Starting phenix.real_space_refine
on Wed Sep 17 06:06:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yht_39300/09_2025/8yht_39300.map"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     C    3724      2.51       5
     N     972      2.21       5
     O    1129      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-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5845
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 5323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5323
          Classifications: {'peptide': 663}
          Link IDs: {'PTRANS': 26, 'TRANS': 636}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 326
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 40, 326
          Classifications: {'peptide': 40}
          Link IDs: {'PTRANS': 1, 'TRANS': 38}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.64, per 1000 atoms: 0.28
  Number of scatterers: 5845
  At special positions: 0
  Unit cell: (52.456, 102.92, 111.552, 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      20     16.00
     O    1129      8.00
     N     972      7.00
     C    3724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 651 " - pdb=" SG  CYS A 696 " 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 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  52 "
      " NAG A 802 " - " ASN A  57 "
      " NAG A 803 " - " ASN A 124 "
      " NAG A 804 " - " ASN A 252 "
      " NAG A 805 " - " ASN A 275 "
      " NAG A 806 " - " ASN A 291 "
      " NAG C   1 " - " ASN A 247 "
      " NAG D   1 " - " ASN A 265 "
      " NAG E   1 " - " ASN A 398 "
      " NAG F   1 " - " ASN A 413 "
  Time building additional restraints: 0.51
  Conformation dependent library (CDL) restraints added in 143.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1354

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 6 sheets defined
      15.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 73
      removed outlier: 3.681A  pdb=" N   ARG A  73 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 4.612A  pdb=" N   ILE A 193 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.850A  pdb=" N   TRP A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 319
      removed outlier: 4.166A  pdb=" N   LEU A 318 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   HIS A 319 " --> pdb=" O   HIS A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 405
      removed outlier: 3.591A  pdb=" N   THR A 400 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   PHE A 401 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   VAL A 402 " --> pdb=" O   GLU A 399 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   SER A 403 " --> pdb=" O   THR A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 546
      removed outlier: 3.726A  pdb=" N   TRP A 546 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 662
    Processing helix  chain 'A' and resid 680 through 684
      removed outlier: 3.569A  pdb=" N   TYR A 683 " --> pdb=" O   PRO A 680 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   HIS A 684 " --> pdb=" O   PRO A 681 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 680 through 684'
    Processing helix  chain 'A' and resid 687 through 691
    Processing helix  chain 'B' and resid 2 through 21
      removed outlier: 3.713A  pdb=" N   LEU B  11 " --> pdb=" O   VAL B   7 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 40
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 4.413A  pdb=" N   THR A  29 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 81
      removed outlier: 6.629A  pdb=" N   LEU A 104 " --> pdb=" O   HIS A 129 " (cutoff:3.500A)
      removed outlier: 7.622A  pdb=" N   LEU A 128 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335
      removed outlier: 6.879A  pdb=" N   ILE A 310 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS A 345 " --> pdb=" O   GLN A 311 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU A 313 " --> pdb=" O   LYS A 345 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
    Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412
      removed outlier: 3.699A  pdb=" N   MET A 486 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   SER A 514 " --> pdb=" O   LEU A 487 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446
      removed outlier: 6.915A  pdb=" N   GLN A 445 " --> pdb=" O   GLN A 470 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LYS A 493 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)

    69 hydrogen bonds defined for protein.
