348 ( 5063)
  covalent geometry    : angle       0.61447 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.579 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7479 (m-80) cc_final: 0.7087 (m-80)
REVERT: A  107 ILE cc_start: 0.8415 (mt) cc_final: 0.8167 (mp)
REVERT: A  265 ASN cc_start: 0.8025 (m-40) cc_final: 0.7795 (m110)
REVERT: B   82 MET cc_start: 0.7888 (mmm) cc_final: 0.7561 (mmm)
REVERT: B   92 LEU cc_start: 0.7276 (mt) cc_final: 0.6966 (mt)
REVERT: B  172 LEU cc_start: 0.8332 (tt) cc_final: 0.7829 (tp)
REVERT: B  265 ASN cc_start: 0.8049 (m-40) cc_final: 0.7718 (m110)
  outliers start: 14
  outliers final: 10
  residues processed: 107
  average time/residue: 0.1939
  time to fit residues: 26.9239
Evaluate side-chains
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  174 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 29 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 47 optimal weight:    6.9990
   chunk 44 optimal weight:    0.3980
   chunk 46 optimal weight:    0.7980
   chunk 41 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4249 r_free = 0.4249 target = 0.171612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.146003 restraints weight = 6421.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3922 rms_B_bonded: 2.05
r_work: 0.3784 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3604 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5064  Z= 0.169
  Angle     :  0.614  11.961   6912  Z= 0.290
  Chirality :  0.042   0.149    872
  Planarity :  0.005   0.042    754
  Dihedral  : 18.230 179.600   1433
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.53 %
    Favored  : 81.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.34), residues: 592
  helix:  2.62 (0.23), residues: 438
  sheet:  2.37 (0.88), residues: 32
  loop : -3.26 (0.47), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 229 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.022   0.002   PHE B 275 
 TYR   0.015   0.002   TYR A 241 
 ARG   0.002   0.000   ARG A 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04356 (  376)
  hydrogen bonds       : angle       4.35839 ( 1122)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       0.40886 (    2)
  covalent geometry    : bond        0.00373 ( 5063)
  covalent geometry    : angle       0.61371 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.503 
Fit side-chains
REVERT: A   65 LEU cc_start: 0.7731 (mp) cc_final: 0.7428 (mt)
REVERT: A   99 TYR cc_start: 0.7538 (m-80) cc_final: 0.7177 (m-80)
REVERT: A  107 ILE cc_start: 0.8427 (mt) cc_final: 0.8200 (mp)
REVERT: A  265 ASN cc_start: 0.8021 (m-40) cc_final: 0.7800 (m110)
REVERT: B   82 MET cc_start: 0.7961 (mmm) cc_final: 0.7609 (mmm)
REVERT: B   92 LEU cc_start: 0.7317 (mt) cc_final: 0.7074 (mt)
REVERT: B  265 ASN cc_start: 0.8054 (m-40) cc_final: 0.7723 (m110)
  outliers start: 12
  outliers final: 9
  residues processed: 105
  average time/residue: 0.1540
  time to fit residues: 21.5267
Evaluate side-chains
  110 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 3 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 304 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.171172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.145422 restraints weight = 6449.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 2.09
r_work: 0.3780 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3597 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5064  Z= 0.168
  Angle     :  0.620  10.197   6912  Z= 0.292
  Chirality :  0.041   0.139    872
  Planarity :  0.005   0.043    754
  Dihedral  : 17.891 178.324   1433
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 15.92 %
    Favored  : 80.61 %
  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:  2.29 (0.34), residues: 592
  helix:  2.56 (0.23), residues: 442
  sheet:  2.59 (0.89), residues: 32
  loop : -3.24 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 229 
 HIS   0.002   0.001   HIS B 214 
 PHE   0.027   0.002   PHE B  70 
 TYR   0.013   0.002   TYR A 241 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  376)
  hydrogen bonds       : angle       4.36112 ( 1122)
  SS BOND              : bond        0.00150 (    1)
  SS BOND              : angle       0.40324 (    2)
  covalent geometry    : bond        0.00375 ( 5063)
  covalent geometry    : angle       0.62019 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7540 (m-80) cc_final: 0.7202 (m-80)
REVERT: A  107 ILE cc_start: 0.8451 (mt) cc_final: 0.8227 (mp)
REVERT: A  172 LEU cc_start: 0.8259 (tt) cc_final: 0.7747 (tp)
REVERT: A  181 MET cc_start: 0.7897 (mtt) cc_final: 0.7692 (mtm)
REVERT: A  265 ASN cc_start: 0.7972 (m-40) cc_final: 0.7749 (m110)
REVERT: B   82 MET cc_start: 0.7943 (mmm) cc_final: 0.7603 (mmm)
REVERT: B   92 LEU cc_start: 0.7317 (mt) cc_final: 0.7062 (mt)
REVERT: B  265 ASN cc_start: 0.8071 (m-40) cc_final: 0.7737 (m110)
  outliers start: 17
  outliers final: 10
  residues processed: 106
  average time/residue: 0.1533
  time to fit residues: 22.0646
Evaluate side-chains
  108 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain B residue  121 GLN
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 38 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 30 optimal weight:   20.0000
   chunk 31 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.4236 r_free = 0.4236 target = 0.170841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.146006 restraints weight = 6425.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3920 rms_B_bonded: 1.99
r_work: 0.3785 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3614 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   5064  Z= 0.183
  Angle     :  0.615   8.374   6912  Z= 0.293
  Chirality :  0.042   0.145    872
  Planarity :  0.005   0.043    754
  Dihedral  : 17.706 176.121   1433
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.37 %
    Favored  : 79.39 %
  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 (0.34), residues: 592
  helix:  2.53 (0.23), residues: 442
  sheet:  2.78 (0.89), residues: 32
  loop : -3.23 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 315 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.024   0.002   PHE B  70 
 TYR   0.013   0.002   TYR A 241 
 ARG   0.002   0.000   ARG B 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04445 (  376)
  hydrogen bonds       : angle       4.40109 ( 1122)
  SS BOND              : bond        0.00164 (    1)
  SS BOND              : angle       0.43508 (    2)
  covalent geometry    : bond        0.00411 ( 5063)
  covalent geometry    : angle       0.61541 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 101
  time to evaluate  : 0.606 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7498 (m-80) cc_final: 0.7229 (m-80)
REVERT: A  265 ASN cc_start: 0.7987 (m-40) cc_final: 0.7761 (m110)
REVERT: B   82 MET cc_start: 0.7915 (mmm) cc_final: 0.7527 (mmm)
REVERT: B   92 LEU cc_start: 0.7308 (mt) cc_final: 0.7061 (mt)
REVERT: B  147 LYS cc_start: 0.7826 (mmmm) cc_final: 0.7495 (mmmm)
REVERT: B  265 ASN cc_start: 0.8078 (m-40) cc_final: 0.7752 (m110)
  outliers start: 11
  outliers final: 8
  residues processed: 105
  average time/residue: 0.1572
  time to fit residues: 22.1335
Evaluate side-chains
  106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  199 MET
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  254 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    0.0670
   chunk 3 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.2980
   chunk 21 optimal weight:    0.5980
   chunk 45 optimal weight:    0.0670
   chunk 1 optimal weight:   30.0000
   chunk 7 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 43 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.2456

