Starting phenix.real_space_refine
on Wed Mar  4 11:49:20 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xym_33522/03_2026/7xym_33522_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2433 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7218      2.51       5
     N    1965      2.21       5
     O    2187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11436
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 3812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 488, 3812
          Classifications: {'peptide': 488}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 21, 'TRANS': 466}
          Unresolved non-hydrogen bonds: 64
          Unresolved non-hydrogen angles: 87
          Unresolved non-hydrogen dihedrals: 55
          Unresolved non-hydrogen chiralities: 10
          Planarities with less than four sites: {'TRP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 28
  Restraints were copied for chains:
    B, C
  Time building chain proxies: 2.65, per 1000 atoms: 0.23
  Number of scatterers: 11436
  At special positions: 0
  Unit cell: (128.199, 132.444, 159.612, 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      66     16.00
     O    2187      8.00
     N    1965      7.00
     C    7218      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  24 " - pdb=" SG  CYS B 384 " distance=1.97
    Simple disulfide: pdb=" SG  CYS A  76 " - pdb=" SG  CYS A  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 111 " - pdb=" SG  CYS A 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 112 " - pdb=" SG  CYS A 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 128 " - pdb=" SG  CYS A 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 279 " - pdb=" SG  CYS A 284 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 384 " - pdb=" SG  CYS C  24 " distance=1.97
    Simple disulfide: pdb=" SG  CYS B  24 " - pdb=" SG  CYS C 384 " distance=1.97
    Simple disulfide: pdb=" SG  CYS B  76 " - pdb=" SG  CYS B  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C  76 " - pdb=" SG  CYS C  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 111 " - pdb=" SG  CYS B 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 111 " - pdb=" SG  CYS C 163 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 112 " - pdb=" SG  CYS B 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 112 " - pdb=" SG  CYS C 137 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 128 " - pdb=" SG  CYS B 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 128 " - pdb=" SG  CYS C 157 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 279 " - pdb=" SG  CYS B 284 " distance=2.06
    Simple disulfide: pdb=" SG  CYS C 279 " - pdb=" SG  CYS C 284 " distance=2.06

  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: 0.90
  Conformation dependent library (CDL) restraints added in 515.0 milliseconds
  

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2718

  Finding SS restraints...
    Secondary structure from input PDB file:
      15 helices and 21 sheets defined
      17.4% alpha, 7.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 313 through 350
      removed outlier: 3.833A  pdb=" N   HIS A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL A 322 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU A 345 " --> pdb=" O   THR A 341 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE A 346 " --> pdb=" O   LEU A 342 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ASN A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 457
    Processing helix  chain 'A' and resid 457 through 469
    Processing helix  chain 'A' and resid 487 through 508
    Processing helix  chain 'B' and resid 101 through 106
    Processing helix  chain 'B' and resid 313 through 350
      removed outlier: 3.833A  pdb=" N   HIS B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 322 " --> pdb=" O   VAL B 318 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU B 345 " --> pdb=" O   THR B 341 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE B 346 " --> pdb=" O   LEU B 342 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN B 347 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 457
    Processing helix  chain 'B' and resid 457 through 469
    Processing helix  chain 'B' and resid 487 through 508
    Processing helix  chain 'C' and resid 101 through 106
    Processing helix  chain 'C' and resid 313 through 350
      removed outlier: 3.833A  pdb=" N   HIS C 319 " --> pdb=" O   ASN C 315 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL C 322 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   LEU C 345 " --> pdb=" O   THR C 341 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   PHE C 346 " --> pdb=" O   LEU C 342 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASN C 347 " --> pdb=" O   SER C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 452 through 457
    Processing helix  chain 'C' and resid 457 through 469
    Processing helix  chain 'C' and resid 487 through 508
    Processing sheet with id=AA1, first strand: chain 'B' and resid 370 through 373
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 49
    Processing sheet with id=AA3, first strand: chain 'A' and resid 77 through 78
      removed outlier: 4.210A  pdb=" N   TYR A 154 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 113
      removed outlier: 3.537A  pdb=" N   CYS A 111 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 180 through 182
      removed outlier: 3.572A  pdb=" N   ALA A 185 " --> pdb=" O   SER A 182 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 232
      removed outlier: 4.255A  pdb=" N   TYR A 261 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 236 through 237
    Processing sheet with id=AA8, first strand: chain 'A' and resid 370 through 373
      removed outlier: 6.166A  pdb=" N   GLN B 421 " --> pdb=" O   THR C  34 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 421 through 422
      removed outlier: 6.166A  pdb=" N   GLN A 421 " --> pdb=" O   THR B  34 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 48 through 49
    Processing sheet with id=AB2, first strand: chain 'B' and resid 77 through 78
      removed outlier: 4.210A  pdb=" N   TYR B 154 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 111 through 113
      removed outlier: 3.537A  pdb=" N   CYS B 111 " --> pdb=" O   HIS B 138 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 180 through 182
      removed outlier: 3.573A  pdb=" N   ALA B 185 " --> pdb=" O   SER B 182 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 228 through 232
      removed outlier: 4.255A  pdb=" N   TYR B 261 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 236 through 237
    Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 49
    Processing sheet with id=AB8, first strand: chain 'C' and resid 77 through 78
      removed outlier: 4.211A  pdb=" N   TYR C 154 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'C' and resid 111 through 113
      removed outlier: 3.537A  pdb=" N   CYS C 111 " --> pdb=" O   HIS C 138 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 180 through 182
      removed outlier: 3.572A  pdb=" N   ALA C 185 " --> pdb=" O   SER C 182 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 228 through 232
      removed outlier: 4.255A  pdb=" N   TYR C 261 " --> pdb=" O   LEU C 272 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 236 through 237