    162 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: 0.63

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1874
        1.34 -     1.46: 1285
        1.46 -     1.58: 2773
        1.58 -     1.70: 0
        1.70 -     1.82: 29
  Bond restraints: 5961
  Sorted by residual:
  bond pdb=" N   ASP A 292 "
       pdb=" CA  ASP A 292 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.29e-02 6.01e+03 5.29e+00
  bond pdb=" N   PHE A 294 "
       pdb=" CA  PHE A 294 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.62e+00
  bond pdb=" N   SER A 293 "
       pdb=" CA  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.454  1.480 -0.026 1.31e-02 5.83e+03 3.96e+00
  bond pdb=" CA  SER A 293 "
       pdb=" CB  SER A 293 "
    ideal  model  delta    sigma   weight residual
    1.534  1.503  0.031 1.60e-02 3.91e+03 3.88e+00
  bond pdb=" C1  NAG A 805 "
       pdb=" O5  NAG A 805 "
    ideal  model  delta    sigma   weight residual
    1.406  1.441 -0.035 2.00e-02 2.50e+03 3.06e+00
  ... (remaining 5956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.57: 7741
        1.57 -     3.14: 291
        3.14 -     4.71: 43
        4.71 -     6.28: 9
        6.28 -     7.85: 1
  Bond angle restraints: 8085
  Sorted by residual:
  angle pdb=" N   ALA A 491 "
        pdb=" CA  ALA A 491 "
        pdb=" C   ALA A 491 "
      ideal   model   delta    sigma   weight residual
     108.63  103.06    5.57 1.60e+00 3.91e-01 1.21e+01
  angle pdb=" CA  SER A 293 "
        pdb=" C   SER A 293 "
        pdb=" O   SER A 293 "
      ideal   model   delta    sigma   weight residual
     121.68  117.84    3.84 1.18e+00 7.18e-01 1.06e+01
  angle pdb=" N   GLU B  15 "
        pdb=" CA  GLU B  15 "
        pdb=" CB  GLU B  15 "
      ideal   model   delta    sigma   weight residual
     110.16  114.68   -4.52 1.48e+00 4.57e-01 9.32e+00
  angle pdb=" CA  VAL A 144 "
        pdb=" C   VAL A 144 "
        pdb=" N   LYS A 145 "
      ideal   model   delta    sigma   weight residual
     116.60  120.92   -4.32 1.45e+00 4.76e-01 8.89e+00
  angle pdb=" C   PHE A 294 "
        pdb=" N   ALA A 295 "
        pdb=" CA  ALA A 295 "
      ideal   model   delta    sigma   weight residual
     120.99  115.82    5.17 1.86e+00 2.89e-01 7.72e+00
  ... (remaining 8080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.41: 3453
       21.41 -    42.83: 290
       42.83 -    64.24: 32
       64.24 -    85.66: 8
       85.66 -   107.07: 8
  Dihedral angle restraints: 3791
    sinusoidal: 1721
      harmonic: 2070
  Sorted by residual:
  dihedral pdb=" CB  CYS A 651 "
           pdb=" SG  CYS A 651 "
           pdb=" SG  CYS A 696 "
           pdb=" CB  CYS A 696 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   12.59   80.41     1      1.00e+01 1.00e-02 8.00e+01
  dihedral pdb=" CB  CYS A 649 "
           pdb=" SG  CYS A 649 "
           pdb=" SG  CYS A 677 "
           pdb=" CB  CYS A 677 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   34.69   58.31     1      1.00e+01 1.00e-02 4.56e+01
  dihedral pdb=" CA  ASN A  61 "
           pdb=" C   ASN A  61 "
           pdb=" N   GLN A  62 "
           pdb=" CA  GLN A  62 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.29   22.71     0      5.00e+00 4.00e-02 2.06e+01
  ... (remaining 3788 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 634
       0.044 -    0.088: 275
       0.088 -    0.131: 59
       0.131 -    0.175: 6
       0.175 -    0.219: 2
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" C1  NAG A 806 "
            pdb=" ND2 ASN A 291 "
            pdb=" C2  NAG A 806 "
            pdb=" O5  NAG A 806 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN A 413 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 8.50e-01
  chirality pdb=" CB  ILE A 591 "
            pdb=" CA  ILE A 591 "
            pdb=" CG1 ILE A 591 "
            pdb=" CG2 ILE A 591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.63e-01
  ... (remaining 973 not shown)

  Planarity restraints: 1024
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 668 "   -0.028 5.00e-02 4.00e+02   4.26e-02 2.91e+00
        pdb=" N   PRO A 669 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 669 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 669 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 291 "    0.008 2.00e-02 2.50e+03   1.68e-02 2.81e+00
        pdb=" C   ASN A 291 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   ASN A 291 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 292 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 631 "    0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO A 632 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 632 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 632 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1021 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 52
        2.58 -     3.16: 4839
        3.16 -     3.74: 8712
        3.74 -     4.32: 12137
        4.32 -     4.90: 19597
