Starting phenix.real_space_refine
on Tue Feb  3 23:33:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ne2_49293/02_2026/9ne2_49293.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.018
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: 4
    Type Number    sf(0)   Gaussians
     S      50      5.16       5
     C    4934      2.51       5
     N    1272      2.21       5
     O    1396      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7652
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3826
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 3826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3826
          Classifications: {'peptide': 468}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 442}
          Chain breaks: 2
  Time building chain proxies: 1.97, per 1000 atoms: 0.26
  Number of scatterers: 7652
  At special positions: 0
  Unit cell: (112.66, 90.855, 86.0094, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      50     16.00
     O    1396      8.00
     N    1272      7.00
     C    4934      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.87
  Conformation dependent library (CDL) restraints added in 305.9 milliseconds
  

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 2 sheets defined
      55.9% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 88
    Processing helix  chain 'A' and resid 112 through 129
    Processing helix  chain 'A' and resid 138 through 142
      removed outlier: 4.241A  pdb=" N   LEU A 141 " --> pdb=" O   SER A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 164
      removed outlier: 3.574A  pdb=" N   VAL A 151 " --> pdb=" O   ASN A 147 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   PHE A 164 " --> pdb=" O   GLN A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
    Processing helix  chain 'A' and resid 190 through 206
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 231 through 241
    Processing helix  chain 'A' and resid 260 through 272
      removed outlier: 3.691A  pdb=" N   ILE A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ILE A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 307
      Proline residue:  A 305  - end of helix
    Processing helix  chain 'A' and resid 317 through 320
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 4.342A  pdb=" N   ASN A 335 " --> pdb=" O   TRP A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 388
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 554 through 565
    Processing helix  chain 'A' and resid 572 through 588
    Processing helix  chain 'A' and resid 588 through 593
      removed outlier: 4.477A  pdb=" N   VAL A 592 " --> pdb=" O   ASN A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 630
      removed outlier: 3.745A  pdb=" N   ASN A 630 " --> pdb=" O   THR A 626 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 634 through 639
    Processing helix  chain 'A' and resid 640 through 663
      removed outlier: 3.620A  pdb=" N   VAL A 644 " --> pdb=" O   MET A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
      removed outlier: 4.359A  pdb=" N   PHE A 681 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG A 682 " --> pdb=" O   PRO A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 677 through 682'
    Processing helix  chain 'A' and resid 683 through 691
    Processing helix  chain 'B' and resid 74 through 88
    Processing helix  chain 'B' and resid 112 through 129
    Processing helix  chain 'B' and resid 138 through 142
      removed outlier: 3.835A  pdb=" N   LEU B 141 " --> pdb=" O   SER B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 164
      removed outlier: 3.672A  pdb=" N   VAL B 151 " --> pdb=" O   ASN B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 190 through 206
    Processing helix  chain 'B' and resid 220 through 224
    Processing helix  chain 'B' and resid 231 through 241
    Processing helix  chain 'B' and resid 260 through 272
      removed outlier: 3.985A  pdb=" N   ILE B 264 " --> pdb=" O   PRO B 260 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   ILE B 270 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 307
      removed outlier: 4.396A  pdb=" N   ARG B 306 " --> pdb=" O   GLU B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 320
    Processing helix  chain 'B' and resid 321 through 334
    Processing helix  chain 'B' and resid 375 through 389
      removed outlier: 4.049A  pdb=" N   GLN B 389 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 392
      No H-bonds generated for 'chain 'B' and resid 390 through 392'
    Processing helix  chain 'B' and resid 554 through 565
    Processing helix  chain 'B' and resid 572 through 588
    Processing helix  chain 'B' and resid 589 through 592
    Processing helix  chain 'B' and resid 600 through 629
    Processing helix  chain 'B' and resid 634 through 639
    Processing helix  chain 'B' and resid 640 through 663
      removed outlier: 3.713A  pdb=" N   VAL B 644 " --> pdb=" O   MET B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 683 through 692
      removed outlier: 3.661A  pdb=" N   LEU B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 66
      removed outlier: 6.621A  pdb=" N   PHE A 133 " --> pdb=" O   SER A 168 " (cutoff:3.500A)
      removed outlier: 7.918A  pdb=" N   ALA A 170 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   TYR A 135 " --> pdb=" O   ALA A 170 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LEU A 172 " --> pdb=" O   TYR A 135 " (cutoff:3.500A)
      removed outlier: 6.413A  pdb=" N   ILE A 137 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 213 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   PHE A 212 " --> pdb=" O   GLU A 246 " (cutoff:3.500A)
      removed outlier: 7.383A  pdb=" N   LEU A 248 " --> pdb=" O   PHE A 212 " (cutoff:3.500A)
      removed outlier: 7.124A  pdb=" N   PHE A 214 " --> pdb=" O   LEU A 248 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   VAL A 247 " --> pdb=" O   VAL A 276 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   TRP A 278 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   TRP A 249 " --> pdb=" O   TRP A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 66
      removed outlier: 5.893A  pdb=" N   CYS B  62 " --> pdb=" O   THR B  92 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   LEU B  94 " --> pdb=" O   CYS B  62 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   VAL B  64 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   PHE B 133 " --> pdb=" O   SER B 168 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   TYR B 135 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.816A  pdb=" N   LEU B 172 " --> pdb=" O   TYR B 135 " (cutoff:3.500A)
      removed outlier: 6.412A  pdb=" N   ILE B 137 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   PHE B 212 " --> pdb=" O   GLU B 246 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   LEU B 248 " --> pdb=" O   PHE B 212 " (cutoff:3.500A)
      removed outlier: 7.213A  pdb=" N   PHE B 214 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 6.173A  pdb=" N   VAL B 247 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 6.906A  pdb=" N   TRP B 278 " --> pdb=" O   VAL B 247 " (cutoff:3.500A)
      removed outlier: 5.969A  pdb=" N   TRP B 249 " --> pdb=" O   TRP B 278 " (cutoff:3.500A)

    367 hydrogen bonds defined for protein.