    259 hydrogen bonds defined for protein.
    714 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: 1.47

  Time building geometry restraints manager: 1.21 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 1878
        1.29 -     1.43: 3210
        1.43 -     1.57: 6546
        1.57 -     1.71: 6
        1.71 -     1.85: 87
  Bond restraints: 11727
  Sorted by residual:
  bond pdb=" C   ILE A 501 "
       pdb=" O   ILE A 501 "
    ideal  model  delta    sigma   weight residual
    1.236  1.459 -0.223 1.19e-02 7.06e+03 3.51e+02
  bond pdb=" C   ILE B 501 "
       pdb=" O   ILE B 501 "
    ideal  model  delta    sigma   weight residual
    1.236  1.459 -0.223 1.19e-02 7.06e+03 3.50e+02
  bond pdb=" C   ILE C 501 "
       pdb=" O   ILE C 501 "
    ideal  model  delta    sigma   weight residual
    1.236  1.459 -0.223 1.19e-02 7.06e+03 3.50e+02
  bond pdb=" CA  SER A 502 "
       pdb=" C   SER A 502 "
    ideal  model  delta    sigma   weight residual
    1.523  1.725 -0.202 1.34e-02 5.57e+03 2.28e+02
  bond pdb=" CA  SER C 502 "
       pdb=" C   SER C 502 "
    ideal  model  delta    sigma   weight residual
    1.523  1.725 -0.202 1.34e-02 5.57e+03 2.27e+02
  ... (remaining 11722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 15377
        3.61 -     7.22: 433
        7.22 -    10.83: 78
       10.83 -    14.44: 42
       14.44 -    18.06: 12
  Bond angle restraints: 15942
  Sorted by residual:
  angle pdb=" CA  ILE C 501 "
        pdb=" C   ILE C 501 "
        pdb=" O   ILE C 501 "
      ideal   model   delta    sigma   weight residual
     120.78  138.17  -17.39 1.25e+00 6.40e-01 1.94e+02
  angle pdb=" CA  ILE A 501 "
        pdb=" C   ILE A 501 "
        pdb=" O   ILE A 501 "
      ideal   model   delta    sigma   weight residual
     120.78  138.15  -17.37 1.25e+00 6.40e-01 1.93e+02
  angle pdb=" CA  ILE B 501 "
        pdb=" C   ILE B 501 "
        pdb=" O   ILE B 501 "
      ideal   model   delta    sigma   weight residual
     120.78  138.12  -17.34 1.25e+00 6.40e-01 1.92e+02
  angle pdb=" N   THR C 299 "
        pdb=" CA  THR C 299 "
        pdb=" C   THR C 299 "
      ideal   model   delta    sigma   weight residual
     113.97  102.74   11.23 1.28e+00 6.10e-01 7.69e+01
  angle pdb=" N   THR B 299 "
        pdb=" CA  THR B 299 "
        pdb=" C   THR B 299 "
      ideal   model   delta    sigma   weight residual
     113.97  102.76   11.21 1.28e+00 6.10e-01 7.67e+01
  ... (remaining 15937 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.47: 5986
       15.47 -    30.94: 698
       30.94 -    46.41: 234
       46.41 -    61.88: 33
       61.88 -    77.35: 18
  Dihedral angle restraints: 6969
    sinusoidal: 2718
      harmonic: 4251
  Sorted by residual:
  dihedral pdb=" CA  CYS C 279 "
           pdb=" C   CYS C 279 "
           pdb=" N   LEU C 280 "
           pdb=" CA  LEU C 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.49   46.51     0      5.00e+00 4.00e-02 8.65e+01
  dihedral pdb=" CA  CYS B 279 "
           pdb=" C   CYS B 279 "
           pdb=" N   LEU B 280 "
           pdb=" CA  LEU B 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.50   46.50     0      5.00e+00 4.00e-02 8.65e+01
  dihedral pdb=" CA  CYS A 279 "
           pdb=" C   CYS A 279 "
           pdb=" N   LEU A 280 "
           pdb=" CA  LEU A 280 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  133.50   46.50     0      5.00e+00 4.00e-02 8.65e+01
  ... (remaining 6966 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1647
       0.139 -    0.277: 63
       0.277 -    0.416: 18
       0.416 -    0.555: 0
       0.555 -    0.693: 3
  Chirality restraints: 1731
  Sorted by residual:
  chirality pdb=" CA  ILE A 501 "
            pdb=" N   ILE A 501 "
            pdb=" C   ILE A 501 "
            pdb=" CB  ILE A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.74    0.69 2.00e-01 2.50e+01 1.20e+01
  chirality pdb=" CA  ILE C 501 "
            pdb=" N   ILE C 501 "
            pdb=" C   ILE C 501 "
            pdb=" CB  ILE C 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.74    0.69 2.00e-01 2.50e+01 1.20e+01
  chirality pdb=" CA  ILE B 501 "
            pdb=" N   ILE B 501 "
            pdb=" C   ILE B 501 "
            pdb=" CB  ILE B 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    1.74    0.69 2.00e-01 2.50e+01 1.20e+01
  ... (remaining 1728 not shown)

