Starting phenix.real_space_refine
on Thu Jul  2 17:54:55 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7xck_33123/07_2026/7xck_33123.cif"
  }
  resolution = 2.5
  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=   0.053
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 4868 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      21      5.16       5
     C    3473      2.51       5
     N     927      2.21       5
     O    1067      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 223, 1688
          Classifications: {'peptide': 223}
          Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 210}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1615
          Classifications: {'peptide': 212}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 200}
    Chain: "M"
      Number of atoms: 2147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 269, 2147
          Classifications: {'peptide': 269}
          Link IDs: {'PTRANS': 16, 'TRANS': 252}
    Chain: "C"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.09, per 1000 atoms: 0.20
  Number of scatterers: 5488
  At special positions: 0
  Unit cell: (113.9, 61.64, 122.61, 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      21     16.00
     O    1067      8.00
     N     927      7.00
     C    3473      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS A 210 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  89 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 134 " - pdb=" SG  CYS B 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 336 " - pdb=" SG  CYS M 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 379 " - pdb=" SG  CYS M 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS M 480 " - pdb=" SG  CYS M 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS M 538 " - pdb=" SG  CYS M 590 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    BETA1-6
      " NAG C   1 " - " FUC C   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG C   1 " - " ASN M 343 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 164.6 milliseconds
  

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1302

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 14 sheets defined
      9.7% alpha, 38.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.646A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 65
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.942A  pdb=" N   THR A  91 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 32
      No H-bonds generated for 'chain 'B' and resid 30 through 32'
    Processing helix  chain 'B' and resid 80 through 84
      removed outlier: 4.031A  pdb=" N   PHE B  84 " --> pdb=" O   PRO B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 188
      removed outlier: 3.542A  pdb=" N   LYS B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 338 through 343
    Processing helix  chain 'M' and resid 365 through 369
    Processing helix  chain 'M' and resid 383 through 390
      removed outlier: 3.529A  pdb=" N   LEU M 387 " --> pdb=" O   PRO M 384 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ASN M 388 " --> pdb=" O   THR M 385 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   LEU M 390 " --> pdb=" O   LEU M 387 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 403 through 410
      removed outlier: 3.521A  pdb=" N   GLU M 406 " --> pdb=" O   ARG M 403 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL M 407 " --> pdb=" O   GLY M 404 " (cutoff:3.500A)
      removed outlier: 4.141A  pdb=" N   ARG M 408 " --> pdb=" O   ASP M 405 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 416 through 422
    Processing helix  chain 'M' and resid 438 through 443
      removed outlier: 3.707A  pdb=" N   SER M 443 " --> pdb=" O   ASN M 439 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.515A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASN A 116 " --> pdb=" O   ARG A  98 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60
      removed outlier: 6.515A  pdb=" N   TRP A  36 " --> pdb=" O   MET A  48 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   TRP A  50 " --> pdb=" O   ILE A  34 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ILE A  34 " --> pdb=" O   TRP A  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.127A  pdb=" N   TYR A 190 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 134 through 138
      removed outlier: 6.127A  pdb=" N   TYR A 190 " --> pdb=" O   ASP A 158 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 165 through 168
    Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 7
    Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.402A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   LEU B  34 " --> pdb=" O   TYR B  50 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   TYR B  50 " --> pdb=" O   LEU B  34 " (cutoff:3.500A)
      removed outlier: 6.548A  pdb=" N   TRP B  36 " --> pdb=" O   LEU B  48 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 13
      removed outlier: 6.402A  pdb=" N   LEU B  11 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 116 through 118
      removed outlier: 3.957A  pdb=" N   VAL B 133 " --> pdb=" O   PHE B 118 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   ASN B 138 " --> pdb=" O   TYR B 173 " (cutoff:3.500A)
      removed outlier: 6.284A  pdb=" N   TYR B 173 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 149
    Processing sheet with id=AB3, first strand: chain 'M' and resid 325 through 328
      removed outlier: 5.842A  pdb=" N   ASP M 574 " --> pdb=" O   ILE M 587 " (cutoff:3.500A)
      removed outlier: 6.577A  pdb=" N   GLY M 566 " --> pdb=" O   ASP M 574 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'M' and resid 354 through 358
    Processing sheet with id=AB5, first strand: chain 'M' and resid 452 through 454

    209 hydrogen bonds defined for protein.