  Nonbonded interactions: 45337
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 416 "
            pdb=" OE2 GLU B  19 "
     model   vdw
     1.995 3.120
  nonbonded pdb=" O   GLU A 363 "
            pdb=" OG  SER A 389 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 387 "
            pdb=" OG1 THR A 415 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" O   ASP A 648 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" NZ  LYS A 201 "
            pdb=" OE2 GLU A 203 "
     model   vdw
     2.285 3.120
  ... (remaining 45332 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             4.560
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.880
  Find NCS groups from input model:        0.040
  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:8.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6217
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   0.036   5979  Z= 0.195
  Angle     :  0.708   7.848   8135  Z= 0.361
  Chirality :  0.047   0.219    976
  Planarity :  0.004   0.043   1014
  Dihedral  : 15.457 107.071   2425
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 12.05 %
    Favored  : 87.80 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  0.31 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.01 (0.32), residues: 697
  helix: -0.67 (0.62), residues: 75
  sheet: -4.11 (0.49), residues: 74
  loop : -2.04 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 689 
 TYR   0.020   0.002   TYR B   6 
 PHE   0.009   0.001   PHE A 119 
 TRP   0.022   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 5961)
  covalent geometry    : angle       0.69978 ( 8085)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       1.10141 (    8)
  hydrogen bonds       : bond        0.23794 (   69)
  hydrogen bonds       : angle       6.97953 (  162)
  link_BETA1-4         : bond        0.00333 (    4)
  link_BETA1-4         : angle       0.89383 (   12)
  link_NAG-ASN         : bond        0.00291 (   10)
  link_NAG-ASN         : angle       1.78916 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 157
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 0
  residues processed: 160
  average time/residue: 0.4371
  time to fit residues: 73.8007
Evaluate side-chains
  68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.3980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 109 ASN
A 169 GLN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 ASN
A 365 ASN
A 538 GLN
A 541 ASN
A 550 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4757 r_free = 0.4757 target = 0.144405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4383 r_free = 0.4383 target = 0.116723 restraints weight = 14336.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.4342 rms_B_bonded: 5.46
r_work (final): 0.4342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   5979  Z= 0.183
  Angle     :  0.804  10.433   8135  Z= 0.385
  Chirality :  0.050   0.441    976
  Planarity :  0.004   0.049   1014
  Dihedral  : 10.169  83.946   1032
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.48 %
    Favored  : 87.52 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 15.36 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.92 (0.31), residues: 697
  helix: -0.59 (0.60), residues: 69
  sheet: -4.00 (0.46), residues: 82
  loop : -1.93 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 394 
 TYR   0.019   0.002   TYR A 307 
 PHE   0.013   0.002   PHE A 574 
 TRP   0.012   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 ( 5961)
  covalent geometry    : angle       0.78620 ( 8085)
  SS BOND              : bond        0.00690 (    4)
  SS BOND              : angle       1.63066 (    8)
  hydrogen bonds       : bond        0.05859 (   69)
  hydrogen bonds       : angle       6.13946 (  162)
  link_BETA1-4         : bond        0.00414 (    4)
  link_BETA1-4         : angle       1.55433 (   12)
  link_NAG-ASN         : bond        0.00807 (   10)
  link_NAG-ASN         : angle       2.66313 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8028 (mm)
REVERT: A  245 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8318 (mm)
REVERT: A  328 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6896 (t0)
REVERT: A  330 LYS cc_start: 0.7753 (tttm) cc_final: 0.7220 (tttp)
REVERT: A  347 ASP cc_start: 0.6207 (m-30) cc_final: 0.5772 (m-30)
REVERT: A  361 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6530 (t0)
REVERT: A  363 GLU cc_start: 0.6806 (tp30) cc_final: 0.5780 (tp30)
REVERT: A  440 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8015 (mp)
REVERT: A  521 ILE cc_start: 0.8740 (mp) cc_final: 0.8540 (mp)
REVERT: A  525 MET cc_start: 0.4816 (OUTLIER) cc_final: 0.3970 (mpt)
REVERT: A  585 LEU cc_start: 0.7974 (mt) cc_final: 0.7719 (mm)
REVERT: A  613 LYS cc_start: 0.8665 (mttt) cc_final: 0.8307 (mmmt)
REVERT: B   27 ARG cc_start: 0.9329 (mmp80) cc_final: 0.9025 (mmp80)
  outliers start: 25
  outliers final: 10
  residues processed: 95
  average time/residue: 0.3277