  Planarity restraints: 2049
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 486 "    0.037 2.00e-02 2.50e+03   6.83e-02 4.66e+01
        pdb=" C   GLY A 486 "   -0.118 2.00e-02 2.50e+03
        pdb=" O   GLY A 486 "    0.041 2.00e-02 2.50e+03
        pdb=" N   TRP A 487 "    0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY C 486 "   -0.037 2.00e-02 2.50e+03   6.83e-02 4.66e+01
        pdb=" C   GLY C 486 "    0.118 2.00e-02 2.50e+03
        pdb=" O   GLY C 486 "   -0.041 2.00e-02 2.50e+03
        pdb=" N   TRP C 487 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 486 "    0.037 2.00e-02 2.50e+03   6.81e-02 4.64e+01
        pdb=" C   GLY B 486 "   -0.118 2.00e-02 2.50e+03
        pdb=" O   GLY B 486 "    0.041 2.00e-02 2.50e+03
        pdb=" N   TRP B 487 "    0.040 2.00e-02 2.50e+03
  ... (remaining 2046 not shown)

  Histogram of nonbonded interaction distances:
        1.03 -     1.80: 6
        1.80 -     2.58: 243
        2.58 -     3.35: 14666
        3.35 -     4.13: 27237
        4.13 -     4.90: 48115
  Nonbonded interactions: 90267
  Sorted by model distance:
  nonbonded pdb=" OG  SER B  74 "
            pdb=" C   ASN B 158 "
     model   vdw
     1.028 3.270
  nonbonded pdb=" OG  SER C  74 "
            pdb=" C   ASN C 158 "
     model   vdw
     1.029 3.270
  nonbonded pdb=" OG  SER A  74 "
            pdb=" C   ASN A 158 "
     model   vdw
     1.029 3.270
  nonbonded pdb=" OG  SER B  74 "
            pdb=" O   ASN B 158 "
     model   vdw
     1.416 3.040
  nonbonded pdb=" OG  SER A  74 "
            pdb=" O   ASN A 158 "
     model   vdw
     1.417 3.040
  ... (remaining 90262 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             10.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.240
  Find NCS groups from input model:        0.080
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7127
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      :  0.009   0.223  11745  Z= 0.674
  Angle     :  1.583  18.056  15978  Z= 0.939
  Chirality :  0.074   0.693   1731
  Planarity :  0.009   0.113   2049
  Dihedral  : 14.866  77.349   4197
  Min Nonbonded Distance : 1.028

Molprobity Statistics.
  All-atom Clashscore : 29.55
  Ramachandran Plot:
    Outliers :  2.88 %
    Allowed  : 25.51 %
    Favored  : 71.60 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  :  0.81 %
    Favored  : 98.71 %
  Cbeta Deviations :  0.44 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.36 %

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: -6.19 (0.16), residues: 1458
  helix: -3.63 (0.20), residues: 315
  sheet: -3.11 (0.37), residues: 171
  loop : -4.84 (0.15), residues: 972

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 404 
 TYR   0.039   0.002   TYR B 212 
 PHE   0.014   0.002   PHE A 208 
 TRP   0.016   0.002   TRP C 161 
 HIS   0.005   0.001   HIS C 397 

Details of bonding type rmsd
  covalent geometry    : bond        0.00922 (11727)
  covalent geometry    : angle       1.57614 (15942)
  SS BOND              : bond        0.02832 (   18)
  SS BOND              : angle       3.56474 (   36)
  hydrogen bonds       : bond        0.19346 (  259)
  hydrogen bonds       : angle      10.97821 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
REVERT: A  189 ASN cc_start: 0.5260 (m110) cc_final: 0.4955 (m110)
REVERT: A  481 LEU cc_start: 0.6174 (mt) cc_final: 0.5901 (mt)
REVERT: C  189 ASN cc_start: 0.5566 (m110) cc_final: 0.5299 (m110)
  outliers start: 6
  outliers final: 2
  residues processed: 93
  average time/residue: 0.0874
  time to fit residues: 12.7476
Evaluate side-chains
  68 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 66
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain C residue  266 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    9.9990
   chunk 77 optimal weight:    0.7980
   chunk 122 optimal weight:    0.2980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.0186

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

Flipped N/Q/H residues before XYZ refinement:
A  29 GLN
A  30 GLN
A 149 ASN
A 413 GLN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  29 GLN
B 149 ASN
B 413 GLN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  29 GLN
C 149 ASN
C 413 GLN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.185020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.120583 restraints weight = 21292.469|
|-----------------------------------------------------------------------------|
r_work (start): 0.3727 rms_B_bonded: 3.65
r_work: 0.3581 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  11745  Z= 0.252
  Angle     :  1.133  12.928  15978  Z= 0.595
  Chirality :  0.058   0.316   1731
  Planarity :  0.007   0.085   2049
  Dihedral  :  9.411  46.678   1594
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 24.21
  Ramachandran Plot:
    Outliers :  2.61 %
    Allowed  : 25.03 %
    Favored  : 72.36 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.00 %
    Favored  : 87.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.43 %