    513 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 0.48 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 948
        1.32 -     1.45: 1605
        1.45 -     1.58: 3044
        1.58 -     1.71: 0
        1.71 -     1.84: 24
  Bond restraints: 5621
  Sorted by residual:
  bond pdb=" C   ALA M 344 "
       pdb=" N   THR M 345 "
    ideal  model  delta    sigma   weight residual
    1.335  1.278  0.057 1.25e-02 6.40e+03 2.05e+01
  bond pdb=" CA  ALA M 344 "
       pdb=" CB  ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.528  1.474  0.054 1.58e-02 4.01e+03 1.15e+01
  bond pdb=" C   ALA M 344 "
       pdb=" O   ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.235  1.201  0.034 1.20e-02 6.94e+03 8.18e+00
  bond pdb=" C   ASN M 343 "
       pdb=" O   ASN M 343 "
    ideal  model  delta    sigma   weight residual
    1.235  1.197  0.038 1.32e-02 5.74e+03 8.17e+00
  bond pdb=" CA  ALA M 344 "
       pdb=" C   ALA M 344 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.038 1.33e-02 5.65e+03 8.00e+00
  ... (remaining 5616 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.21: 7496
        2.21 -     4.43: 120
        4.43 -     6.64: 25
        6.64 -     8.85: 2
        8.85 -    11.07: 1
  Bond angle restraints: 7644
  Sorted by residual:
  angle pdb=" CA  ASN M 334 "
        pdb=" C   ASN M 334 "
        pdb=" O   ASN M 334 "
      ideal   model   delta    sigma   weight residual
     121.15  116.26    4.89 1.10e+00 8.26e-01 1.98e+01
  angle pdb=" C   VAL B 150 "
        pdb=" N   ASP B 151 "
        pdb=" CA  ASP B 151 "
      ideal   model   delta    sigma   weight residual
     121.54  129.19   -7.65 1.91e+00 2.74e-01 1.60e+01
  angle pdb=" C   ASN M 343 "
        pdb=" CA  ASN M 343 "
        pdb=" CB  ASN M 343 "
      ideal   model   delta    sigma   weight residual
     111.02  104.60    6.42 1.61e+00 3.86e-01 1.59e+01
  angle pdb=" C   PRO A 161 "
        pdb=" N   GLU A 162 "
        pdb=" CA  GLU A 162 "
      ideal   model   delta    sigma   weight residual
     120.26  125.14   -4.88 1.34e+00 5.57e-01 1.33e+01
  angle pdb=" C   SER B  95 "
        pdb=" CA  SER B  95 "
        pdb=" CB  SER B  95 "
      ideal   model   delta    sigma   weight residual
     115.89  111.20    4.69 1.32e+00 5.74e-01 1.26e+01
  ... (remaining 7639 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3057
       17.59 -    35.17: 220
       35.17 -    52.76: 47
       52.76 -    70.34: 5
       70.34 -    87.93: 4
  Dihedral angle restraints: 3333
    sinusoidal: 1297
      harmonic: 2036
  Sorted by residual:
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS A 210 "
           pdb=" CB  CYS A 210 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.64  -69.64     1      1.00e+01 1.00e-02 6.26e+01
  dihedral pdb=" CB  CYS M 538 "
           pdb=" SG  CYS M 538 "
           pdb=" SG  CYS M 590 "
           pdb=" CB  CYS M 590 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.35  -47.65     1      1.00e+01 1.00e-02 3.13e+01
  dihedral pdb=" CB  CYS M 379 "
           pdb=" SG  CYS M 379 "
           pdb=" SG  CYS M 432 "
           pdb=" CB  CYS M 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -51.56  -34.44     1      1.00e+01 1.00e-02 1.68e+01
  ... (remaining 3330 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.142: 855
       0.142 -    0.284: 2
       0.284 -    0.425: 0
       0.425 -    0.567: 0
       0.567 -    0.709: 1
  Chirality restraints: 858
  Sorted by residual:
  chirality pdb=" C1  FUC C   3 "
            pdb=" O6  NAG C   1 "
            pdb=" C2  FUC C   3 "
            pdb=" O5  FUC C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.31   -0.09 2.00e-02 2.50e+03 2.19e+01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN M 343 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.69   -0.71 2.00e-01 2.50e+01 1.26e+01
  chirality pdb=" CA  VAL A  37 "
            pdb=" N   VAL A  37 "
            pdb=" C   VAL A  37 "
            pdb=" CB  VAL A  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.60   -0.16 2.00e-01 2.50e+01 6.69e-01
  ... (remaining 855 not shown)

  Planarity restraints: 982
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   1 "   -0.045 2.00e-02 2.50e+03   3.72e-02 1.73e+01
        pdb=" C7  NAG C   1 "    0.011 2.00e-02 2.50e+03
        pdb=" C8  NAG C   1 "   -0.034 2.00e-02 2.50e+03
        pdb=" N2  NAG C   1 "    0.060 2.00e-02 2.50e+03
        pdb=" O7  NAG C   1 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG C   2 "    0.041 2.00e-02 2.50e+03   3.36e-02 1.41e+01
        pdb=" C7  NAG C   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG C   2 "    0.032 2.00e-02 2.50e+03
        pdb=" N2  NAG C   2 "   -0.052 2.00e-02 2.50e+03
        pdb=" O7  NAG C   2 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA M 520 "    0.043 5.00e-02 4.00e+02   6.51e-02 6.78e+00
        pdb=" N   PRO M 521 "   -0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO M 521 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO M 521 "    0.036 5.00e-02 4.00e+02