    1053 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: 1.26

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2433
        1.34 -     1.46: 1715
        1.46 -     1.57: 3634
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 7860
  Sorted by residual:
  bond pdb=" N   GLU A  66 "
       pdb=" CA  GLU A  66 "
    ideal  model  delta    sigma   weight residual
    1.463  1.487 -0.024 1.31e-02 5.83e+03 3.37e+00
  bond pdb=" C   PHE A 681 "
       pdb=" N   ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.327  1.338 -0.011 1.06e-02 8.90e+03 1.10e+00
  bond pdb=" CA  ARG A 682 "
       pdb=" CB  ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.513  1.538 -0.024 2.59e-02 1.49e+03 8.91e-01
  bond pdb=" CA  ILE B 270 "
       pdb=" CB  ILE B 270 "
    ideal  model  delta    sigma   weight residual
    1.545  1.535  0.010 1.05e-02 9.07e+03 8.77e-01
  bond pdb=" C   ILE B 304 "
       pdb=" N   PRO B 305 "
    ideal  model  delta    sigma   weight residual
    1.335  1.346 -0.012 1.28e-02 6.10e+03 8.30e-01
  ... (remaining 7855 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.95: 10062
        0.95 -     1.89: 460
        1.89 -     2.84: 74
        2.84 -     3.79: 36
        3.79 -     4.74: 8
  Bond angle restraints: 10640
  Sorted by residual:
  angle pdb=" CA  GLU A  66 "
        pdb=" C   GLU A  66 "
        pdb=" O   GLU A  66 "
      ideal   model   delta    sigma   weight residual
     122.37  117.63    4.74 1.15e+00 7.56e-01 1.70e+01
  angle pdb=" N   ILE B 270 "
        pdb=" CA  ILE B 270 "
        pdb=" C   ILE B 270 "
      ideal   model   delta    sigma   weight residual
     111.67  109.14    2.53 9.50e-01 1.11e+00 7.07e+00
  angle pdb=" C   ASN B  91 "
        pdb=" N   THR B  92 "
        pdb=" CA  THR B  92 "
      ideal   model   delta    sigma   weight residual
     122.74  118.82    3.92 1.54e+00 4.22e-01 6.48e+00
  angle pdb=" C   THR B 554 "
        pdb=" N   LEU B 555 "
        pdb=" CA  LEU B 555 "
      ideal   model   delta    sigma   weight residual
     120.38  123.82   -3.44 1.37e+00 5.33e-01 6.29e+00
  angle pdb=" C   CYS A  62 "
        pdb=" N   GLY A  63 "
        pdb=" CA  GLY A  63 "
      ideal   model   delta    sigma   weight residual
     120.51  117.54    2.97 1.22e+00 6.72e-01 5.91e+00
  ... (remaining 10635 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.79: 4541
       17.79 -    35.57: 110
       35.57 -    53.36: 24
       53.36 -    71.15: 7
       71.15 -    88.94: 2
  Dihedral angle restraints: 4684
    sinusoidal: 1938
      harmonic: 2746
  Sorted by residual:
  dihedral pdb=" CA  GLY B  63 "
           pdb=" C   GLY B  63 "
           pdb=" N   VAL B  64 "
           pdb=" CA  VAL B  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.93  -16.07     0      5.00e+00 4.00e-02 1.03e+01
  dihedral pdb=" CA  PHE B 565 "
           pdb=" C   PHE B 565 "
           pdb=" N   TYR B 566 "
           pdb=" CA  TYR B 566 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.16  -15.84     0      5.00e+00 4.00e-02 1.00e+01
  dihedral pdb=" CA  TYR B 286 "
           pdb=" C   TYR B 286 "
           pdb=" N   ASP B 287 "
           pdb=" CA  ASP B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.27   15.73     0      5.00e+00 4.00e-02 9.90e+00
  ... (remaining 4681 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 648
       0.026 -    0.051: 276
       0.051 -    0.077: 112
       0.077 -    0.102: 43
       0.102 -    0.128: 35
  Chirality restraints: 1114
  Sorted by residual:
  chirality pdb=" CA  ARG A 682 "
            pdb=" N   ARG A 682 "
            pdb=" C   ARG A 682 "
            pdb=" CB  ARG A 682 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  VAL B 393 "
            pdb=" N   VAL B 393 "
            pdb=" C   VAL B 393 "
            pdb=" CB  VAL B 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.07e-01
  chirality pdb=" CA  VAL A 393 "
            pdb=" N   VAL A 393 "
            pdb=" C   VAL A 393 "
            pdb=" CB  VAL A 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 3.95e-01
  ... (remaining 1111 not shown)

  Planarity restraints: 1362
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 327 "   -0.009 2.00e-02 2.50e+03   1.89e-02 3.57e+00
        pdb=" C   THR B 327 "    0.033 2.00e-02 2.50e+03
        pdb=" O   THR B 327 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU B 328 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 323 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.24e+00
        pdb=" C   VAL B 323 "    0.031 2.00e-02 2.50e+03
        pdb=" O   VAL B 323 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ALA B 324 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 324 "   -0.009 2.00e-02 2.50e+03   1.77e-02 3.12e+00
        pdb=" C   ALA B 324 "    0.031 2.00e-02 2.50e+03