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: -5.47 (0.18), residues: 1458
  helix: -1.87 (0.27), residues: 297
  sheet: -2.90 (0.42), residues: 141
  loop : -4.69 (0.14), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 199 
 TYR   0.038   0.002   TYR C 212 
 PHE   0.019   0.002   PHE B 225 
 TRP   0.025   0.002   TRP C 405 
 HIS   0.005   0.001   HIS C 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 (11727)
  covalent geometry    : angle       1.13124 (15942)
  SS BOND              : bond        0.00819 (   18)
  SS BOND              : angle       1.71374 (   36)
  hydrogen bonds       : bond        0.13171 (  259)
  hydrogen bonds       : angle       8.29617 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.417 
Fit side-chains
REVERT: A  266 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7845 (p0)
REVERT: A  380 MET cc_start: 0.8290 (tpp) cc_final: 0.8009 (tpp)
REVERT: C  196 GLU cc_start: 0.4084 (tt0) cc_final: 0.3798 (pp20)
REVERT: C  266 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7925 (p0)
  outliers start: 17
  outliers final: 4
  residues processed: 84
  average time/residue: 0.0624
  time to fit residues: 8.8254
Evaluate side-chains
  67 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  468 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 5 optimal weight:    6.9990
   chunk 72 optimal weight:    0.7980
   chunk 109 optimal weight:    9.9990
   chunk 4 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 61 optimal weight:    8.9990
   chunk 73 optimal weight:    0.3980
   chunk 129 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 106 optimal weight:    4.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 293 ASN
A 413 GLN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  30 GLN
B 293 ASN
B 413 GLN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  30 GLN
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 293 ASN
C 413 GLN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.179595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.115594 restraints weight = 21314.056|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 3.57
r_work: 0.3510 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.073  11745  Z= 0.298
  Angle     :  1.126  12.510  15978  Z= 0.588
  Chirality :  0.059   0.359   1731
  Planarity :  0.007   0.075   2049
  Dihedral  :  9.414  45.447   1594
  Min Nonbonded Distance : 2.069

Molprobity Statistics.
  All-atom Clashscore : 28.87
  Ramachandran Plot:
    Outliers :  2.47 %
    Allowed  : 26.68 %
    Favored  : 70.85 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.23 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.58 %

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: -5.34 (0.18), residues: 1458
  helix: -1.59 (0.29), residues: 300
  sheet: -2.92 (0.41), residues: 141
  loop : -4.66 (0.15), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 199 
 TYR   0.030   0.002   TYR A 212 
 PHE   0.024   0.002   PHE B 225 
 TRP   0.033   0.002   TRP C 405 
 HIS   0.005   0.001   HIS A 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00658 (11727)
  covalent geometry    : angle       1.12290 (15942)
  SS BOND              : bond        0.01589 (   18)
  SS BOND              : angle       2.03297 (   36)
  hydrogen bonds       : bond        0.12866 (  259)
  hydrogen bonds       : angle       8.26909 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 58
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  405 TRP cc_start: 0.4610 (OUTLIER) cc_final: 0.3625 (m100)
REVERT: B  225 PHE cc_start: 0.7735 (OUTLIER) cc_final: 0.6863 (m-10)
REVERT: B  268 TYR cc_start: 0.8447 (m-10) cc_final: 0.8228 (m-10)
REVERT: B  405 TRP cc_start: 0.4563 (OUTLIER) cc_final: 0.3334 (m100)
REVERT: B  465 MET cc_start: 0.8287 (mtm) cc_final: 0.7678 (mtm)
REVERT: C  225 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6973 (m-10)
REVERT: C  266 ASN cc_start: 0.8338 (OUTLIER) cc_final: 0.8047 (p0)
REVERT: C  380 MET cc_start: 0.8485 (tpp) cc_final: 0.8155 (tpp)
REVERT: C  405 TRP cc_start: 0.4593 (OUTLIER) cc_final: 0.3834 (m100)
REVERT: C  413 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8136 (mt0)
REVERT: C  465 MET cc_start: 0.8185 (mtm) cc_final: 0.7711 (mtm)
  outliers start: 32
  outliers final: 12
  residues processed: 89
  average time/residue: 0.0690
  time to fit residues: 10.3637
Evaluate side-chains
  73 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 54
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  225 PHE
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  468 THR
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  225 PHE
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain B residue  468 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  225 PHE
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  405 TRP
Chi-restraints excluded: chain C residue  413 GLN
Chi-restraints excluded: chain C residue  468 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 98 optimal weight:    0.0030
   chunk 113 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0870
   chunk 99 optimal weight:    0.9980
   chunk 59 optimal weight:    8.9990
   chunk 45 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 87 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.5970

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

Flipped N/Q/H residues before XYZ refinement:
A 266 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 GLN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4548 r_free = 0.4548 target = 0.186358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.125919 restraints weight = 21428.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3781 rms_B_bonded: 4.06
r_work: 0.3595 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.3181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  11745  Z= 0.206
  Angle     :  1.011  12.060  15978  Z= 0.526
  Chirality :  0.053   0.278   1731
  Planarity :  0.006   0.071   2049
  Dihedral  :  8.987  45.955   1592
  Min Nonbonded Distance : 2.098

Molprobity Statistics.
  All-atom Clashscore : 22.95
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 24.76 %
    Favored  : 73.39 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 17.64 %
    Favored  : 77.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.65 %

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: -5.06 (0.19), residues: 1458
  helix: -0.97 (0.32), residues: 291
  sheet: -2.75 (0.42), residues: 141
  loop : -4.58 (0.15), residues: 1026