  ... (remaining 979 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 246
        2.72 -     3.27: 5007
        3.27 -     3.81: 8362
        3.81 -     4.36: 10652
        4.36 -     4.90: 18600
  Nonbonded interactions: 42867
  Sorted by model distance:
  nonbonded pdb=" OH  TYR M 369 "
            pdb=" O   PRO M 384 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER B  64 "
            pdb=" OG1 THR B  75 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OG1 THR A 149 "
            pdb=" O   VAL A 198 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU B 105 "
            pdb=" OH  TYR B 173 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   ASP M 442 "
            pdb=" ND2 ASN M 448 "
     model   vdw
     2.307 3.120
  ... (remaining 42862 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             11.090
  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:          0.160
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.000
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.540
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8057
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      :  0.004   0.057   5632  Z= 0.203
  Angle     :  0.723  11.067   7669  Z= 0.392
  Chirality :  0.052   0.709    858
  Planarity :  0.006   0.065    981
  Dihedral  : 12.659  87.930   2007
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.60 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.89 (0.32), residues: 696
  helix: -3.99 (0.85), residues: 20
  sheet:  0.21 (0.33), residues: 271
  loop : -0.98 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 346 
 TYR   0.007   0.001   TYR A 159 
 PHE   0.012   0.001   PHE M 374 
 TRP   0.008   0.001   TRP M 436 
 HIS   0.004   0.001   HIS M 519 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00357 /  0.20 ( 5621)
  covalent geometry    : angle       0.71268 /  0.39 ( 7644)
  SS BOND              : bond        0.00609 /  0.28 (    8)
  SS BOND              : angle       1.26856 /  0.94 (   16)
  hydrogen bonds       : bond        0.14772 /  9.92 (  181)
  hydrogen bonds       : angle       7.19690 /  4.82 (  513)
  link_BETA1-4         : bond        0.00179 /  0.09 (    1)
  link_BETA1-4         : angle       2.72332 /  1.50 (    3)
  link_BETA1-6         : bond        0.01807 /  0.95 (    1)
  link_BETA1-6         : angle       2.90036 /  1.53 (    3)
  link_NAG-ASN         : bond        0.02761 /  1.45 (    1)
  link_NAG-ASN         : angle       4.16457 /  2.19 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.6100
  time to fit residues: 43.7753
Evaluate side-chains
  57 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.4980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 155 GLN
M 417 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.183133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.117666 restraints weight = 6217.314|
|-----------------------------------------------------------------------------|
r_work (start): 0.3414 rms_B_bonded: 2.56
r_work: 0.3272 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.0800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5632  Z= 0.126
  Angle     :  0.600   8.946   7669  Z= 0.309
  Chirality :  0.046   0.139    858
  Planarity :  0.005   0.060    981
  Dihedral  :  4.698  19.304    764
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  5.92 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.33), residues: 696
  helix: -4.39 (0.53), residues: 26
  sheet:  0.36 (0.33), residues: 268
  loop : -0.94 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.008   0.001   TYR A 159 
 PHE   0.013   0.001   PHE M 377 
 TRP   0.009   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 ( 5621)
  covalent geometry    : angle       0.59459 /  0.31 ( 7644)
  SS BOND              : bond        0.00547 /  0.27 (    8)
  SS BOND              : angle       1.44799 /  1.07 (   16)
  hydrogen bonds       : bond        0.03584 /  2.42 (  181)
  hydrogen bonds       : angle       5.76035 /  3.91 (  513)
  link_BETA1-4         : bond        0.00108 /  0.06 (    1)
  link_BETA1-4         : angle       1.57852 /  0.83 (    3)
  link_BETA1-6         : bond        0.00260 /  0.14 (    1)
  link_BETA1-6         : angle       1.82130 /  0.96 (    3)
  link_NAG-ASN         : bond        0.00446 /  0.23 (    1)
  link_NAG-ASN         : angle       1.93095 /  1.12 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7313 (mp10)
REVERT: A   82 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7651 (tp30)
REVERT: B  117 ILE cc_start: 0.6504 (tt) cc_final: 0.6069 (mm)
REVERT: M  357 ARG cc_start: 0.8717 (ttp-170) cc_final: 0.8301 (ttp80)
REVERT: M  405 ASP cc_start: 0.7837 (p0) cc_final: 0.7591 (p0)
REVERT: M  586 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7949 (m-30)
  outliers start: 15
  outliers final: 5
  residues processed: 70
  average time/residue: 0.5715
  time to fit residues: 41.8765
Evaluate side-chains
  64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 57