        pdb=" O   ALA B 324 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ILE B 325 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1359 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 1757
        2.78 -     3.31: 7218
        3.31 -     3.84: 12795
        3.84 -     4.37: 14906
        4.37 -     4.90: 25064
  Nonbonded interactions: 61740
  Sorted by model distance:
  nonbonded pdb=" N   ASN B 315 "
            pdb=" OD1 ASN B 321 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   THR A 626 "
            pdb=" OG  SER A 629 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" OH  TYR B 111 "
            pdb=" OH  TYR B 135 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   ASP A  99 "
            pdb=" NH1 ARG B 634 "
     model   vdw
     2.343 3.120
  nonbonded pdb=" O   ALA B 324 "
            pdb=" OG1 THR B 327 "
     model   vdw
     2.347 3.040
  ... (remaining 61735 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.970
  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:             0.020
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     9.240
  Find NCS groups from input model:        0.100
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
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      :  0.003   0.033   7860  Z= 0.142
  Angle     :  0.503   4.737  10640  Z= 0.290
  Chirality :  0.040   0.128   1114
  Planarity :  0.004   0.027   1362
  Dihedral  :  9.483  88.937   2916
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.84 %
    Favored  : 99.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.27), residues: 924
  helix:  2.61 (0.24), residues: 448
  sheet:  0.27 (0.58), residues: 86
  loop :  0.25 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 682 
 TYR   0.009   0.001   TYR B 296 
 PHE   0.017   0.001   PHE A 191 
 TRP   0.013   0.001   TRP A 278 
 HIS   0.002   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 7860)
  covalent geometry    : angle       0.50308 (10640)
  hydrogen bonds       : bond        0.13932 (  367)
  hydrogen bonds       : angle       5.23322 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  617 MET cc_start: 0.8450 (mmm) cc_final: 0.8205 (mmm)
REVERT: B  175 ASP cc_start: 0.8356 (m-30) cc_final: 0.8118 (p0)
REVERT: B  286 TYR cc_start: 0.7393 (p90) cc_final: 0.7185 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1078
  time to fit residues: 22.5628
Evaluate side-chains
  76 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 666 HIS
A 690 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.086504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.071472 restraints weight = 24870.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.074047 restraints weight = 13112.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.075799 restraints weight = 8494.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.076963 restraints weight = 6244.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.077763 restraints weight = 5020.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7997
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7860  Z= 0.140
  Angle     :  0.569   8.674  10640  Z= 0.299
  Chirality :  0.041   0.132   1114
  Planarity :  0.004   0.025   1362
  Dihedral  :  4.235  20.839   1030
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  6.39 %
    Favored  : 92.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.28), residues: 924
  helix:  2.81 (0.24), residues: 450
  sheet:  0.18 (0.58), residues: 86
  loop :  0.26 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 235 
 TYR   0.024   0.001   TYR B 638 
 PHE   0.017   0.002   PHE A 191 
 TRP   0.013   0.001   TRP B 278 
 HIS   0.012   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7860)
  covalent geometry    : angle       0.56898 (10640)
  hydrogen bonds       : bond        0.04488 (  367)
  hydrogen bonds       : angle       4.45115 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  168 SER cc_start: 0.7847 (m) cc_final: 0.7151 (p)
REVERT: A  224 CYS cc_start: 0.8423 (m) cc_final: 0.8005 (m)
REVERT: A  618 CYS cc_start: 0.8646 (m) cc_final: 0.7871 (m)
REVERT: A  624 MET cc_start: 0.8873 (tmm) cc_final: 0.8390 (tmm)
REVERT: A  646 ASP cc_start: 0.8812 (m-30) cc_final: 0.8530 (m-30)
REVERT: A  651 MET cc_start: 0.9242 (mmm) cc_final: 0.8445 (mmm)
REVERT: B   75 MET cc_start: 0.7020 (tpp) cc_final: 0.6700 (tpp)
REVERT: B  180 MET cc_start: 0.7203 (mtp) cc_final: 0.6998 (ttp)
REVERT: B  281 ILE cc_start: 0.9151 (tt) cc_final: 0.8947 (tp)
REVERT: B  690 GLN cc_start: 0.9336 (tp40) cc_final: 0.9111 (tp-100)
  outliers start: 11
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0680
  time to fit residues: 9.2874
Evaluate side-chains
  69 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  639 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 90 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0060