  time to fit residues: 33.5724
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  154 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  361 ASN
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  490 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 44 optimal weight:    0.2980
   chunk 2 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 47 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:   10.0000
   chunk 46 optimal weight:    0.0370
   chunk 8 optimal weight:    5.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    1.3462

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

Flipped N/Q/H residues before XYZ refinement:
** A  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4743 r_free = 0.4743 target = 0.143274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4369 r_free = 0.4369 target = 0.115774 restraints weight = 14092.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.4325 rms_B_bonded: 5.40
r_work (final): 0.4325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6698
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5979  Z= 0.159
  Angle     :  0.758   7.927   8135  Z= 0.362
  Chirality :  0.049   0.462    976
  Planarity :  0.004   0.051   1014
  Dihedral  :  8.709  65.618   1032
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 18.59 %
    Favored  : 77.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.31), residues: 697
  helix: -0.47 (0.60), residues: 68
  sheet: -4.12 (0.45), residues: 80
  loop : -1.88 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 394 
 TYR   0.016   0.002   TYR B   5 
 PHE   0.012   0.001   PHE A 333 
 TRP   0.011   0.001   TRP A 452 
 HIS   0.006   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 ( 5961)
  covalent geometry    : angle       0.74590 ( 8085)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       1.06756 (    8)
  hydrogen bonds       : bond        0.05367 (   69)
  hydrogen bonds       : angle       5.82930 (  162)
  link_BETA1-4         : bond        0.00496 (    4)
  link_BETA1-4         : angle       1.36866 (   12)
  link_NAG-ASN         : bond        0.00843 (   10)
  link_NAG-ASN         : angle       2.23595 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.229 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8089 (mm)
REVERT: A  201 LYS cc_start: 0.8202 (tmmm) cc_final: 0.7880 (ptmm)
REVERT: A  330 LYS cc_start: 0.7778 (tttm) cc_final: 0.7335 (ttmp)
REVERT: A  347 ASP cc_start: 0.6294 (m-30) cc_final: 0.5881 (m-30)
REVERT: A  363 GLU cc_start: 0.6811 (tp30) cc_final: 0.5869 (tp30)
REVERT: A  525 MET cc_start: 0.4886 (OUTLIER) cc_final: 0.4001 (mpt)
REVERT: A  575 ASP cc_start: 0.7455 (m-30) cc_final: 0.7123 (m-30)
REVERT: A  585 LEU cc_start: 0.8129 (mt) cc_final: 0.7841 (mm)
REVERT: A  613 LYS cc_start: 0.8612 (mttt) cc_final: 0.8222 (mmmt)
REVERT: B    8 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8920 (ptpt)
REVERT: B   27 ARG cc_start: 0.9317 (mmp80) cc_final: 0.9054 (mmp80)
  outliers start: 24
  outliers final: 11
  residues processed: 84
  average time/residue: 0.3641
  time to fit residues: 32.8679
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  122 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 13 optimal weight:    9.9990
   chunk 69 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 52 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  96 GLN
** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** 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 = 0.4738 r_free = 0.4738 target = 0.142453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.115360 restraints weight = 14634.525|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 5.50
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6733
moved from start:          0.3583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5979  Z= 0.159
  Angle     :  0.777  17.602   8135  Z= 0.359
  Chirality :  0.048   0.438    976
  Planarity :  0.004   0.051   1014
  Dihedral  :  7.580  53.989   1032
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 20.43 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.88 (0.31), residues: 697
  helix: -0.42 (0.60), residues: 69
  sheet: -4.17 (0.46), residues: 75
  loop : -1.93 (0.27), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 394 
 TYR   0.019   0.002   TYR B   6 
 PHE   0.011   0.001   PHE A 119 
 TRP   0.011   0.001   TRP A 452 
 HIS   0.003   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 5961)
  covalent geometry    : angle       0.76391 ( 8085)
  SS BOND              : bond        0.00878 (    4)
  SS BOND              : angle       1.42628 (    8)
  hydrogen bonds       : bond        0.05005 (   69)
  hydrogen bonds       : angle       5.67242 (  162)
  link_BETA1-4         : bond        0.00529 (    4)
  link_BETA1-4         : angle       1.56321 (   12)
  link_NAG-ASN         : bond        0.00755 (   10)
  link_NAG-ASN         : angle       2.17622 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 68