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  586 ASP
Chi-restraints excluded: chain M residue  588 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    0.0980
   chunk 40 optimal weight:    0.0570
   chunk 3 optimal weight:    2.9990
   chunk 55 optimal weight:    5.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    9.9990
   chunk 6 optimal weight:    3.9990
   chunk 37 optimal weight:   10.0000
   overall best weight:    1.2102

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.181347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.116017 restraints weight = 6120.500|
|-----------------------------------------------------------------------------|
r_work (start): 0.3392 rms_B_bonded: 2.52
r_work: 0.3248 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3113 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5632  Z= 0.159
  Angle     :  0.614   7.955   7669  Z= 0.318
  Chirality :  0.046   0.148    858
  Planarity :  0.005   0.059    981
  Dihedral  :  4.853  18.312    764
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 11.18 %
    Favored  : 86.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.87 (0.32), residues: 696
  helix: -4.41 (0.47), residues: 26
  sheet:  0.33 (0.33), residues: 271
  loop : -0.96 (0.31), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 346 
 TYR   0.010   0.001   TYR B  37 
 PHE   0.017   0.001   PHE M 377 
 TRP   0.011   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00380 /  0.16 ( 5621)
  covalent geometry    : angle       0.60737 /  0.32 ( 7644)
  SS BOND              : bond        0.00766 /  0.35 (    8)
  SS BOND              : angle       1.63375 /  1.20 (   16)
  hydrogen bonds       : bond        0.03669 /  2.46 (  181)
  hydrogen bonds       : angle       5.58700 /  3.81 (  513)
  link_BETA1-4         : bond        0.00236 /  0.12 (    1)
  link_BETA1-4         : angle       1.93090 /  1.02 (    3)
  link_BETA1-6         : bond        0.00012 /  0.01 (    1)
  link_BETA1-6         : angle       1.45775 /  0.78 (    3)
  link_NAG-ASN         : bond        0.00559 /  0.29 (    1)
  link_NAG-ASN         : angle       1.64454 /  0.96 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.214 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7375 (mp10)
REVERT: A   89 ASP cc_start: 0.8165 (m-30) cc_final: 0.7272 (t0)
REVERT: B  117 ILE cc_start: 0.6571 (tt) cc_final: 0.6187 (mm)
REVERT: M  357 ARG cc_start: 0.8752 (ttp-170) cc_final: 0.8392 (ttp-170)
REVERT: M  403 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.6819 (ttt-90)
REVERT: M  405 ASP cc_start: 0.7868 (p0) cc_final: 0.6857 (p0)
REVERT: M  461 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7271 (pp)
REVERT: M  574 ASP cc_start: 0.7862 (p0) cc_final: 0.7347 (p0)
REVERT: M  586 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7873 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 71
  average time/residue: 0.5143
  time to fit residues: 38.1692
Evaluate side-chains
  71 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  470 THR
Chi-restraints excluded: chain M residue  553 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 11 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    6.9990
   chunk 49 optimal weight:   20.0000
   chunk 62 optimal weight:    0.0020
   chunk 22 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.9190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 160 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.182579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.117954 restraints weight = 6057.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.49
r_work: 0.3265 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.1164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   5632  Z= 0.131
  Angle     :  0.585  10.490   7669  Z= 0.301
  Chirality :  0.045   0.141    858
  Planarity :  0.005   0.059    981
  Dihedral  :  4.672  18.096    764
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 14.47 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.75 (0.32), residues: 696
  helix: -4.28 (0.52), residues: 26
  sheet:  0.47 (0.33), residues: 268
  loop : -0.92 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  78 
 TYR   0.008   0.001   TYR B  37 
 PHE   0.014   0.001   PHE M 377 
 TRP   0.012   0.001   TRP A  47 
 HIS   0.005   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.13 ( 5621)
  covalent geometry    : angle       0.57967 /  0.30 ( 7644)
  SS BOND              : bond        0.00690 /  0.31 (    8)
  SS BOND              : angle       1.35347 /  0.99 (   16)
  hydrogen bonds       : bond        0.03304 /  2.20 (  181)
  hydrogen bonds       : angle       5.40159 /  3.69 (  513)
  link_BETA1-4         : bond        0.00244 /  0.13 (    1)
  link_BETA1-4         : angle       1.85123 /  0.97 (    3)
  link_BETA1-6         : bond        0.00068 /  0.04 (    1)
  link_BETA1-6         : angle       1.39477 /  0.75 (    3)
  link_NAG-ASN         : bond        0.00508 /  0.27 (    1)