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 199 
 TYR   0.030   0.001   TYR B 212 
 PHE   0.016   0.002   PHE C 208 
 TRP   0.028   0.002   TRP C 405 
 HIS   0.004   0.001   HIS C 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (11727)
  covalent geometry    : angle       1.00810 (15942)
  SS BOND              : bond        0.00680 (   18)
  SS BOND              : angle       1.88117 (   36)
  hydrogen bonds       : bond        0.11263 (  259)
  hydrogen bonds       : angle       8.04091 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 71
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 GLU cc_start: 0.7195 (tm-30) cc_final: 0.6720 (tm-30)
REVERT: B  157 CYS cc_start: 0.1677 (OUTLIER) cc_final: 0.1237 (p)
REVERT: B  405 TRP cc_start: 0.4632 (OUTLIER) cc_final: 0.4305 (m100)
REVERT: B  465 MET cc_start: 0.8314 (mtm) cc_final: 0.7756 (mtm)
REVERT: B  478 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6657 (tm-30)
  outliers start: 55
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0806
  time to fit residues: 15.1388
Evaluate side-chains
  76 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain B residue  453 PHE
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  453 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 34 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 12 optimal weight:    8.9990
   chunk 110 optimal weight:    7.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 266 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.180421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.119406 restraints weight = 21144.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.3703 rms_B_bonded: 3.81
r_work: 0.3511 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7810
moved from start:          0.3689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.083  11745  Z= 0.296
  Angle     :  1.093  15.883  15978  Z= 0.566
  Chirality :  0.059   0.434   1731
  Planarity :  0.007   0.061   2049
  Dihedral  :  9.040  40.996   1590
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 25.60
  Ramachandran Plot:
    Outliers :  1.99 %
    Allowed  : 27.09 %
    Favored  : 70.92 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 19.01 %
    Favored  : 76.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.72 %

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: -5.22 (0.19), residues: 1458
  helix: -1.30 (0.30), residues: 315
  sheet: -2.90 (0.40), residues: 141
  loop : -4.68 (0.15), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 199 
 TYR   0.035   0.002   TYR B 212 
 PHE   0.016   0.002   PHE A 208 
 TRP   0.037   0.002   TRP B 405 
 HIS   0.005   0.001   HIS C  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00662 (11727)
  covalent geometry    : angle       1.08821 (15942)
  SS BOND              : bond        0.01290 (   18)
  SS BOND              : angle       2.40160 (   36)
  hydrogen bonds       : bond        0.12118 (  259)
  hydrogen bonds       : angle       8.01233 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 65
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1876 (OUTLIER) cc_final: 0.1364 (p)
REVERT: A  405 TRP cc_start: 0.5705 (OUTLIER) cc_final: 0.4934 (m100)
REVERT: B  157 CYS cc_start: 0.1976 (OUTLIER) cc_final: 0.1583 (p)
REVERT: B  405 TRP cc_start: 0.5406 (OUTLIER) cc_final: 0.5102 (m100)
REVERT: B  465 MET cc_start: 0.8495 (mtm) cc_final: 0.8112 (mtm)
REVERT: C  157 CYS cc_start: 0.1636 (OUTLIER) cc_final: 0.1090 (p)
REVERT: C  404 ARG cc_start: 0.6531 (mmt-90) cc_final: 0.6309 (ttt90)
REVERT: C  465 MET cc_start: 0.8299 (mtp) cc_final: 0.8027 (mtm)
  outliers start: 54
  outliers final: 26
  residues processed: 113
  average time/residue: 0.0784
  time to fit residues: 14.4307
Evaluate side-chains
  93 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 62
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   48 ILE
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  192 LEU
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain B residue  415 PHE
Chi-restraints excluded: chain B residue  453 PHE
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   48 ILE
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  453 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 58 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 107 optimal weight:    9.9990
   chunk 17 optimal weight:    0.6980
   chunk 102 optimal weight:    9.9990
   chunk 84 optimal weight:    0.0670
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 21 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 132 optimal weight:    0.9990
   overall best weight:    0.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  65 HIS
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  65 HIS
C 266 ASN
** C 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.188634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.132913 restraints weight = 20449.529|
|-----------------------------------------------------------------------------|
r_work (start): 0.3823 rms_B_bonded: 3.37
r_work: 0.3627 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  11745  Z= 0.203
  Angle     :  1.001  14.363  15978  Z= 0.516
  Chirality :  0.053   0.462   1731
  Planarity :  0.006   0.063   2049
  Dihedral  :  8.837  44.582   1590
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 22.01
  Ramachandran Plot:
    Outliers :  1.65 %
    Allowed  : 25.51 %
    Favored  : 72.84 %
  Rotamer:
    Outliers :  4.45 %
    Allowed  : 19.42 %
    Favored  : 76.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.58 %