   chunk 1 optimal weight:    0.3980
   chunk 47 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 195 GLN
A 666 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.085769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.070669 restraints weight = 25021.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.073216 restraints weight = 13468.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.074895 restraints weight = 8840.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.076006 restraints weight = 6591.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.076757 restraints weight = 5352.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.2688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7860  Z= 0.105
  Angle     :  0.500   7.806  10640  Z= 0.259
  Chirality :  0.039   0.125   1114
  Planarity :  0.003   0.023   1362
  Dihedral  :  4.029  19.400   1030
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  7.47 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.28 (0.28), residues: 924
  helix:  2.90 (0.23), residues: 450
  sheet:  0.15 (0.57), residues: 86
  loop :  0.19 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 691 
 TYR   0.018   0.001   TYR B 638 
 PHE   0.018   0.001   PHE A 191 
 TRP   0.036   0.002   TRP A 679 
 HIS   0.013   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7860)
  covalent geometry    : angle       0.49990 (10640)
  hydrogen bonds       : bond        0.03812 (  367)
  hydrogen bonds       : angle       4.18727 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8996 (mmm) cc_final: 0.8618 (mmm)
REVERT: A  168 SER cc_start: 0.7825 (m) cc_final: 0.7219 (p)
REVERT: A  224 CYS cc_start: 0.8279 (m) cc_final: 0.7789 (m)
REVERT: A  617 MET cc_start: 0.9039 (mmm) cc_final: 0.8190 (mmm)
REVERT: A  618 CYS cc_start: 0.8563 (m) cc_final: 0.7925 (m)
REVERT: A  624 MET cc_start: 0.8910 (tmm) cc_final: 0.8363 (tmm)
REVERT: A  646 ASP cc_start: 0.8671 (m-30) cc_final: 0.8410 (m-30)
REVERT: A  651 MET cc_start: 0.9164 (mmm) cc_final: 0.8346 (mmm)
REVERT: B   75 MET cc_start: 0.7162 (tpp) cc_final: 0.6830 (tpp)
REVERT: B  281 ILE cc_start: 0.9133 (tt) cc_final: 0.8929 (tp)
REVERT: B  332 TYR cc_start: 0.8609 (t80) cc_final: 0.8353 (t80)
REVERT: B  622 MET cc_start: 0.8503 (mpp) cc_final: 0.7788 (mpp)
REVERT: B  639 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8208 (m-30)
  outliers start: 11
  outliers final: 7
  residues processed: 82
  average time/residue: 0.0672
  time to fit residues: 8.4550
Evaluate side-chains
  70 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  110 MET
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  639 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0270
   chunk 56 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.1844

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

Flipped N/Q/H residues before XYZ refinement:
A 204 GLN
A 666 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.081352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.065360 restraints weight = 25111.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.067911 restraints weight = 12971.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.069696 restraints weight = 8331.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.070888 restraints weight = 6097.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.071709 restraints weight = 4893.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7797
moved from start:          0.3071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7860  Z= 0.150
  Angle     :  0.526   7.616  10640  Z= 0.272
  Chirality :  0.040   0.128   1114
  Planarity :  0.003   0.029   1362
  Dihedral  :  4.068  15.457   1030
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  :  7.83 %
    Favored  : 90.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.27 (0.28), residues: 924
  helix:  2.98 (0.23), residues: 450
  sheet: -0.03 (0.58), residues: 86
  loop :  0.12 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B  71 
 TYR   0.013   0.001   TYR B 296 
 PHE   0.012   0.001   PHE B 191 
 TRP   0.021   0.002   TRP A 679 
 HIS   0.008   0.001   HIS A 666 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 7860)
  covalent geometry    : angle       0.52574 (10640)
  hydrogen bonds       : bond        0.03838 (  367)
  hydrogen bonds       : angle       4.12672 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9042 (mmm) cc_final: 0.8596 (mmm)
REVERT: A  168 SER cc_start: 0.7542 (m) cc_final: 0.6735 (p)
REVERT: A  224 CYS cc_start: 0.8344 (m) cc_final: 0.8043 (p)
REVERT: A  617 MET cc_start: 0.9074 (mmm) cc_final: 0.8257 (mmm)
REVERT: A  622 MET cc_start: 0.8903 (tpp) cc_final: 0.8353 (mtt)
REVERT: A  624 MET cc_start: 0.8629 (tmm) cc_final: 0.8207 (tmm)