  link_NAG-ASN         : angle       1.61132 /  0.94 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7520 (mp10)
REVERT: A   89 ASP cc_start: 0.8196 (m-30) cc_final: 0.7334 (t0)
REVERT: B  117 ILE cc_start: 0.6586 (tt) cc_final: 0.6213 (mm)
REVERT: B  166 GLN cc_start: 0.6913 (tt0) cc_final: 0.6576 (tt0)
REVERT: M  357 ARG cc_start: 0.8805 (ttp-170) cc_final: 0.8245 (ttp80)
REVERT: M  403 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6831 (ttt-90)
REVERT: M  405 ASP cc_start: 0.7958 (p0) cc_final: 0.6900 (p0)
REVERT: M  461 LEU cc_start: 0.7635 (OUTLIER) cc_final: 0.7140 (pp)
REVERT: M  465 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7967 (tt0)
REVERT: M  574 ASP cc_start: 0.7934 (p0) cc_final: 0.7401 (p0)
REVERT: M  586 ASP cc_start: 0.8282 (OUTLIER) cc_final: 0.7975 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 69
  average time/residue: 0.5191
  time to fit residues: 37.4089
Evaluate side-chains
  72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  465 GLU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 21 optimal weight:    0.0370
   chunk 49 optimal weight:   20.0000
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   chunk 50 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 58 optimal weight:    4.9990
   chunk 43 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   overall best weight:    0.5658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.183992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.119559 restraints weight = 6236.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.3438 rms_B_bonded: 2.51
r_work: 0.3291 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3156 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5632  Z= 0.103
  Angle     :  0.549   7.562   7669  Z= 0.283
  Chirality :  0.044   0.135    858
  Planarity :  0.005   0.056    981
  Dihedral  :  4.443  17.672    764
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 15.13 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.32), residues: 696
  helix: -4.15 (0.60), residues: 26
  sheet:  0.61 (0.33), residues: 262
  loop : -0.85 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  78 
 TYR   0.013   0.001   TYR M 489 
 PHE   0.010   0.001   PHE M 377 
 TRP   0.010   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.10 ( 5621)
  covalent geometry    : angle       0.54546 /  0.28 ( 7644)
  SS BOND              : bond        0.00585 /  0.25 (    8)
  SS BOND              : angle       1.00119 /  0.71 (   16)
  hydrogen bonds       : bond        0.02976 /  1.98 (  181)
  hydrogen bonds       : angle       5.27521 /  3.62 (  513)
  link_BETA1-4         : bond        0.00277 /  0.15 (    1)
  link_BETA1-4         : angle       1.73962 /  0.91 (    3)
  link_BETA1-6         : bond        0.00027 /  0.01 (    1)
  link_BETA1-6         : angle       1.32756 /  0.72 (    3)
  link_NAG-ASN         : bond        0.00418 /  0.22 (    1)
  link_NAG-ASN         : angle       1.64900 /  0.96 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7492 (mp10)
REVERT: A   89 ASP cc_start: 0.8189 (m-30) cc_final: 0.7345 (t0)
REVERT: B  117 ILE cc_start: 0.6504 (tt) cc_final: 0.6151 (mm)
REVERT: B  166 GLN cc_start: 0.6912 (tt0) cc_final: 0.6514 (tt0)
REVERT: M  357 ARG cc_start: 0.8798 (ttp-170) cc_final: 0.8253 (ttp80)
REVERT: M  403 ARG cc_start: 0.7934 (OUTLIER) cc_final: 0.6807 (ttt-90)
REVERT: M  405 ASP cc_start: 0.7966 (p0) cc_final: 0.6931 (p0)
REVERT: M  461 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7072 (pp)
REVERT: M  574 ASP cc_start: 0.7895 (p0) cc_final: 0.7346 (p0)
REVERT: M  586 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7956 (m-30)
  outliers start: 14
  outliers final: 5
  residues processed: 70
  average time/residue: 0.5494
  time to fit residues: 40.2268
Evaluate side-chains
  67 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 64 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   overall best weight:    1.9988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  59 ASN
B  27 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.183052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.119520 restraints weight = 6086.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 2.42
r_work: 0.3316 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   5632  Z= 0.239
  Angle     :  0.694   9.310   7669  Z= 0.360
  Chirality :  0.050   0.274    858
  Planarity :  0.006   0.063    981
  Dihedral  :  5.123  19.439    764
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.30 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.32), residues: 696
  helix: -4.23 (0.55), residues: 26
  sheet:  0.45 (0.33), residues: 268
  loop : -1.03 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  62 
 TYR   0.015   0.002   TYR M 380 
 PHE   0.024   0.002   PHE M 377 
 TRP   0.015   0.002   TRP A  50 
 HIS   0.007   0.002   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00582 /  0.24 ( 5621)
  covalent geometry    : angle       0.68597 /  0.36 ( 7644)
  SS BOND              : bond        0.01314 /  0.53 (    8)
