Starting phenix.real_space_refine
on Wed Sep 17 05:17:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjp_39345/09_2025/8yjp_39345.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjp_39345/09_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_39345/09_2025/8yjp_39345.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjp_39345/09_2025/8yjp_39345.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjp_39345/09_2025/8yjp_39345.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjp_39345/09_2025/8yjp_39345.cif"
  }
  resolution = 3.09
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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, 'HIS:plan': 3, 'ASP:plan': 1}
          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, 'HIS:plan': 3, 'ASP:plan': 1}
          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: 1.50, per 1000 atoms: 0.30
  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: 0.50
  Conformation dependent library (CDL) restraints added in 191.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.13
  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: 0.73

  Time building geometry restraints manager: 0.61 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:             1.060
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.470
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.880
-------------------------------------------------------------------------------
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 : 17.61
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (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
 ARG   0.003   0.000   ARG B 123 
 TYR   0.015   0.002   TYR A 241 
 PHE   0.008   0.002   PHE B 105 
 TRP   0.046   0.002   TRP A 229 
 HIS   0.001   0.000   HIS B  73 

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

*********************** 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  : 0.169 
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: 0.0661
  time to fit residues: 9.6531
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  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4267 r_free = 0.4267 target = 0.172850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.147031 restraints weight = 6575.528|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.02
r_work: 0.3802 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3628 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5064  Z= 0.185
  Angle     :  0.688   8.979   6912  Z= 0.321
  Chirality :  0.044   0.151    872
  Planarity :  0.005   0.042    754
  Dihedral  : 22.744 178.977   1433
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.61 %
    Allowed  : 10.20 %
    Favored  : 89.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.89 (0.34), residues: 592
  helix:  2.37 (0.23), residues: 438
  sheet:  1.44 (0.84), residues: 32
  loop : -3.26 (0.46), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.014   0.002   TYR A 241 
 PHE   0.012   0.002   PHE B 105 
 TRP   0.017   0.001   TRP A 229 
 HIS   0.001   0.000   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5063)
  covalent geometry    : angle       0.68773 ( 6910)
  SS BOND              : bond        0.00340 (    1)
  SS BOND              : angle       0.83051 (    2)
  hydrogen bonds       : bond        0.04562 (  376)
  hydrogen bonds       : angle       4.54693 ( 1122)

*********************** 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
  105 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 0.162 
Fit side-chains
REVERT: A  265 ASN cc_start: 0.8013 (m-40) cc_final: 0.7790 (m110)
REVERT: B   82 MET cc_start: 0.7809 (mmm) cc_final: 0.7497 (mmm)
REVERT: B  118 THR cc_start: 0.7982 (m) cc_final: 0.7775 (t)
REVERT: B  194 ILE cc_start: 0.7925 (pt) cc_final: 0.7705 (pt)
REVERT: B  265 ASN cc_start: 0.8102 (m-40) cc_final: 0.7783 (m110)
  outliers start: 3
  outliers final: 2
  residues processed: 103
  average time/residue: 0.0702
  time to fit residues: 9.4800
Evaluate side-chains
  98 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
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 22 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 35 optimal weight:    0.4980
   chunk 17 optimal weight:    5.9990
   chunk 29 optimal weight:    0.0870
   chunk 0 optimal weight:   10.9990
   chunk 50 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.4253 r_free = 0.4253 target = 0.172509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.146539 restraints weight = 6413.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3929 rms_B_bonded: 2.07
r_work: 0.3797 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3623 rms_B_bonded: 4.76 restraints_weight: 0.2500
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5064  Z= 0.164
  Angle     :  0.641  11.875   6912  Z= 0.300
  Chirality :  0.042   0.141    872
  Planarity :  0.005   0.043    754
  Dihedral  : 20.845 179.296   1433
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 13.27 %
    Favored  : 84.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.34), residues: 592
  helix:  2.50 (0.23), residues: 438
  sheet:  1.81 (0.84), residues: 32
  loop : -3.22 (0.46), residues: 122