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: -5.00 (0.19), residues: 1458
  helix: -0.78 (0.32), residues: 297
  sheet: -2.91 (0.40), residues: 141
  loop : -4.57 (0.15), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 199 
 TYR   0.034   0.002   TYR B 212 
 PHE   0.017   0.001   PHE A 208 
 TRP   0.029   0.002   TRP B 405 
 HIS   0.004   0.001   HIS C 407 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (11727)
  covalent geometry    : angle       0.99491 (15942)
  SS BOND              : bond        0.01023 (   18)
  SS BOND              : angle       2.45890 (   36)
  hydrogen bonds       : bond        0.10804 (  259)
  hydrogen bonds       : angle       7.85205 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 66
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1556 (OUTLIER) cc_final: 0.0998 (p)
REVERT: A  266 ASN cc_start: 0.8119 (OUTLIER) cc_final: 0.7884 (p0)
REVERT: A  268 TYR cc_start: 0.8341 (m-10) cc_final: 0.7973 (m-10)
REVERT: A  405 TRP cc_start: 0.5746 (OUTLIER) cc_final: 0.5046 (m100)
REVERT: A  478 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6801 (tm-30)
REVERT: B   68 TYR cc_start: 0.3053 (OUTLIER) cc_final: 0.2530 (t80)
REVERT: B  157 CYS cc_start: 0.1923 (OUTLIER) cc_final: 0.1413 (p)
REVERT: B  405 TRP cc_start: 0.5253 (OUTLIER) cc_final: 0.4923 (m100)
REVERT: B  465 MET cc_start: 0.8394 (mtm) cc_final: 0.8110 (mtm)
REVERT: B  478 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6714 (tm-30)
REVERT: C  157 CYS cc_start: 0.1401 (OUTLIER) cc_final: 0.0889 (p)
REVERT: C  478 GLU cc_start: 0.7180 (tm-30) cc_final: 0.6643 (tm-30)
  outliers start: 55
  outliers final: 23
  residues processed: 115
  average time/residue: 0.0743
  time to fit residues: 13.7561
Evaluate side-chains
  90 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 60
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain B residue  415 PHE
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  415 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   chunk 131 optimal weight:    0.6980
   chunk 117 optimal weight:    0.8980
   chunk 13 optimal weight:   10.0000
   chunk 122 optimal weight:    0.7980
   chunk 86 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0970
   chunk 141 optimal weight:    0.2980
   chunk 140 optimal weight:    0.5980
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 266 ASN
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
C 413 GLN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4585 r_free = 0.4585 target = 0.189436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.133135 restraints weight = 20296.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3828 rms_B_bonded: 3.32
r_work: 0.3644 rms_B_bonded: 3.55 restraints_weight: 0.5000
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.4175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  11745  Z= 0.196
  Angle     :  0.995  11.848  15978  Z= 0.511
  Chirality :  0.054   0.315   1731
  Planarity :  0.006   0.050   2049
  Dihedral  :  8.631  40.362   1590
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 21.97
  Ramachandran Plot:
    Outliers :  1.85 %
    Allowed  : 24.76 %
    Favored  : 73.39 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 20.71 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 2.36 %

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: -4.86 (0.19), residues: 1458
  helix: -0.42 (0.33), residues: 297
  sheet: -2.80 (0.40), residues: 141
  loop : -4.58 (0.15), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 404 
 TYR   0.036   0.001   TYR B 212 
 PHE   0.018   0.001   PHE A 208 
 TRP   0.029   0.002   TRP B 405 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (11727)
  covalent geometry    : angle       0.99159 (15942)
  SS BOND              : bond        0.00729 (   18)
  SS BOND              : angle       1.98726 (   36)
  hydrogen bonds       : bond        0.10399 (  259)
  hydrogen bonds       : angle       7.68444 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 76
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1583 (OUTLIER) cc_final: 0.1031 (p)
REVERT: A  268 TYR cc_start: 0.8287 (m-10) cc_final: 0.7958 (m-10)
REVERT: A  405 TRP cc_start: 0.5820 (OUTLIER) cc_final: 0.5489 (m100)
REVERT: A  478 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6756 (tm-30)
REVERT: A  481 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7121 (mt)
REVERT: B   68 TYR cc_start: 0.3061 (OUTLIER) cc_final: 0.2548 (t80)
REVERT: B  157 CYS cc_start: 0.1751 (OUTLIER) cc_final: 0.1306 (p)
REVERT: B  465 MET cc_start: 0.8340 (mtm) cc_final: 0.8110 (mtm)
REVERT: B  478 GLU cc_start: 0.7110 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: C  157 CYS cc_start: 0.1481 (OUTLIER) cc_final: 0.0986 (p)
REVERT: C  335 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8718 (tt)
REVERT: C  478 GLU cc_start: 0.7064 (tm-30) cc_final: 0.6552 (tm-30)
  outliers start: 52
  outliers final: 24
  residues processed: 121
  average time/residue: 0.0790
  time to fit residues: 15.2936
Evaluate side-chains
  96 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   68 TYR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  266 ASN
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  415 PHE
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  196 GLU
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  415 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 70 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 88 optimal weight:    3.9990
   chunk 43 optimal weight:    0.7980
   chunk 75 optimal weight:    0.5980
   chunk 139 optimal weight:    0.9990
   chunk 108 optimal weight:    9.9990
   chunk 22 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 367 GLN
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.187400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.131265 restraints weight = 20198.760|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 3.60
r_work: 0.3590 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.4377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  11745  Z= 0.215
  Angle     :  1.007  13.675  15978  Z= 0.517
  Chirality :  0.055   0.320   1731
  Planarity :  0.006   0.049   2049
  Dihedral  :  8.678  42.131   1590
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 22.33
  Ramachandran Plot:
    Outliers :  1.78 %
    Allowed  : 26.06 %
    Favored  : 72.15 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 22.09 %
    Favored  : 74.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 2.36 %

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: -4.84 (0.19), residues: 1458
  helix: -0.45 (0.33), residues: 300
  sheet: -2.80 (0.40), residues: 141
  loop : -4.55 (0.15), residues: 1017