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  119 PHE cc_start: 0.7430 (p90) cc_final: 0.7058 (p90)
REVERT: A  201 LYS cc_start: 0.8181 (tmmm) cc_final: 0.7665 (tmmm)
REVERT: A  330 LYS cc_start: 0.7760 (tttm) cc_final: 0.7369 (tttp)
REVERT: A  347 ASP cc_start: 0.6499 (m-30) cc_final: 0.6054 (m-30)
REVERT: A  363 GLU cc_start: 0.6837 (tp30) cc_final: 0.6083 (tp30)
REVERT: A  525 MET cc_start: 0.5042 (OUTLIER) cc_final: 0.3899 (mpt)
REVERT: A  575 ASP cc_start: 0.7543 (m-30) cc_final: 0.7210 (m-30)
REVERT: A  585 LEU cc_start: 0.8147 (mt) cc_final: 0.7879 (mm)
REVERT: A  613 LYS cc_start: 0.8609 (mttt) cc_final: 0.8180 (mmmt)
REVERT: B    8 LYS cc_start: 0.9238 (mtmm) cc_final: 0.9002 (mtmm)
REVERT: B   27 ARG cc_start: 0.9315 (mmp80) cc_final: 0.9038 (mmp80)
  outliers start: 25
  outliers final: 12
  residues processed: 85
  average time/residue: 0.3673
  time to fit residues: 33.5025
Evaluate side-chains
  68 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 55
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   95 CYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  570 GLU
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 8 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0670
   chunk 54 optimal weight:    0.0000
   chunk 1 optimal weight:   10.0000
   chunk 14 optimal weight:    0.5980
   chunk 64 optimal weight:    8.9990
   chunk 63 optimal weight:    0.3980
   chunk 35 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.3722

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

Flipped N/Q/H residues before XYZ refinement:
A 133 ASN
A 207 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4766 r_free = 0.4766 target = 0.144594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.118353 restraints weight = 14458.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.4369 rms_B_bonded: 5.42
r_work (final): 0.4369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6676
moved from start:          0.3819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   5979  Z= 0.130
  Angle     :  0.761  10.069   8135  Z= 0.355
  Chirality :  0.050   0.655    976
  Planarity :  0.004   0.048   1014
  Dihedral  :  7.105  54.017   1032
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  9.90 %
    Favored  : 89.96 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 21.66 %
    Favored  : 74.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (0.31), residues: 697
  helix: -0.35 (0.60), residues: 69
  sheet: -3.97 (0.48), residues: 75
  loop : -1.96 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.023   0.002   TYR B   6 
 PHE   0.009   0.001   PHE A 119 
 TRP   0.009   0.001   TRP A 452 
 HIS   0.009   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 5961)
  covalent geometry    : angle       0.74208 ( 8085)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       1.88817 (    8)
  hydrogen bonds       : bond        0.04709 (   69)
  hydrogen bonds       : angle       5.36733 (  162)
  link_BETA1-4         : bond        0.00549 (    4)
  link_BETA1-4         : angle       1.83505 (   12)
  link_NAG-ASN         : bond        0.00581 (   10)
  link_NAG-ASN         : angle       2.50767 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 67
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ASN cc_start: 0.8680 (m110) cc_final: 0.6971 (t0)
REVERT: A  201 LYS cc_start: 0.8180 (tmmm) cc_final: 0.7662 (tmmm)
REVERT: A  330 LYS cc_start: 0.7657 (tttm) cc_final: 0.7235 (tppt)
REVERT: A  347 ASP cc_start: 0.6486 (m-30) cc_final: 0.6049 (m-30)
REVERT: A  437 ASP cc_start: 0.6554 (t70) cc_final: 0.6319 (t0)
REVERT: A  525 MET cc_start: 0.5159 (OUTLIER) cc_final: 0.4266 (mpt)
REVERT: A  575 ASP cc_start: 0.7563 (m-30) cc_final: 0.7201 (m-30)
REVERT: A  613 LYS cc_start: 0.8437 (mttt) cc_final: 0.8087 (mmmt)
REVERT: B    8 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8965 (mtmm)
REVERT: B   15 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8684 (mm-30)
REVERT: B   27 ARG cc_start: 0.9305 (mmp80) cc_final: 0.9031 (mmp80)
REVERT: B   31 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8711 (mm-30)
  outliers start: 24
  outliers final: 10
  residues processed: 83
  average time/residue: 0.3571
  time to fit residues: 31.8611
Evaluate side-chains
  70 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  667 ASN
Chi-restraints excluded: chain B residue   30 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 59 optimal weight:    4.9990
   chunk 21 optimal weight:   10.0000
   chunk 57 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4708 r_free = 0.4708 target = 0.140552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.113762 restraints weight = 14826.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.4286 rms_B_bonded: 5.48
r_work (final): 0.4286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6806
moved from start:          0.4077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   5979  Z= 0.182
  Angle     :  0.794   9.314   8135  Z= 0.370