-------------------------------------------------------------------------------
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 = 0.4264 r_free = 0.4264 target = 0.173283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.148068 restraints weight = 6505.312|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.08
r_work: 0.3808 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7377
moved from start:          0.2260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5064  Z= 0.123
  Angle     :  0.577   9.289   6912  Z= 0.277
  Chirality :  0.040   0.150    872
  Planarity :  0.004   0.043    754
  Dihedral  : 17.279 179.451   1433
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 19.80 %
    Favored  : 78.16 %
  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:  2.57 (0.34), residues: 592
  helix:  2.75 (0.23), residues: 442
  sheet:  2.98 (0.90), residues: 32
  loop : -3.18 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 315 
 HIS   0.003   0.000   HIS B 214 
 PHE   0.017   0.001   PHE B 275 
 TYR   0.023   0.001   TYR A 241 
 ARG   0.002   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (  376)
  hydrogen bonds       : angle       4.22294 ( 1122)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.19854 (    2)
  covalent geometry    : bond        0.00257 ( 5063)
  covalent geometry    : angle       0.57671 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 1.361 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7486 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  107 ILE cc_start: 0.8442 (mt) cc_final: 0.8226 (mp)
REVERT: B   82 MET cc_start: 0.7909 (mmm) cc_final: 0.7554 (mmm)
REVERT: B   92 LEU cc_start: 0.7250 (mt) cc_final: 0.7017 (mt)
REVERT: B  147 LYS cc_start: 0.7873 (mmmm) cc_final: 0.7515 (mmmm)
REVERT: B  265 ASN cc_start: 0.8053 (m-40) cc_final: 0.7786 (m110)
  outliers start: 10
  outliers final: 4
  residues processed: 105
  average time/residue: 0.1601
  time to fit residues: 23.2537
Evaluate side-chains
  101 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.549 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue  148 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 43 optimal weight:    0.1980
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
B 311 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.171852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.146748 restraints weight = 6480.539|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.03
r_work: 0.3794 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3620 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5064  Z= 0.157
  Angle     :  0.639  12.713   6912  Z= 0.297
  Chirality :  0.042   0.153    872
  Planarity :  0.005   0.043    754
  Dihedral  : 17.193 178.363   1433
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.39 %
    Favored  : 78.78 %
  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:  2.52 (0.34), residues: 592
  helix:  2.78 (0.23), residues: 430
  sheet:  3.01 (0.88), residues: 32
  loop : -2.90 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 229 
 HIS   0.002   0.001   HIS A 282 
 PHE   0.019   0.002   PHE B  70 
 TYR   0.023   0.002   TYR A 241 
 ARG   0.007   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04306 (  376)
  hydrogen bonds       : angle       4.34341 ( 1122)
  SS BOND              : bond        0.00160 (    1)
  SS BOND              : angle       0.33018 (    2)
  covalent geometry    : bond        0.00350 ( 5063)
  covalent geometry    : angle       0.63898 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.499 
Fit side-chains
REVERT: A   65 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7406 (mt)
REVERT: A   99 TYR cc_start: 0.7541 (m-80) cc_final: 0.7241 (m-80)
REVERT: A  107 ILE cc_start: 0.8463 (mt) cc_final: 0.8263 (mp)
REVERT: B   82 MET cc_start: 0.7918 (mmm) cc_final: 0.7560 (mmm)
REVERT: B   92 LEU cc_start: 0.7280 (mt) cc_final: 0.7044 (mt)
REVERT: B  147 LYS cc_start: 0.7859 (mmmm) cc_final: 0.7505 (mmmm)
REVERT: B  265 ASN cc_start: 0.8064 (m-40) cc_final: 0.7776 (m110)
  outliers start: 9
  outliers final: 6
  residues processed: 104
  average time/residue: 0.1489
  time to fit residues: 20.5807
Evaluate side-chains
  106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0870
   chunk 21 optimal weight:    0.5980
   chunk 38 optimal weight:    0.2980
   chunk 12 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.4256 r_free = 0.4256 target = 0.172508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.147507 restraints weight = 6495.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3935 rms_B_bonded: 2.02
r_work: 0.3803 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3627 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.2401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5064  Z= 0.143
  Angle     :  0.626  12.724   6912  Z= 0.293
  Chirality :  0.041   0.142    872
  Planarity :  0.004   0.043    754
  Dihedral  : 16.978 173.503   1433
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 19.59 %
    Favored  : 78.57 %
  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 (0.34), residues: 592
  helix:  2.77 (0.23), residues: 430
  sheet:  3.02 (0.86), residues: 32
  loop : -2.85 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 229 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.017   0.001   PHE B  70 
 TYR   0.020   0.002   TYR A 241 
 ARG   0.004   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04253 (  376)
  hydrogen bonds       : angle       4.32547 ( 1122)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.26619 (    2)
  covalent geometry    : bond        0.00315 ( 5063)
  covalent geometry    : angle       0.62657 ( 6910)