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 279 
 TYR   0.024   0.002   TYR A 241 
 PHE   0.018   0.002   PHE B 275 
 TRP   0.006   0.001   TRP B 229 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5063)
  covalent geometry    : angle       0.64074 ( 6910)
  SS BOND              : bond        0.00124 (    1)
  SS BOND              : angle       0.63195 (    2)
  hydrogen bonds       : bond        0.04450 (  376)
  hydrogen bonds       : angle       4.43012 ( 1122)

*********************** 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
  113 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A   65 LEU cc_start: 0.7672 (mp) cc_final: 0.7458 (mt)
REVERT: A  172 LEU cc_start: 0.8158 (tt) cc_final: 0.7616 (tp)
REVERT: A  229 TRP cc_start: 0.6221 (m-10) cc_final: 0.6010 (m100)
REVERT: A  265 ASN cc_start: 0.8025 (m-40) cc_final: 0.7778 (m110)
REVERT: B   82 MET cc_start: 0.7924 (mmm) cc_final: 0.7608 (mmm)
REVERT: B  118 THR cc_start: 0.7971 (m) cc_final: 0.7737 (t)
REVERT: B  265 ASN cc_start: 0.8030 (m-40) cc_final: 0.7714 (m110)
  outliers start: 10
  outliers final: 7
  residues processed: 105
  average time/residue: 0.0664
  time to fit residues: 9.1688
Evaluate side-chains
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.173 
-------------------------------------------------------------------------------
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  199 MET
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  174 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 25 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 18 optimal weight:    0.3980
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.172240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.146282 restraints weight = 6419.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.06
r_work: 0.3784 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3605 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3605
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5064  Z= 0.160
  Angle     :  0.625  10.713   6912  Z= 0.294
  Chirality :  0.042   0.138    872
  Planarity :  0.005   0.043    754
  Dihedral  : 18.792 176.553   1433
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.71 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.34), residues: 592
  helix:  2.65 (0.23), residues: 430
  sheet:  1.95 (0.86), residues: 32
  loop : -2.95 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 279 
 TYR   0.018   0.002   TYR A 241 
 PHE   0.026   0.002   PHE B 275 
 TRP   0.005   0.001   TRP A 143 
 HIS   0.002   0.000   HIS B  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 5063)
  covalent geometry    : angle       0.62458 ( 6910)
  SS BOND              : bond        0.00132 (    1)
  SS BOND              : angle       0.50006 (    2)
  hydrogen bonds       : bond        0.04365 (  376)
  hydrogen bonds       : angle       4.34656 ( 1122)

*********************** 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
  113 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 0.187 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7509 (m-80) cc_final: 0.7242 (m-80)
REVERT: A  229 TRP cc_start: 0.6241 (m-10) cc_final: 0.6011 (m100)
REVERT: A  265 ASN cc_start: 0.8021 (m-40) cc_final: 0.7780 (m110)
REVERT: B   82 MET cc_start: 0.7993 (mmm) cc_final: 0.7646 (mmm)
REVERT: B  147 LYS cc_start: 0.7831 (mmmm) cc_final: 0.7505 (mmmm)
REVERT: B  172 LEU cc_start: 0.8338 (tt) cc_final: 0.7689 (tp)
REVERT: B  265 ASN cc_start: 0.8042 (m-40) cc_final: 0.7707 (m110)
  outliers start: 11
  outliers final: 7
  residues processed: 106
  average time/residue: 0.0684
  time to fit residues: 9.5832
Evaluate side-chains
  102 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  118 THR
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 B residue  148 VAL
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 20 optimal weight:    0.8980
   chunk 18 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 4 optimal weight:    0.5980
   chunk 24 optimal weight:    0.3980
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 33 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4230 r_free = 0.4230 target = 0.170526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.145510 restraints weight = 6543.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3915 rms_B_bonded: 1.99
r_work: 0.3781 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3606 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3606
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7427
moved from start:          0.1991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5064  Z= 0.191
  Angle     :  0.623   8.135   6912  Z= 0.297
  Chirality :  0.042   0.146    872
  Planarity :  0.005   0.043    754
  Dihedral  : 18.359 177.182   1433
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 16.94 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.16 (0.33), residues: 592
  helix:  2.56 (0.23), residues: 430
  sheet:  2.14 (0.85), residues: 32
  loop : -2.96 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 123 
 TYR   0.015   0.002   TYR A 241 
 PHE   0.019   0.002   PHE B 275 
 TRP   0.005   0.001   TRP B 183 
 HIS   0.003   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 5063)
  covalent geometry    : angle       0.62296 ( 6910)
  SS BOND              : bond        0.00172 (    1)
  SS BOND              : angle       0.48624 (    2)
  hydrogen bonds       : bond        0.04524 (  376)
  hydrogen bonds       : angle       4.42699 ( 1122)