  Chirality :  0.050   0.522    976
  Planarity :  0.005   0.057   1014
  Dihedral  :  6.881  54.121   1032
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.91 %
    Favored  : 87.09 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 21.66 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.84 (0.31), residues: 697
  helix: -0.44 (0.60), residues: 69
  sheet: -3.91 (0.50), residues: 74
  loop : -1.94 (0.27), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.028   0.003   TYR B   5 
 PHE   0.023   0.001   PHE A 119 
 TRP   0.010   0.001   TRP A 452 
 HIS   0.004   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5961)
  covalent geometry    : angle       0.77804 ( 8085)
  SS BOND              : bond        0.00324 (    4)
  SS BOND              : angle       0.75752 (    8)
  hydrogen bonds       : bond        0.05390 (   69)
  hydrogen bonds       : angle       5.40756 (  162)
  link_BETA1-4         : bond        0.00460 (    4)
  link_BETA1-4         : angle       1.68402 (   12)
  link_NAG-ASN         : bond        0.00751 (   10)
  link_NAG-ASN         : angle       2.55138 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 68
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.8186 (tmmm) cc_final: 0.7680 (tmmm)
REVERT: A  330 LYS cc_start: 0.7666 (tttm) cc_final: 0.7230 (tppt)
REVERT: A  347 ASP cc_start: 0.6656 (m-30) cc_final: 0.6166 (m-30)
REVERT: A  525 MET cc_start: 0.5330 (OUTLIER) cc_final: 0.4333 (mpt)
REVERT: A  575 ASP cc_start: 0.7641 (m-30) cc_final: 0.7374 (m-30)
REVERT: A  613 LYS cc_start: 0.8628 (mttt) cc_final: 0.8325 (mppt)
  outliers start: 28
  outliers final: 15
  residues processed: 88
  average time/residue: 0.2979
  time to fit residues: 28.3943
Evaluate side-chains
  80 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 64
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 13 optimal weight:   10.0000
   chunk 64 optimal weight:    8.9990
   chunk 8 optimal weight:   10.0000
   chunk 66 optimal weight:    0.9990
   chunk 44 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4684 r_free = 0.4684 target = 0.138645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.111733 restraints weight = 14882.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.4259 rms_B_bonded: 5.44
r_work (final): 0.4259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6854
moved from start:          0.4366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   5979  Z= 0.200
  Angle     :  0.832  10.841   8135  Z= 0.386
  Chirality :  0.050   0.502    976
  Planarity :  0.005   0.052   1014
  Dihedral  :  6.842  53.960   1032
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  4.76 %
    Allowed  : 23.50 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.02 (0.31), residues: 697
  helix: -0.71 (0.57), residues: 75
  sheet: -4.04 (0.49), residues: 73
  loop : -2.06 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.035   0.003   TYR B   6 
 PHE   0.011   0.001   PHE A 557 
 TRP   0.012   0.001   TRP A 452 
 HIS   0.004   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 5961)
  covalent geometry    : angle       0.81684 ( 8085)
  SS BOND              : bond        0.00478 (    4)
  SS BOND              : angle       1.30858 (    8)
  hydrogen bonds       : bond        0.05571 (   69)
  hydrogen bonds       : angle       5.58100 (  162)
  link_BETA1-4         : bond        0.00351 (    4)
  link_BETA1-4         : angle       1.60741 (   12)
  link_NAG-ASN         : bond        0.00748 (   10)
  link_NAG-ASN         : angle       2.52517 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 65
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7630 (tmmm)
REVERT: A  330 LYS cc_start: 0.7709 (tttm) cc_final: 0.7274 (tppt)
REVERT: A  347 ASP cc_start: 0.6806 (m-30) cc_final: 0.6332 (m-30)
REVERT: A  525 MET cc_start: 0.5475 (OUTLIER) cc_final: 0.4512 (mpt)
REVERT: A  575 ASP cc_start: 0.7695 (m-30) cc_final: 0.7443 (m-30)
REVERT: A  613 LYS cc_start: 0.8698 (mttt) cc_final: 0.8285 (mmmt)
REVERT: B    8 LYS cc_start: 0.9218 (mttp) cc_final: 0.8947 (pttm)
  outliers start: 31
  outliers final: 16
  residues processed: 87
  average time/residue: 0.3081
  time to fit residues: 29.0389
Evaluate side-chains
  78 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 THR
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  413 ASN
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 8 optimal weight:    8.9990
   chunk 1 optimal weight:    9.9990
   chunk 13 optimal weight:   10.0000
   chunk 54 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.141027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.114697 restraints weight = 14504.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.4316 rms_B_bonded: 5.43
r_work (final): 0.4316
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.4519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5979  Z= 0.134
  Angle     :  0.811  11.341   8135  Z= 0.366