  SS BOND              : angle       2.08245 /  1.52 (   16)
  hydrogen bonds       : bond        0.04181 /  2.81 (  181)
  hydrogen bonds       : angle       5.52797 /  3.75 (  513)
  link_BETA1-4         : bond        0.00245 /  0.13 (    1)
  link_BETA1-4         : angle       2.50090 /  1.33 (    3)
  link_BETA1-6         : bond        0.00239 /  0.13 (    1)
  link_BETA1-6         : angle       1.43711 /  0.76 (    3)
  link_NAG-ASN         : bond        0.00700 /  0.37 (    1)
  link_NAG-ASN         : angle       1.26958 /  0.74 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 60
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7975 (mp10)
REVERT: B  117 ILE cc_start: 0.6796 (tt) cc_final: 0.6458 (mm)
REVERT: M  403 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7167 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7638 (pp)
REVERT: M  574 ASP cc_start: 0.8154 (p0) cc_final: 0.7673 (p0)
REVERT: M  586 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.8172 (m-30)
  outliers start: 17
  outliers final: 7
  residues processed: 71
  average time/residue: 0.5510
  time to fit residues: 40.9317
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  105 GLU
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 54 optimal weight:    0.6980
   chunk 55 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0370
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    0.3980
   chunk 18 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.6262

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.185946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.123127 restraints weight = 6185.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 2.45
r_work: 0.3362 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3228 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3228
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5632  Z= 0.119
  Angle     :  0.627  11.694   7669  Z= 0.317
  Chirality :  0.046   0.302    858
  Planarity :  0.005   0.063    981
  Dihedral  :  4.714  19.432    764
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.45 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.69 (0.32), residues: 696
  helix: -4.09 (0.62), residues: 26
  sheet:  0.61 (0.33), residues: 262
  loop : -0.95 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG M 357 
 TYR   0.010   0.001   TYR M 380 
 PHE   0.014   0.001   PHE M 377 
 TRP   0.011   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5621)
  covalent geometry    : angle       0.61909 /  0.31 ( 7644)
  SS BOND              : bond        0.00900 /  0.35 (    8)
  SS BOND              : angle       1.90903 /  1.38 (   16)
  hydrogen bonds       : bond        0.03215 /  2.17 (  181)
  hydrogen bonds       : angle       5.27389 /  3.60 (  513)
  link_BETA1-4         : bond        0.00408 /  0.21 (    1)
  link_BETA1-4         : angle       1.80798 /  0.95 (    3)
  link_BETA1-6         : bond        0.00092 /  0.05 (    1)
  link_BETA1-6         : angle       1.33433 /  0.71 (    3)
  link_NAG-ASN         : bond        0.00466 /  0.25 (    1)
  link_NAG-ASN         : angle       1.55447 /  0.91 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 57
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7893 (mp10)
REVERT: B  117 ILE cc_start: 0.6712 (tt) cc_final: 0.6352 (mm)
REVERT: B  166 GLN cc_start: 0.7208 (tt0) cc_final: 0.6799 (tt0)
REVERT: M  357 ARG cc_start: 0.8901 (ttp-170) cc_final: 0.8499 (ttp80)
REVERT: M  403 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7049 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7253 (pp)
REVERT: M  574 ASP cc_start: 0.8138 (p0) cc_final: 0.7664 (p0)
REVERT: M  586 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8143 (m-30)
  outliers start: 15
  outliers final: 8
  residues processed: 67
  average time/residue: 0.5689
  time to fit residues: 39.7935
Evaluate side-chains
  68 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 34 optimal weight:   10.0000
   chunk 46 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 47 optimal weight:    6.9990
   chunk 3 optimal weight:    0.5980
   chunk 38 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 20 optimal weight:    9.9990
   overall best weight:    1.6386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.183540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.120152 restraints weight = 6061.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3479 rms_B_bonded: 2.44
r_work: 0.3329 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.1473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   5632  Z= 0.203
  Angle     :  0.683  11.176   7669  Z= 0.348
  Chirality :  0.049   0.297    858
  Planarity :  0.006   0.065    981
  Dihedral  :  4.986  19.154    764
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.78 %
    Favored  : 80.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.78 (0.32), residues: 696
  helix: -4.18 (0.57), residues: 26
  sheet:  0.51 (0.33), residues: 268