*********************** 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
  106 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.180 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7549 (m-80) cc_final: 0.7193 (m-80)
REVERT: A  229 TRP cc_start: 0.6300 (m-10) cc_final: 0.6043 (m100)
REVERT: A  265 ASN cc_start: 0.8002 (m-40) cc_final: 0.7777 (m110)
REVERT: B   82 MET cc_start: 0.7910 (mmm) cc_final: 0.7580 (mmm)
REVERT: B  265 ASN cc_start: 0.8061 (m-40) cc_final: 0.7743 (m110)
  outliers start: 13
  outliers final: 8
  residues processed: 98
  average time/residue: 0.0726
  time to fit residues: 9.3129
Evaluate side-chains
  98 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 90
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 36 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 34 optimal weight:    0.0470
   chunk 32 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 12 optimal weight:    0.9990
   chunk 29 optimal weight:    9.9990
   overall best weight:    0.4878

-------------------------------------------------------------------------------
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 = 0.4238 r_free = 0.4238 target = 0.171543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.146360 restraints weight = 6582.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.03
r_work: 0.3787 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3612 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2073

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= 0.147
  Angle     :  0.572   7.532   6912  Z= 0.278
  Chirality :  0.040   0.137    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.931 177.767   1433
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 18.16 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.36 (0.34), residues: 592
  helix:  2.60 (0.23), residues: 442
  sheet:  2.65 (0.89), residues: 32
  loop : -3.21 (0.47), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 144 
 TYR   0.026   0.002   TYR A 241 
 PHE   0.017   0.001   PHE B  70 
 TRP   0.006   0.001   TRP B 315 
 HIS   0.002   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5063)
  covalent geometry    : angle       0.57173 ( 6910)
  SS BOND              : bond        0.00116 (    1)
  SS BOND              : angle       0.34310 (    2)
  hydrogen bonds       : bond        0.04257 (  376)
  hydrogen bonds       : angle       4.29578 ( 1122)

*********************** 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
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 98
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7530 (m-80) cc_final: 0.7040 (m-80)
REVERT: A  173 LEU cc_start: 0.8115 (mt) cc_final: 0.7907 (mt)
REVERT: A  229 TRP cc_start: 0.6328 (m-10) cc_final: 0.6065 (m100)
REVERT: A  265 ASN cc_start: 0.7938 (m-40) cc_final: 0.7707 (m110)
REVERT: B  265 ASN cc_start: 0.8043 (m-40) cc_final: 0.7756 (m110)
  outliers start: 9
  outliers final: 7
  residues processed: 101
  average time/residue: 0.0738
  time to fit residues: 9.7105
Evaluate side-chains
  104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 49 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 19 optimal weight:    2.9990
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.170730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.145642 restraints weight = 6466.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3918 rms_B_bonded: 1.99
r_work: 0.3785 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   5064  Z= 0.172
  Angle     :  0.607   9.777   6912  Z= 0.290
  Chirality :  0.042   0.156    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.772 175.304   1433
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 18.98 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.28 (0.34), residues: 592
  helix:  2.53 (0.22), residues: 442
  sheet:  2.78 (0.89), residues: 32
  loop : -3.21 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 123 
 TYR   0.020   0.002   TYR A 241 
 PHE   0.019   0.001   PHE B 275 
 TRP   0.011   0.001   TRP B 229 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 5063)
  covalent geometry    : angle       0.60700 ( 6910)
  SS BOND              : bond        0.00165 (    1)
  SS BOND              : angle       0.41173 (    2)
  hydrogen bonds       : bond        0.04387 (  376)
  hydrogen bonds       : angle       4.38692 ( 1122)