  Chirality :  0.049   0.492    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.536  54.008   1032
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.33 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 25.96 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.88 (0.31), residues: 697
  helix: -0.54 (0.60), residues: 69
  sheet: -3.90 (0.52), residues: 74
  loop : -1.97 (0.26), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.038   0.003   TYR B   6 
 PHE   0.027   0.001   PHE A 119 
 TRP   0.012   0.001   TRP A 546 
 HIS   0.002   0.000   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 5961)
  covalent geometry    : angle       0.79617 ( 8085)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       0.85732 (    8)
  hydrogen bonds       : bond        0.04953 (   69)
  hydrogen bonds       : angle       5.41105 (  162)
  link_BETA1-4         : bond        0.00426 (    4)
  link_BETA1-4         : angle       1.55393 (   12)
  link_NAG-ASN         : bond        0.00672 (   10)
  link_NAG-ASN         : angle       2.48108 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 67
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.8191 (tmmm) cc_final: 0.7558 (tmmm)
REVERT: A  330 LYS cc_start: 0.7681 (tttm) cc_final: 0.7272 (tppt)
REVERT: A  347 ASP cc_start: 0.6702 (m-30) cc_final: 0.6226 (m-30)
REVERT: A  440 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7717 (tt)
REVERT: A  525 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.4541 (mpt)
REVERT: A  575 ASP cc_start: 0.7687 (m-30) cc_final: 0.7435 (m-30)
REVERT: A  613 LYS cc_start: 0.8565 (mttt) cc_final: 0.8167 (mmmt)
REVERT: B    5 TYR cc_start: 0.8292 (t80) cc_final: 0.7975 (t80)
REVERT: B    8 LYS cc_start: 0.9167 (mttp) cc_final: 0.8950 (pttp)
REVERT: B   19 GLU cc_start: 0.8858 (tm-30) cc_final: 0.8432 (OUTLIER)
REVERT: B   27 ARG cc_start: 0.9315 (mmp80) cc_final: 0.8972 (mmp80)
  outliers start: 22
  outliers final: 16
  residues processed: 83
  average time/residue: 0.3500
  time to fit residues: 31.3467
Evaluate side-chains
  79 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  440 LEU
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 69 optimal weight:   10.0000
   chunk 37 optimal weight:    2.9990
   chunk 13 optimal weight:    8.9990
   chunk 24 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 8 optimal weight:   10.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
A 172 ASN
** A 259 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 = 0.4686 r_free = 0.4686 target = 0.138465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.111853 restraints weight = 14657.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.4272 rms_B_bonded: 5.39
r_work (final): 0.4272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6857
moved from start:          0.4712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   5979  Z= 0.198
  Angle     :  0.870  13.518   8135  Z= 0.398
  Chirality :  0.052   0.637    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.683  54.058   1032
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 14.06 %
    Favored  : 85.80 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 25.65 %
    Favored  : 70.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.95 (0.31), residues: 697
  helix: -0.59 (0.60), residues: 69
  sheet: -4.03 (0.49), residues: 78
  loop : -1.98 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.025   0.003   TYR B   6 
 PHE   0.011   0.001   PHE A 557 
 TRP   0.011   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00474 ( 5961)
  covalent geometry    : angle       0.84353 ( 8085)
  SS BOND              : bond        0.00407 (    4)
  SS BOND              : angle       1.02424 (    8)
  hydrogen bonds       : bond        0.05602 (   69)
  hydrogen bonds       : angle       5.59756 (  162)
  link_BETA1-4         : bond        0.00502 (    4)
  link_BETA1-4         : angle       1.59911 (   12)
  link_NAG-ASN         : bond        0.00945 (   10)
  link_NAG-ASN         : angle       3.47484 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.8513 (p90) cc_final: 0.7716 (p90)
REVERT: A  201 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7753 (tmmm)
REVERT: A  330 LYS cc_start: 0.7669 (tttm) cc_final: 0.7281 (tppt)
REVERT: A  347 ASP cc_start: 0.6821 (m-30) cc_final: 0.6366 (m-30)
REVERT: A  525 MET cc_start: 0.5539 (OUTLIER) cc_final: 0.4555 (mpt)
REVERT: A  575 ASP cc_start: 0.7706 (m-30) cc_final: 0.7441 (m-30)
  outliers start: 24
  outliers final: 14
  residues processed: 77
  average time/residue: 0.3479
  time to fit residues: 28.8220
Evaluate side-chains
  71 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 55
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 54 optimal weight:    0.2980
   chunk 42 optimal weight:    0.4980
   chunk 23 optimal weight:    9.9990
   chunk 57 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 68 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 1 optimal weight:   10.0000