REVERT: A  646 ASP cc_start: 0.8905 (m-30) cc_final: 0.8691 (m-30)
REVERT: A  651 MET cc_start: 0.9225 (mmm) cc_final: 0.8713 (mmm)
REVERT: B   75 MET cc_start: 0.7074 (tpp) cc_final: 0.6713 (tpp)
REVERT: B  180 MET cc_start: 0.7638 (mtp) cc_final: 0.7266 (ttp)
REVERT: B  639 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8226 (m-30)
REVERT: B  646 ASP cc_start: 0.8980 (p0) cc_final: 0.8606 (p0)
  outliers start: 13
  outliers final: 11
  residues processed: 80
  average time/residue: 0.0678
  time to fit residues: 8.3383
Evaluate side-chains
  73 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  640 MET
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  639 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    4.9990
   chunk 1 optimal weight:    0.4980
   chunk 80 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 17 optimal weight:    0.1980
   overall best weight:    0.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.083558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.068294 restraints weight = 25025.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.070728 restraints weight = 13642.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.072373 restraints weight = 9022.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.073507 restraints weight = 6747.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.074268 restraints weight = 5479.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7860  Z= 0.104
  Angle     :  0.480   8.334  10640  Z= 0.248
  Chirality :  0.039   0.125   1114
  Planarity :  0.003   0.022   1362
  Dihedral  :  3.927  14.250   1030
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.55 %
    Favored  : 89.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.28), residues: 924
  helix:  3.18 (0.24), residues: 438
  sheet: -0.07 (0.58), residues: 86
  loop :  0.22 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  71 
 TYR   0.009   0.001   TYR B 296 
 PHE   0.014   0.001   PHE B 191 
 TRP   0.013   0.001   TRP A 679 
 HIS   0.002   0.000   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 7860)
  covalent geometry    : angle       0.47982 (10640)
  hydrogen bonds       : bond        0.03465 (  367)
  hydrogen bonds       : angle       4.03945 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8902 (mmm) cc_final: 0.8427 (mmm)
REVERT: A  168 SER cc_start: 0.7915 (m) cc_final: 0.7308 (p)
REVERT: A  224 CYS cc_start: 0.8352 (m) cc_final: 0.7981 (p)
REVERT: A  589 SER cc_start: 0.8727 (p) cc_final: 0.8396 (m)
REVERT: A  617 MET cc_start: 0.8934 (mmm) cc_final: 0.8264 (mmm)
REVERT: A  622 MET cc_start: 0.8624 (tpp) cc_final: 0.8391 (mtt)
REVERT: A  624 MET cc_start: 0.8909 (tmm) cc_final: 0.8330 (tmm)
REVERT: A  646 ASP cc_start: 0.8713 (m-30) cc_final: 0.8442 (m-30)
REVERT: B   75 MET cc_start: 0.6834 (tpp) cc_final: 0.6578 (tpp)
REVERT: B  622 MET cc_start: 0.8431 (mpp) cc_final: 0.7797 (mpp)
REVERT: B  639 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8204 (m-30)
REVERT: B  646 ASP cc_start: 0.8838 (p0) cc_final: 0.8429 (p0)
  outliers start: 14
  outliers final: 11
  residues processed: 79
  average time/residue: 0.0645
  time to fit residues: 7.9757
Evaluate side-chains
  74 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  640 MET
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  384 LEU
Chi-restraints excluded: chain B residue  639 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 89 optimal weight:    0.0170
   chunk 53 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 68 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 50 optimal weight:    6.9990
   overall best weight:    0.9420

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

Flipped N/Q/H residues before XYZ refinement:
A 588 ASN
B 676 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.081003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.065568 restraints weight = 24992.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.068044 restraints weight = 12966.860|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.069758 restraints weight = 8309.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070953 restraints weight = 6080.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.071772 restraints weight = 4856.948|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.3577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7860  Z= 0.126
  Angle     :  0.489   8.257  10640  Z= 0.253
  Chirality :  0.039   0.125   1114
  Planarity :  0.003   0.024   1362
  Dihedral  :  3.895  13.440   1030
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.76 %
    Favored  : 89.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.28), residues: 924
  helix:  3.05 (0.24), residues: 442
  sheet: -0.24 (0.58), residues: 86
  loop :  0.12 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 664 