*********************** 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
  103 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7510 (m-80) cc_final: 0.7083 (m-80)
REVERT: A  229 TRP cc_start: 0.6371 (m-10) cc_final: 0.6070 (m100)
REVERT: A  265 ASN cc_start: 0.7929 (m-40) cc_final: 0.7710 (m110)
REVERT: B   82 MET cc_start: 0.7918 (mmm) cc_final: 0.7533 (mmm)
REVERT: B  147 LYS cc_start: 0.7827 (mmmm) cc_final: 0.7495 (mmmm)
REVERT: B  265 ASN cc_start: 0.8052 (m-40) cc_final: 0.7746 (m110)
  outliers start: 11
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0623
  time to fit residues: 7.9452
Evaluate side-chains
  100 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 91
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    0.0870
   chunk 47 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.4980
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.4233 r_free = 0.4233 target = 0.170729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.145051 restraints weight = 6521.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3909 rms_B_bonded: 2.09
r_work: 0.3770 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3589 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2214

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= 0.167
  Angle     :  0.596   9.329   6912  Z= 0.286
  Chirality :  0.041   0.162    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.560 176.495   1433
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 18.78 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.34), residues: 592
  helix:  2.55 (0.23), residues: 442
  sheet:  2.82 (0.89), residues: 32
  loop : -3.20 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 144 
 TYR   0.019   0.002   TYR A 241 
 PHE   0.016   0.001   PHE B 275 
 TRP   0.008   0.001   TRP B 229 
 HIS   0.002   0.000   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 5063)
  covalent geometry    : angle       0.59570 ( 6910)
  SS BOND              : bond        0.00152 (    1)
  SS BOND              : angle       0.35490 (    2)
  hydrogen bonds       : bond        0.04377 (  376)
  hydrogen bonds       : angle       4.38780 ( 1122)

*********************** 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
  107 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7512 (m-80) cc_final: 0.7092 (m-80)
REVERT: A  265 ASN cc_start: 0.7953 (m-40) cc_final: 0.7731 (m110)
REVERT: B   82 MET cc_start: 0.7968 (mmm) cc_final: 0.7614 (mmm)
REVERT: B  147 LYS cc_start: 0.7863 (mmmm) cc_final: 0.7506 (mmmm)
REVERT: B  265 ASN cc_start: 0.8056 (m-40) cc_final: 0.7730 (m110)
REVERT: B  314 GLN cc_start: 0.6715 (OUTLIER) cc_final: 0.6470 (mp10)
  outliers start: 15
  outliers final: 9
  residues processed: 100
  average time/residue: 0.0656
  time to fit residues: 8.6835
Evaluate side-chains
  102 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
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  177 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
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  314 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4223 r_free = 0.4223 target = 0.169618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.144127 restraints weight = 6504.928|
|-----------------------------------------------------------------------------|
r_work (start): 0.3896 rms_B_bonded: 2.07
r_work: 0.3759 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3581 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7449
moved from start:          0.2349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5064  Z= 0.215
  Angle     :  0.638   9.181   6912  Z= 0.307
  Chirality :  0.044   0.170    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.532 174.968   1433
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.20 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.34), residues: 592
  helix:  2.37 (0.23), residues: 442
  sheet:  2.81 (0.86), residues: 32
  loop : -3.26 (0.48), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 123 
 TYR   0.019   0.002   TYR A 241 
 PHE   0.014   0.002   PHE B  70 
 TRP   0.013   0.002   TRP A 229 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 5063)
  covalent geometry    : angle       0.63823 ( 6910)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       0.46691 (    2)
  hydrogen bonds       : bond        0.04671 (  376)
  hydrogen bonds       : angle       4.55753 ( 1122)