  loop : -0.99 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 357 
 TYR   0.012   0.002   TYR B  37 
 PHE   0.020   0.002   PHE M 377 
 TRP   0.014   0.001   TRP A  50 
 HIS   0.006   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.20 ( 5621)
  covalent geometry    : angle       0.67541 /  0.35 ( 7644)
  SS BOND              : bond        0.01257 /  0.49 (    8)
  SS BOND              : angle       2.04338 /  1.47 (   16)
  hydrogen bonds       : bond        0.03802 /  2.54 (  181)
  hydrogen bonds       : angle       5.41890 /  3.69 (  513)
  link_BETA1-4         : bond        0.00280 /  0.15 (    1)
  link_BETA1-4         : angle       2.26330 /  1.20 (    3)
  link_BETA1-6         : bond        0.00267 /  0.14 (    1)
  link_BETA1-6         : angle       1.37911 /  0.73 (    3)
  link_NAG-ASN         : bond        0.00620 /  0.33 (    1)
  link_NAG-ASN         : angle       1.31022 /  0.76 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 59
  time to evaluate  : 0.216 
Fit side-chains
REVERT: A   43 GLN cc_start: 0.8505 (mm-40) cc_final: 0.7965 (mp10)
REVERT: B   24 ARG cc_start: 0.7563 (ttm110) cc_final: 0.7276 (tpp-160)
REVERT: B  117 ILE cc_start: 0.6817 (tt) cc_final: 0.6446 (mm)
REVERT: B  166 GLN cc_start: 0.7224 (tt0) cc_final: 0.6854 (tt0)
REVERT: M  403 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7146 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7557 (pp)
REVERT: M  574 ASP cc_start: 0.8164 (p0) cc_final: 0.7682 (p0)
REVERT: M  586 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.8162 (m-30)
  outliers start: 15
  outliers final: 9
  residues processed: 71
  average time/residue: 0.5612
  time to fit residues: 41.5927
Evaluate side-chains
  70 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain B residue   34 LEU
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 46 optimal weight:    2.9990
   chunk 20 optimal weight:   20.0000
   chunk 64 optimal weight:    2.9990
   chunk 16 optimal weight:    6.9990
   chunk 40 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
M 505 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.182324 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.118808 restraints weight = 6079.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.44
r_work: 0.3313 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3180 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.1613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   5632  Z= 0.254
  Angle     :  0.760  13.544   7669  Z= 0.387
  Chirality :  0.051   0.329    858
  Planarity :  0.006   0.068    981
  Dihedral  :  5.423  24.911    764
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.76 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.32), residues: 696
  helix: -4.42 (0.47), residues: 26
  sheet:  0.27 (0.32), residues: 277
  loop : -1.10 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  78 
 TYR   0.016   0.002   TYR B  37 
 PHE   0.027   0.002   PHE M 377 
 TRP   0.016   0.002   TRP A  50 
 HIS   0.007   0.002   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00617 /  0.25 ( 5621)
  covalent geometry    : angle       0.75199 /  0.38 ( 7644)
  SS BOND              : bond        0.01459 /  0.57 (    8)
  SS BOND              : angle       2.15819 /  1.57 (   16)
  hydrogen bonds       : bond        0.04219 /  2.83 (  181)
  hydrogen bonds       : angle       5.62095 /  3.81 (  513)
  link_BETA1-4         : bond        0.00264 /  0.14 (    1)
  link_BETA1-4         : angle       2.45828 /  1.30 (    3)
  link_BETA1-6         : bond        0.00247 /  0.13 (    1)
  link_BETA1-6         : angle       1.48206 /  0.78 (    3)
  link_NAG-ASN         : bond        0.00677 /  0.36 (    1)
  link_NAG-ASN         : angle       1.27068 /  0.74 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 55
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8482 (mm-40) cc_final: 0.7931 (mp10)
REVERT: B  166 GLN cc_start: 0.7283 (tt0) cc_final: 0.6866 (tt0)
REVERT: M  357 ARG cc_start: 0.8929 (ttp-170) cc_final: 0.8576 (ttp-170)
REVERT: M  403 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7238 (ttt-90)
REVERT: M  461 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7674 (pp)
REVERT: M  586 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8214 (m-30)
  outliers start: 14
  outliers final: 8
  residues processed: 67
  average time/residue: 0.5763
  time to fit residues: 40.2245
Evaluate side-chains
  64 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 53
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 51 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 49 optimal weight:    0.3980
   overall best weight:    1.4386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.183813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.120635 restraints weight = 6057.265|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 2.44
r_work: 0.3334 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.3199 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5632  Z= 0.183
  Angle     :  0.697  13.001   7669  Z= 0.354