 TYR   0.010   0.001   TYR B 296 
 PHE   0.016   0.001   PHE B 538 
 TRP   0.012   0.001   TRP B 278 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7860)
  covalent geometry    : angle       0.48901 (10640)
  hydrogen bonds       : bond        0.03461 (  367)
  hydrogen bonds       : angle       4.00972 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9037 (mmm) cc_final: 0.8507 (mmm)
REVERT: A  168 SER cc_start: 0.7585 (m) cc_final: 0.6772 (p)
REVERT: A  224 CYS cc_start: 0.8231 (m) cc_final: 0.7845 (p)
REVERT: A  588 ASN cc_start: 0.7379 (m-40) cc_final: 0.6955 (t0)
REVERT: A  589 SER cc_start: 0.8777 (p) cc_final: 0.8341 (m)
REVERT: A  617 MET cc_start: 0.8954 (mmm) cc_final: 0.8230 (mmm)
REVERT: A  622 MET cc_start: 0.8760 (tpp) cc_final: 0.8319 (mtt)
REVERT: A  624 MET cc_start: 0.8475 (tmm) cc_final: 0.7921 (tmm)
REVERT: A  646 ASP cc_start: 0.8899 (m-30) cc_final: 0.8671 (m-30)
REVERT: A  688 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8482 (mm-30)
REVERT: B  332 TYR cc_start: 0.8794 (t80) cc_final: 0.8561 (t80)
REVERT: B  622 MET cc_start: 0.8358 (mpp) cc_final: 0.7785 (mpp)
  outliers start: 10
  outliers final: 10
  residues processed: 72
  average time/residue: 0.0658
  time to fit residues: 7.4066
Evaluate side-chains
  74 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    0.1980
   chunk 5 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0470
   chunk 16 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 21 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
** B 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.082290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.066844 restraints weight = 24366.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.069416 restraints weight = 12573.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.071161 restraints weight = 8010.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.072345 restraints weight = 5836.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.073197 restraints weight = 4659.826|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7860  Z= 0.091
  Angle     :  0.472   8.348  10640  Z= 0.240
  Chirality :  0.038   0.127   1114
  Planarity :  0.003   0.024   1362
  Dihedral  :  3.780  13.588   1030
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  :  9.88 %
    Favored  : 88.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.28), residues: 924
  helix:  2.96 (0.24), residues: 454
  sheet: -0.21 (0.57), residues: 86
  loop :  0.02 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 664 
 TYR   0.009   0.001   TYR B 322 
 PHE   0.018   0.001   PHE B 538 
 TRP   0.012   0.001   TRP A 584 
 HIS   0.002   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00200 ( 7860)
  covalent geometry    : angle       0.47249 (10640)
  hydrogen bonds       : bond        0.03155 (  367)
  hydrogen bonds       : angle       3.91358 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9020 (mmm) cc_final: 0.8458 (mmm)
REVERT: A  168 SER cc_start: 0.7512 (m) cc_final: 0.6710 (p)
REVERT: A  224 CYS cc_start: 0.8196 (m) cc_final: 0.7785 (p)
REVERT: A  588 ASN cc_start: 0.7409 (m-40) cc_final: 0.7198 (t0)
REVERT: A  589 SER cc_start: 0.8787 (p) cc_final: 0.8357 (m)
REVERT: A  617 MET cc_start: 0.8890 (mmm) cc_final: 0.8244 (mmm)
REVERT: A  646 ASP cc_start: 0.8889 (m-30) cc_final: 0.8652 (m-30)
REVERT: A  688 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8475 (mm-30)
REVERT: B   75 MET cc_start: 0.8050 (mmm) cc_final: 0.7311 (ttt)
REVERT: B  622 MET cc_start: 0.8200 (mpp) cc_final: 0.7691 (mpp)
REVERT: B  690 GLN cc_start: 0.9507 (tp-100) cc_final: 0.9160 (tp-100)
  outliers start: 11
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0716
  time to fit residues: 8.0815
Evaluate side-chains
  72 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 46 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 54 optimal weight:    0.4980
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3436 r_free = 0.3436 target = 0.081334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.065900 restraints weight = 24875.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.068429 restraints weight = 12870.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.070183 restraints weight = 8195.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.071380 restraints weight = 5972.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.072191 restraints weight = 4744.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7860  Z= 0.119
  Angle     :  0.505  10.140  10640  Z= 0.252
  Chirality :  0.039   0.128   1114
  Planarity :  0.003   0.024   1362
  Dihedral  :  3.775  13.240   1030
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 10.36 %
    Favored  : 88.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.13 (0.28), residues: 924