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.141582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.115562 restraints weight = 14549.294|
|-----------------------------------------------------------------------------|
r_work (start): 0.4340 rms_B_bonded: 5.43
r_work (final): 0.4340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6767
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   5979  Z= 0.133
  Angle     :  0.852  13.242   8135  Z= 0.386
  Chirality :  0.054   0.772    976
  Planarity :  0.004   0.051   1014
  Dihedral  :  6.676  53.955   1032
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.19 %
    Favored  : 88.67 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 26.88 %
    Favored  : 70.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.84 (0.31), residues: 697
  helix: -0.53 (0.61), residues: 69
  sheet: -3.85 (0.58), residues: 67
  loop : -1.97 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 394 
 TYR   0.016   0.002   TYR B  16 
 PHE   0.028   0.001   PHE A 119 
 TRP   0.013   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 5961)
  covalent geometry    : angle       0.82751 ( 8085)
  SS BOND              : bond        0.00302 (    4)
  SS BOND              : angle       0.81384 (    8)
  hydrogen bonds       : bond        0.05224 (   69)
  hydrogen bonds       : angle       5.54192 (  162)
  link_BETA1-4         : bond        0.00382 (    4)
  link_BETA1-4         : angle       1.46264 (   12)
  link_NAG-ASN         : bond        0.01015 (   10)
  link_NAG-ASN         : angle       3.34881 (   30)

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

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

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1394 Ramachandran restraints generated.
    697 Oldfield, 0 Emsley, 697 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 62
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 PHE cc_start: 0.8470 (p90) cc_final: 0.7679 (p90)
REVERT: A  201 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7743 (tmmm)
REVERT: A  330 LYS cc_start: 0.7714 (tttm) cc_final: 0.7295 (tppt)
REVERT: A  347 ASP cc_start: 0.6774 (m-30) cc_final: 0.6304 (m-30)
REVERT: A  525 MET cc_start: 0.5584 (OUTLIER) cc_final: 0.4646 (mpt)
REVERT: A  575 ASP cc_start: 0.7698 (m-30) cc_final: 0.7434 (m-30)
REVERT: B   27 ARG cc_start: 0.9321 (mmp80) cc_final: 0.9000 (mmp80)
  outliers start: 19
  outliers final: 15
  residues processed: 77
  average time/residue: 0.3676
  time to fit residues: 30.4419
Evaluate side-chains
  75 residues out of total 651 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 58
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   86 THR
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  201 LYS
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  370 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  448 THR
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 ILE
Chi-restraints excluded: chain A residue  525 MET
Chi-restraints excluded: chain A residue  529 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  667 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    4.9990
   chunk 30 optimal weight:    3.9990
   chunk 13 optimal weight:    0.8980
   chunk 21 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4702 r_free = 0.4702 target = 0.139732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.113399 restraints weight = 14462.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 5.37
r_work (final): 0.4295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6830
moved from start:          0.4947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   5979  Z= 0.172
  Angle     :  0.858  14.528   8135  Z= 0.396
  Chirality :  0.056   0.875    976
  Planarity :  0.004   0.050   1014
  Dihedral  :  6.459  54.176   1032
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.20 %
    Favored  : 86.66 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 27.34 %
    Favored  : 69.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.86 (0.31), residues: 697
  helix: -0.53 (0.62), residues: 69
  sheet: -3.74 (0.52), residues: 80
  loop : -1.94 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  12 
 TYR   0.025   0.002   TYR B  16 
 PHE   0.017   0.001   PHE A  71 
 TRP   0.011   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 108 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 5961)
  covalent geometry    : angle       0.82534 ( 8085)
  SS BOND              : bond        0.00363 (    4)
  SS BOND              : angle       0.92658 (    8)
  hydrogen bonds       : bond        0.05543 (   69)
  hydrogen bonds       : angle       5.63317 (  162)
  link_BETA1-4         : bond        0.00491 (    4)
  link_BETA1-4         : angle       1.33989 (   12)
  link_NAG-ASN         : bond        0.00928 (   10)
  link_NAG-ASN         : angle       3.87730 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2025.22 seconds
wall clock time: 35 minutes 28.47 seconds (2128.47 seconds total)