  Chirality :  0.048   0.288    858
  Planarity :  0.006   0.071    981
  Dihedral  :  5.147  24.117    764
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 18.26 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.32), residues: 696
  helix: -4.40 (0.48), residues: 26
  sheet:  0.51 (0.33), residues: 261
  loop : -1.14 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG M 357 
 TYR   0.011   0.001   TYR B  37 
 PHE   0.019   0.002   PHE M 377 
 TRP   0.013   0.001   TRP A  50 
 HIS   0.006   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00442 /  0.18 ( 5621)
  covalent geometry    : angle       0.69037 /  0.35 ( 7644)
  SS BOND              : bond        0.01196 /  0.47 (    8)
  SS BOND              : angle       1.87661 /  1.34 (   16)
  hydrogen bonds       : bond        0.03689 /  2.48 (  181)
  hydrogen bonds       : angle       5.48632 /  3.73 (  513)
  link_BETA1-4         : bond        0.00292 /  0.15 (    1)
  link_BETA1-4         : angle       2.10403 /  1.11 (    3)
  link_BETA1-6         : bond        0.00135 /  0.07 (    1)
  link_BETA1-6         : angle       1.42103 /  0.76 (    3)
  link_NAG-ASN         : bond        0.00585 /  0.31 (    1)
  link_NAG-ASN         : angle       1.35950 /  0.79 (    3)

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

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

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1392 Ramachandran restraints generated.
    696 Oldfield, 0 Emsley, 696 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 56
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7883 (mp10)
REVERT: B   24 ARG cc_start: 0.7555 (ttm110) cc_final: 0.7138 (tpp-160)
REVERT: B  166 GLN cc_start: 0.7265 (tt0) cc_final: 0.6836 (tt0)
REVERT: M  357 ARG cc_start: 0.8892 (ttp-170) cc_final: 0.8537 (ttp-170)
REVERT: M  403 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7015 (ttt-90)
REVERT: M  461 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7525 (pp)
REVERT: M  574 ASP cc_start: 0.8152 (p0) cc_final: 0.7820 (p0)
REVERT: M  586 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8145 (m-30)
  outliers start: 12
  outliers final: 8
  residues processed: 64
  average time/residue: 0.6044
  time to fit residues: 40.3359
Evaluate side-chains
  66 residues out of total 608 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 55
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 GLN
Chi-restraints excluded: chain B residue   64 SER
Chi-restraints excluded: chain B residue  132 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain M residue  332 ILE
Chi-restraints excluded: chain M residue  333 THR
Chi-restraints excluded: chain M residue  403 ARG
Chi-restraints excluded: chain M residue  461 LEU
Chi-restraints excluded: chain M residue  572 THR
Chi-restraints excluded: chain M residue  581 THR
Chi-restraints excluded: chain M residue  586 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 20 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 18 optimal weight:    6.9990
   chunk 3 optimal weight:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  27 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.185275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122354 restraints weight = 6137.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3505 rms_B_bonded: 2.45
r_work: 0.3355 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3221 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3221
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5632  Z= 0.134
  Angle     :  0.651  11.907   7669  Z= 0.329
  Chirality :  0.046   0.257    858
  Planarity :  0.005   0.068    981
  Dihedral  :  4.859  23.583    764
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 17.93 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 7.69 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.32), residues: 696
  helix: -4.31 (0.53), residues: 26
  sheet:  0.58 (0.34), residues: 261
  loop : -1.07 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG M 357 
 TYR   0.008   0.001   TYR B 140 
 PHE   0.015   0.001   PHE M 377 
 TRP   0.011   0.001   TRP A  47 
 HIS   0.004   0.001   HIS B  92 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.13 ( 5621)
  covalent geometry    : angle       0.64606 /  0.33 ( 7644)
  SS BOND              : bond        0.01036 /  0.40 (    8)
  SS BOND              : angle       1.54504 /  1.07 (   16)
  hydrogen bonds       : bond        0.03290 /  2.22 (  181)
  hydrogen bonds       : angle       5.33997 /  3.64 (  513)
  link_BETA1-4         : bond        0.00281 /  0.15 (    1)
  link_BETA1-4         : angle       1.89339 /  0.99 (    3)
  link_BETA1-6         : bond        0.00023 /  0.01 (    1)
  link_BETA1-6         : angle       1.32567 /  0.71 (    3)
  link_NAG-ASN         : bond        0.00506 /  0.27 (    1)
  link_NAG-ASN         : angle       1.40952 /  0.82 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2970.33 seconds
wall clock time: 51 minutes 8.42 seconds (3068.42 seconds total)