  helix:  2.91 (0.24), residues: 454
  sheet: -0.28 (0.57), residues: 86
  loop :  0.01 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 664 
 TYR   0.008   0.001   TYR B 296 
 PHE   0.018   0.001   PHE B 538 
 TRP   0.012   0.001   TRP B 278 
 HIS   0.002   0.001   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7860)
  covalent geometry    : angle       0.50459 (10640)
  hydrogen bonds       : bond        0.03304 (  367)
  hydrogen bonds       : angle       3.94611 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9032 (mmm) cc_final: 0.8462 (mmm)
REVERT: A  168 SER cc_start: 0.7530 (m) cc_final: 0.6704 (p)
REVERT: A  193 HIS cc_start: 0.9193 (OUTLIER) cc_final: 0.8480 (m90)
REVERT: A  224 CYS cc_start: 0.8198 (m) cc_final: 0.7820 (p)
REVERT: A  588 ASN cc_start: 0.7447 (m-40) cc_final: 0.7204 (t0)
REVERT: A  589 SER cc_start: 0.8838 (p) cc_final: 0.8319 (m)
REVERT: A  617 MET cc_start: 0.8847 (mmm) cc_final: 0.8644 (mtt)
REVERT: A  622 MET cc_start: 0.8751 (tpp) cc_final: 0.8167 (mtm)
REVERT: A  646 ASP cc_start: 0.8905 (m-30) cc_final: 0.8671 (m-30)
REVERT: A  651 MET cc_start: 0.9115 (mmm) cc_final: 0.8318 (tpt)
REVERT: A  688 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8472 (mm-30)
REVERT: B  622 MET cc_start: 0.8261 (mpp) cc_final: 0.7743 (mpp)
REVERT: B  690 GLN cc_start: 0.9501 (tp-100) cc_final: 0.9134 (tp-100)
  outliers start: 12
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0664
  time to fit residues: 7.6770
Evaluate side-chains
  71 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   chunk 7 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 90 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3441 r_free = 0.3441 target = 0.081282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.065744 restraints weight = 24922.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.068355 restraints weight = 12802.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.070146 restraints weight = 8112.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.071361 restraints weight = 5871.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.072180 restraints weight = 4652.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.3997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7860  Z= 0.110
  Angle     :  0.512   9.031  10640  Z= 0.255
  Chirality :  0.038   0.130   1114
  Planarity :  0.003   0.024   1362
  Dihedral  :  3.744  13.137   1030
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 10.60 %
    Favored  : 87.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 924
  helix:  2.89 (0.24), residues: 456
  sheet: -0.33 (0.57), residues: 86
  loop : -0.06 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 664 
 TYR   0.010   0.001   TYR B 203 
 PHE   0.012   0.001   PHE B 191 
 TRP   0.011   0.001   TRP B 278 
 HIS   0.002   0.000   HIS A 282 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 7860)
  covalent geometry    : angle       0.51153 (10640)
  hydrogen bonds       : bond        0.03152 (  367)
  hydrogen bonds       : angle       3.92515 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.9013 (mmm) cc_final: 0.8375 (mmm)
REVERT: A  168 SER cc_start: 0.7504 (m) cc_final: 0.6686 (p)
REVERT: A  193 HIS cc_start: 0.9173 (OUTLIER) cc_final: 0.8467 (m90)
REVERT: A  224 CYS cc_start: 0.8184 (m) cc_final: 0.7806 (p)
REVERT: A  574 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8067 (tppt)
REVERT: A  588 ASN cc_start: 0.7399 (m-40) cc_final: 0.6839 (t0)
REVERT: A  589 SER cc_start: 0.8872 (p) cc_final: 0.8290 (m)
REVERT: A  617 MET cc_start: 0.8874 (mmm) cc_final: 0.8556 (mtt)
REVERT: A  622 MET cc_start: 0.8661 (tpp) cc_final: 0.8126 (mtt)
REVERT: A  646 ASP cc_start: 0.8894 (m-30) cc_final: 0.8651 (m-30)
REVERT: A  688 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8403 (mm-30)
REVERT: B   75 MET cc_start: 0.7911 (mmm) cc_final: 0.7215 (ttt)
REVERT: B  622 MET cc_start: 0.8257 (mpp) cc_final: 0.7723 (mpp)
REVERT: B  659 GLN cc_start: 0.8959 (mt0) cc_final: 0.8745 (tm-30)
REVERT: B  690 GLN cc_start: 0.9494 (tp-100) cc_final: 0.9127 (tp-100)
  outliers start: 13
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0690
  time to fit residues: 7.7512
Evaluate side-chains
  73 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 61
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 ASP
Chi-restraints excluded: chain A residue  177 ASP
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  336 MET
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  574 LYS
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 5 optimal weight:    0.0970
   chunk 75 optimal weight:    0.0770
   chunk 77 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.3734