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 404 
 TYR   0.036   0.002   TYR B 212 
 PHE   0.017   0.002   PHE A 208 
 TRP   0.018   0.002   TRP A 405 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00446 (11727)
  covalent geometry    : angle       1.00195 (15942)
  SS BOND              : bond        0.00689 (   18)
  SS BOND              : angle       2.29538 (   36)
  hydrogen bonds       : bond        0.10480 (  259)
  hydrogen bonds       : angle       7.61900 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 67
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1591 (OUTLIER) cc_final: 0.1044 (p)
REVERT: A  268 TYR cc_start: 0.8419 (m-10) cc_final: 0.8100 (m-10)
REVERT: A  405 TRP cc_start: 0.5811 (OUTLIER) cc_final: 0.5531 (m100)
REVERT: A  478 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6807 (tm-30)
REVERT: A  481 LEU cc_start: 0.7299 (OUTLIER) cc_final: 0.7089 (mt)
REVERT: B   68 TYR cc_start: 0.2924 (OUTLIER) cc_final: 0.2502 (t80)
REVERT: B  157 CYS cc_start: 0.1506 (OUTLIER) cc_final: 0.1056 (p)
REVERT: B  208 PHE cc_start: 0.5027 (m-80) cc_final: 0.4496 (m-80)
REVERT: B  405 TRP cc_start: 0.5989 (OUTLIER) cc_final: 0.5514 (m100)
REVERT: B  465 MET cc_start: 0.8391 (mtm) cc_final: 0.8163 (mtm)
REVERT: B  478 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6654 (tm-30)
REVERT: C  157 CYS cc_start: 0.1422 (OUTLIER) cc_final: 0.0906 (p)
REVERT: C  335 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8711 (tt)
REVERT: C  405 TRP cc_start: 0.6158 (OUTLIER) cc_final: 0.5063 (m100)
REVERT: C  478 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6680 (tm-30)
  outliers start: 44
  outliers final: 23
  residues processed: 105
  average time/residue: 0.0812
  time to fit residues: 13.3917
Evaluate side-chains
  97 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 65
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  405 TRP
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain A residue  481 LEU
Chi-restraints excluded: chain B residue   21 ILE
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  192 LEU
Chi-restraints excluded: chain C residue  193 ILE
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  405 TRP
Chi-restraints excluded: chain C residue  415 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 138 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 126 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 104 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 68 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.185435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.121999 restraints weight = 20974.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 3.49
r_work: 0.3597 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  11745  Z= 0.200
  Angle     :  0.984  13.234  15978  Z= 0.505
  Chirality :  0.054   0.363   1731
  Planarity :  0.006   0.045   2049
  Dihedral  :  8.663  41.059   1590
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  1.92 %
    Allowed  : 25.31 %
    Favored  : 72.77 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 21.76 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 2.43 %

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: -4.69 (0.20), residues: 1458
  helix: -0.22 (0.33), residues: 297
  sheet: -2.35 (0.41), residues: 162
  loop : -4.57 (0.15), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 404 
 TYR   0.037   0.002   TYR A 212 
 PHE   0.018   0.002   PHE A 208 
 TRP   0.033   0.002   TRP C 121 
 HIS   0.008   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (11727)
  covalent geometry    : angle       0.97949 (15942)
  SS BOND              : bond        0.00945 (   18)
  SS BOND              : angle       2.18427 (   36)
  hydrogen bonds       : bond        0.10174 (  259)
  hydrogen bonds       : angle       7.63606 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 65
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1456 (OUTLIER) cc_final: 0.0886 (p)
REVERT: A  183 MET cc_start: 0.7816 (mmm) cc_final: 0.6940 (ppp)
REVERT: A  268 TYR cc_start: 0.8397 (m-10) cc_final: 0.8007 (m-10)
REVERT: A  404 ARG cc_start: 0.6421 (mpt180) cc_final: 0.5933 (mtt90)
REVERT: A  478 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6548 (tm-30)
REVERT: B   68 TYR cc_start: 0.2845 (OUTLIER) cc_final: 0.2438 (t80)
REVERT: B  157 CYS cc_start: 0.1846 (OUTLIER) cc_final: 0.1365 (p)
REVERT: B  405 TRP cc_start: 0.5276 (OUTLIER) cc_final: 0.4516 (m100)
REVERT: B  465 MET cc_start: 0.8245 (mtm) cc_final: 0.7823 (mtm)
REVERT: B  478 GLU cc_start: 0.7038 (tm-30) cc_final: 0.6465 (tm-30)
REVERT: C  157 CYS cc_start: 0.1348 (OUTLIER) cc_final: 0.0812 (p)
REVERT: C  335 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8575 (tt)
REVERT: C  384 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7581 (m)
REVERT: C  478 GLU cc_start: 0.7008 (tm-30) cc_final: 0.6452 (tm-30)
  outliers start: 42
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0835
  time to fit residues: 13.6951
Evaluate side-chains
  91 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 64
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  298 ASP
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  384 CYS
Chi-restraints excluded: chain C residue  415 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 17 optimal weight:    0.1980
   chunk 131 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 141 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0000
   chunk 21 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 100 optimal weight:    9.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4547 r_free = 0.4547 target = 0.186220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.128837 restraints weight = 21035.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.3830 rms_B_bonded: 4.36
r_work: 0.3566 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.4693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  11745  Z= 0.194
  Angle     :  1.011  18.660  15978  Z= 0.518
  Chirality :  0.055   0.462   1731
  Planarity :  0.006   0.094   2049
  Dihedral  :  8.717  42.545   1590
  Min Nonbonded Distance : 2.124