*********************** 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
  104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.182 
Fit side-chains
REVERT: A   99 TYR cc_start: 0.7540 (m-80) cc_final: 0.7193 (m-80)
REVERT: A  265 ASN cc_start: 0.8014 (m-40) cc_final: 0.7776 (m110)
REVERT: B   82 MET cc_start: 0.7999 (mmm) cc_final: 0.7583 (mmm)
REVERT: B  147 LYS cc_start: 0.7854 (mmmm) cc_final: 0.7477 (mmmm)
REVERT: B  265 ASN cc_start: 0.8042 (m-40) cc_final: 0.7702 (m110)
REVERT: B  314 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6488 (mp10)
  outliers start: 13
  outliers final: 9
  residues processed: 96
  average time/residue: 0.0709
  time to fit residues: 9.0754
Evaluate side-chains
  99 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
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  177 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 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
Chi-restraints excluded: chain B residue  314 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 21 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 23 optimal weight:    0.6980
   chunk 30 optimal weight:   10.0000
   chunk 50 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.170476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.144799 restraints weight = 6467.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3907 rms_B_bonded: 2.08
r_work: 0.3770 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3594 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5064  Z= 0.176
  Angle     :  0.625   9.849   6912  Z= 0.297
  Chirality :  0.042   0.169    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.380 175.976   1433
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 11.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 20.41 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.34), residues: 592
  helix:  2.45 (0.23), residues: 442
  sheet:  2.92 (0.86), residues: 32
  loop : -3.25 (0.47), residues: 118

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 144 
 TYR   0.018   0.002   TYR A 241 
 PHE   0.013   0.001   PHE B 275 
 TRP   0.008   0.001   TRP A 229 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 5063)
  covalent geometry    : angle       0.62492 ( 6910)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.34716 (    2)
  hydrogen bonds       : bond        0.04473 (  376)
  hydrogen bonds       : angle       4.47797 ( 1122)

********************** 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
  104 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 TYR cc_start: 0.7507 (m-80) cc_final: 0.7085 (m-80)
REVERT: A  265 ASN cc_start: 0.8019 (m-40) cc_final: 0.7770 (m110)
REVERT: B   82 MET cc_start: 0.7972 (mmm) cc_final: 0.7564 (mmm)
REVERT: B  147 LYS cc_start: 0.7855 (mmmm) cc_final: 0.7477 (mmmm)
REVERT: B  265 ASN cc_start: 0.8018 (m-40) cc_final: 0.7690 (m110)
REVERT: B  314 GLN cc_start: 0.6748 (OUTLIER) cc_final: 0.6503 (mp10)
  outliers start: 11
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0659
  time to fit residues: 8.5812
Evaluate side-chains
  102 residues out of total 532 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 92
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 GLU
Chi-restraints excluded: chain A residue  121 GLN
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  177 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  227 LEU
Chi-restraints excluded: chain A residue  249 VAL
Chi-restraints excluded: chain B residue  148 VAL
Chi-restraints excluded: chain B residue  160 ILE
Chi-restraints excluded: chain B residue  314 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 38 optimal weight:    0.4980
   chunk 40 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 12 optimal weight:    0.3980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.4239 r_free = 0.4239 target = 0.171121 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.145943 restraints weight = 6531.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.02
r_work: 0.3790 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3617 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.2389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5064  Z= 0.158
  Angle     :  0.608   9.710   6912  Z= 0.290
  Chirality :  0.042   0.154    872
  Planarity :  0.005   0.044    754
  Dihedral  : 17.210 177.673   1433
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.00 %
    Favored  : 77.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.37 (0.34), residues: 592
  helix:  2.65 (0.23), residues: 430
  sheet:  3.03 (0.85), residues: 32
  loop : -2.92 (0.47), residues: 130

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 144 
 TYR   0.017   0.002   TYR A 241 
 PHE   0.012   0.001   PHE B 275 
 TRP   0.007   0.001   TRP A 229 
 HIS   0.002   0.000   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 5063)
  covalent geometry    : angle       0.60811 ( 6910)
  SS BOND              : bond        0.00137 (    1)
  SS BOND              : angle       0.25858 (    2)
  hydrogen bonds       : bond        0.04336 (  376)
  hydrogen bonds       : angle       4.40607 ( 1122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1496.90 seconds
wall clock time: 26 minutes 24.47 seconds (1584.47 seconds total)