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

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

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1184 Ramachandran restraints generated.
    592 Oldfield, 0 Emsley, 592 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.752 
Fit side-chains
REVERT: A   65 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7469 (mt)
REVERT: A   99 TYR cc_start: 0.7531 (m-80) cc_final: 0.7230 (m-80)
REVERT: B   82 MET cc_start: 0.7938 (mmm) cc_final: 0.7536 (mmm)
REVERT: B   92 LEU cc_start: 0.7267 (mt) cc_final: 0.7048 (mt)
REVERT: B  147 LYS cc_start: 0.7852 (mmmm) cc_final: 0.7500 (mmmm)
REVERT: B  166 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.7904 (mm)
REVERT: B  265 ASN cc_start: 0.8058 (m-40) cc_final: 0.7767 (m110)
  outliers start: 9
  outliers final: 6
  residues processed: 103
  average time/residue: 0.2181
  time to fit residues: 29.8017
Evaluate side-chains
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  166 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 24 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0970
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 23 optimal weight:    0.2980
   chunk 4 optimal weight:    0.5980
   chunk 31 optimal weight:    0.4980
   chunk 56 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.4178

-------------------------------------------------------------------------------
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 = 0.4254 r_free = 0.4254 target = 0.172465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.147629 restraints weight = 6484.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3936 rms_B_bonded: 2.01
r_work: 0.3807 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3634 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5064  Z= 0.144
  Angle     :  0.632  12.504   6912  Z= 0.298
  Chirality :  0.041   0.141    872
  Planarity :  0.005   0.043    754
  Dihedral  : 16.861 173.414   1433
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 20.41 %
    Favored  : 77.96 %
  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:  2.54 (0.34), residues: 592
  helix:  2.78 (0.23), residues: 430
  sheet:  3.06 (0.85), residues: 32
  loop : -2.82 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 229 
 HIS   0.002   0.000   HIS B 214 
 PHE   0.017   0.001   PHE B  70 
 TYR   0.021   0.002   TYR A 241 
 ARG   0.004   0.000   ARG B 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  376)
  hydrogen bonds       : angle       4.33560 ( 1122)
  SS BOND              : bond        0.00129 (    1)
  SS BOND              : angle       0.27972 (    2)
  covalent geometry    : bond        0.00317 ( 5063)
  covalent geometry    : angle       0.63242 ( 6910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3539.44 seconds
wall clock time: 64 minutes 21.02 seconds (3861.02 seconds total)