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.082494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.066913 restraints weight = 24653.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.069584 restraints weight = 12585.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.071363 restraints weight = 8013.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.072581 restraints weight = 5818.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.073417 restraints weight = 4611.274|
|-----------------------------------------------------------------------------|
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.4103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   7860  Z= 0.090
  Angle     :  0.493   8.971  10640  Z= 0.244
  Chirality :  0.038   0.129   1114
  Planarity :  0.003   0.026   1362
  Dihedral  :  3.686  13.793   1030
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 10.84 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.09 (0.28), residues: 924
  helix:  2.89 (0.24), residues: 456
  sheet: -0.26 (0.57), residues: 86
  loop : -0.07 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 664 
 TYR   0.009   0.001   TYR B 332 
 PHE   0.013   0.001   PHE B 191 
 TRP   0.012   0.001   TRP A 584 
 HIS   0.002   0.000   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 7860)
  covalent geometry    : angle       0.49258 (10640)
  hydrogen bonds       : bond        0.02946 (  367)
  hydrogen bonds       : angle       3.87792 ( 1053)

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

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

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1848 Ramachandran restraints generated.
    924 Oldfield, 0 Emsley, 924 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 65
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8989 (mmm) cc_final: 0.8389 (mmm)
REVERT: A  168 SER cc_start: 0.7455 (m) cc_final: 0.6613 (p)
REVERT: A  193 HIS cc_start: 0.9108 (OUTLIER) cc_final: 0.8392 (m90)
REVERT: A  224 CYS cc_start: 0.8152 (m) cc_final: 0.7817 (p)
REVERT: A  588 ASN cc_start: 0.7518 (m-40) cc_final: 0.7056 (t0)
REVERT: A  589 SER cc_start: 0.8867 (p) cc_final: 0.8295 (m)
REVERT: A  605 GLU cc_start: 0.9246 (mm-30) cc_final: 0.8787 (mm-30)
REVERT: A  622 MET cc_start: 0.8596 (tpp) cc_final: 0.8069 (mtt)
REVERT: A  646 ASP cc_start: 0.8879 (m-30) cc_final: 0.8630 (m-30)
REVERT: A  651 MET cc_start: 0.9186 (mmm) cc_final: 0.8594 (tpt)
REVERT: A  688 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8430 (mm-30)
REVERT: B   75 MET cc_start: 0.7776 (mmm) cc_final: 0.7097 (ttt)
REVERT: B  622 MET cc_start: 0.8165 (mpp) cc_final: 0.7626 (mpp)
REVERT: B  690 GLN cc_start: 0.9426 (tp-100) cc_final: 0.9130 (tp-100)
  outliers start: 9
  outliers final: 7
  residues processed: 72
  average time/residue: 0.0724
  time to fit residues: 7.9315
Evaluate side-chains
  68 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  193 HIS
Chi-restraints excluded: chain A residue  213 LEU
Chi-restraints excluded: chain A residue  217 THR
Chi-restraints excluded: chain A residue  384 LEU
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain B residue  255 VAL
Chi-restraints excluded: chain B residue  384 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 70 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0040
   chunk 7 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
A 577 GLN
B 577 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.081648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.066066 restraints weight = 24823.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.068698 restraints weight = 12838.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.070496 restraints weight = 8210.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.071703 restraints weight = 5969.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.072520 restraints weight = 4749.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.4221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7860  Z= 0.114
  Angle     :  0.512   8.972  10640  Z= 0.257
  Chirality :  0.039   0.126   1114
  Planarity :  0.003   0.026   1362
  Dihedral  :  3.758  16.074   1030
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 11.08 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.04 (0.28), residues: 924
  helix:  2.87 (0.24), residues: 456
  sheet: -0.31 (0.58), residues: 86
  loop : -0.11 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 664 
 TYR   0.011   0.001   TYR B 332 
 PHE   0.014   0.001   PHE B  68 
 TRP   0.011   0.001   TRP B 278 
 HIS   0.002   0.001   HIS B 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 7860)
  covalent geometry    : angle       0.51210 (10640)
  hydrogen bonds       : bond        0.03100 (  367)
  hydrogen bonds       : angle       3.94018 ( 1053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1301.50 seconds
wall clock time: 23 minutes 24.79 seconds (1404.79 seconds total)