Molprobity Statistics.
  All-atom Clashscore : 21.52
  Ramachandran Plot:
    Outliers :  1.78 %
    Allowed  : 25.24 %
    Favored  : 72.98 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 21.93 %
    Favored  : 75.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.59 %
    Twisted General : 2.43 %

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: -4.64 (0.20), residues: 1458
  helix: -0.12 (0.33), residues: 297
  sheet: -2.27 (0.42), residues: 162
  loop : -4.57 (0.15), residues: 999

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 404 
 TYR   0.037   0.002   TYR A 212 
 PHE   0.019   0.001   PHE A 208 
 TRP   0.031   0.002   TRP C 121 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (11727)
  covalent geometry    : angle       0.99980 (15942)
  SS BOND              : bond        0.01170 (   18)
  SS BOND              : angle       3.26607 (   36)
  hydrogen bonds       : bond        0.09961 (  259)
  hydrogen bonds       : angle       7.62544 (  714)

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

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

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2916 Ramachandran restraints generated.
    1458 Oldfield, 0 Emsley, 1458 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 65
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  157 CYS cc_start: 0.1385 (OUTLIER) cc_final: 0.0810 (p)
REVERT: A  183 MET cc_start: 0.7840 (mmm) cc_final: 0.6979 (ppp)
REVERT: A  478 GLU cc_start: 0.7087 (tm-30) cc_final: 0.6578 (tm-30)
REVERT: B   68 TYR cc_start: 0.2785 (OUTLIER) cc_final: 0.2438 (t80)
REVERT: B  157 CYS cc_start: 0.1725 (OUTLIER) cc_final: 0.1226 (p)
REVERT: B  405 TRP cc_start: 0.4921 (OUTLIER) cc_final: 0.4252 (m100)
REVERT: B  465 MET cc_start: 0.8253 (mtm) cc_final: 0.7849 (mtm)
REVERT: B  478 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6476 (tm-30)
REVERT: C  157 CYS cc_start: 0.1417 (OUTLIER) cc_final: 0.0871 (p)
REVERT: C  335 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8594 (tt)
REVERT: C  384 CYS cc_start: 0.8015 (OUTLIER) cc_final: 0.7631 (m)
REVERT: C  478 GLU cc_start: 0.6996 (tm-30) cc_final: 0.6438 (tm-30)
  outliers start: 35
  outliers final: 22
  residues processed: 98
  average time/residue: 0.0758
  time to fit residues: 11.9707
Evaluate side-chains
  94 residues out of total 1287 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ILE
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  157 CYS
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  212 TYR
Chi-restraints excluded: chain A residue  453 PHE
Chi-restraints excluded: chain B residue   34 THR
Chi-restraints excluded: chain B residue   36 VAL
Chi-restraints excluded: chain B residue   68 TYR
Chi-restraints excluded: chain B residue   98 THR
Chi-restraints excluded: chain B residue  157 CYS
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  193 ILE
Chi-restraints excluded: chain B residue  201 THR
Chi-restraints excluded: chain B residue  212 TYR
Chi-restraints excluded: chain B residue  279 CYS
Chi-restraints excluded: chain B residue  333 SER
Chi-restraints excluded: chain B residue  405 TRP
Chi-restraints excluded: chain C residue   34 THR
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  157 CYS
Chi-restraints excluded: chain C residue  170 ILE
Chi-restraints excluded: chain C residue  181 VAL
Chi-restraints excluded: chain C residue  201 THR
Chi-restraints excluded: chain C residue  212 TYR
Chi-restraints excluded: chain C residue  266 ASN
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  384 CYS
Chi-restraints excluded: chain C residue  415 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 1 optimal weight:    0.3980
   chunk 137 optimal weight:    1.9990
   chunk 98 optimal weight:    0.1980
   chunk 72 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 125 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 266 ASN
** C 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.185731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.122296 restraints weight = 21227.510|
|-----------------------------------------------------------------------------|
r_work (start): 0.3735 rms_B_bonded: 3.51
r_work: 0.3581 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.4823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11745  Z= 0.197
  Angle     :  0.990  12.771  15978  Z= 0.509
  Chirality :  0.054   0.348   1731
  Planarity :  0.006   0.092   2049
  Dihedral  :  8.653  41.618   1590
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 21.88
  Ramachandran Plot:
    Outliers :  1.78 %
    Allowed  : 25.45 %
    Favored  : 72.77 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 22.49 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 2.43 %

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: -4.61 (0.20), residues: 1458
  helix:  0.23 (0.33), residues: 285
  sheet: -2.19 (0.42), residues: 162
  loop : -4.62 (0.15), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.024   0.001   ARG C 404 
 TYR   0.038   0.002   TYR A 212 
 PHE   0.019   0.001   PHE A 208 
 TRP   0.031   0.002   TRP A 121 
 HIS   0.007   0.001   HIS A  65 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (11727)
  covalent geometry    : angle       0.98097 (15942)
  SS BOND              : bond        0.01046 (   18)
  SS BOND              : angle       2.99846 (   36)
  hydrogen bonds       : bond        0.09935 (  259)
  hydrogen bonds       : angle       7.63104 (  714)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3638.28 seconds
wall clock time: 62 minutes 52.94 seconds (3772.94 seconds total)