Starting phenix.real_space_refine
on Tue Feb  3 18:14:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9l6q_62862/02_2026/9l6q_62862_trim.cif"
  }
  resolution = 2.78
  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=   0.039
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      26      5.16       5
     C    3846      2.51       5
     N     947      2.21       5
     O    1032      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5853
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 5363
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 665, 5363
          Classifications: {'peptide': 665}
          Incomplete info: {'truncation_to_alanine': 36}
          Link IDs: {'PTRANS': 33, 'TRANS': 631}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 152
          Unresolved non-hydrogen angles: 185
          Unresolved non-hydrogen dihedrals: 125
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 9, 'GLN:plan1': 5, 'PHE:plan': 2}
          Unresolved non-hydrogen planarities: 97
    Chain: "C"
      Number of atoms: 238
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 238
          Classifications: {'peptide': 32}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 24
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 17
    Chain: "B"
      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: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 157
          Unusual residues: {'1L3': 1, '6PL': 2, 'CLR': 1}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   6PL A 801 " occ=0.73
      ... (48 atoms not shown)
      pdb=" P   6PL A 801 " occ=0.73
    residue:
      pdb=" N   6PL A 802 " occ=0.91
      ... (44 atoms not shown)
      pdb=" P   6PL A 802 " occ=0.91
  Time building chain proxies: 1.50, per 1000 atoms: 0.26
  Number of scatterers: 5853
  At special positions: 0
  Unit cell: (94.16, 105.93, 86.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      26     16.00
     P       2     15.00
     O    1032      8.00
     N     947      7.00
     C    3846      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  99 " - pdb=" SG  CYS A 450 " 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 B   1 " - " NAG B   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 550 "
      " NAG D   1 " - " ASN A 570 "
      " NAG E   1 " - " ASN A 605 "
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 125.7 milliseconds
  

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1322

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      58.2% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 39
    Processing helix  chain 'A' and resid 41 through 46
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 61 through 82
      Proline residue:  A  80  - end of helix
    Processing helix  chain 'A' and resid 84 through 86
      No H-bonds generated for 'chain 'A' and resid 84 through 86'
    Processing helix  chain 'A' and resid 87 through 92
    Processing helix  chain 'A' and resid 111 through 132
    Processing helix  chain 'A' and resid 134 through 153
      Proline residue:  A 145  - end of helix
      removed outlier: 3.697A  pdb=" N   ASP A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 154 through 157
      removed outlier: 3.540A  pdb=" N   TRP A 157 " --> pdb=" O   LYS A 154 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 154 through 157'
    Processing helix  chain 'A' and resid 158 through 174
      removed outlier: 3.970A  pdb=" N   PHE A 173 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 3.506A  pdb=" N   LEU A 185 " --> pdb=" O   SER A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 219
    Processing helix  chain 'A' and resid 220 through 225
    Processing helix  chain 'A' and resid 235 through 237
      No H-bonds generated for 'chain 'A' and resid 235 through 237'
    Processing helix  chain 'A' and resid 238 through 245
      removed outlier: 3.915A  pdb=" N   LEU A 244 " --> pdb=" O   PRO A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 254
    Processing helix  chain 'A' and resid 256 through 272
      removed outlier: 4.797A  pdb=" N   GLY A 267 " --> pdb=" O   ASP A 263 " (cutoff:3.500A)
      removed outlier: 5.067A  pdb=" N   PHE A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 294
    Processing helix  chain 'A' and resid 298 through 307
    Processing helix  chain 'A' and resid 308 through 310
      No H-bonds generated for 'chain 'A' and resid 308 through 310'
    Processing helix  chain 'A' and resid 314 through 323
    Processing helix  chain 'A' and resid 357 through 377
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 384 through 388
      removed outlier: 3.644A  pdb=" N   TYR A 387 " --> pdb=" O   THR A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 439
    Processing helix  chain 'A' and resid 440 through 455
    Processing helix  chain 'A' and resid 456 through 459
    Processing helix  chain 'A' and resid 487 through 491
    Processing helix  chain 'A' and resid 506 through 511
      Proline residue:  A 511  - end of helix
    Processing helix  chain 'A' and resid 512 through 523
    Processing helix  chain 'A' and resid 605 through 625
    Processing helix  chain 'A' and resid 654 through 675
    Processing helix  chain 'A' and resid 676 through 708
    Processing helix  chain 'A' and resid 712 through 724
    Processing helix  chain 'C' and resid 33 through 38
    Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 59
    Processing sheet with id=AA2, first strand: chain 'A' and resid 479 through 480
      removed outlier: 6.161A  pdb=" N   GLN A 464 " --> pdb=" O   TYR A 415 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   TYR A 415 " --> pdb=" O   GLN A 464 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   TYR A 466 " --> pdb=" O   ILE A 413 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   ILE A 413 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ASP A 468 " --> pdb=" O   VAL A 411 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   VAL A 411 " --> pdb=" O   ASP A 468 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   TRP A 470 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ILE A 413 " --> pdb=" O   LEU A 426 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   TYR A 425 " --> pdb=" O   LEU C  32 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 528 through 534
      removed outlier: 6.269A  pdb=" N   CYS A 598 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR A 551 " --> pdb=" O   LEU A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 539 through 543
      removed outlier: 3.891A  pdb=" N   VAL A 560 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    855 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.10

  Time building geometry restraints manager: 0.78 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 878
        1.31 -     1.43: 1760
        1.43 -     1.56: 3319
        1.56 -     1.68: 15
        1.68 -     1.81: 43
  Bond restraints: 6015
  Sorted by residual:
  bond pdb=" C02 1L3 A 804 "
       pdb=" C03 1L3 A 804 "
    ideal  model  delta    sigma   weight residual
    1.348  1.502 -0.154 2.00e-02 2.50e+03 5.90e+01
  bond pdb=" C16 1L3 A 804 "
       pdb=" C18 1L3 A 804 "
    ideal  model  delta    sigma   weight residual
    1.507  1.607 -0.100 2.00e-02 2.50e+03 2.48e+01
  bond pdb=" C04 1L3 A 804 "
       pdb=" C06 1L3 A 804 "
    ideal  model  delta    sigma   weight residual
    1.482  1.571 -0.089 2.00e-02 2.50e+03 1.99e+01
  bond pdb=" C21 1L3 A 804 "
       pdb=" C23 1L3 A 804 "
    ideal  model  delta    sigma   weight residual
    1.506  1.594 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C11 1L3 A 804 "
       pdb=" C12 1L3 A 804 "
    ideal  model  delta    sigma   weight residual
    1.480  1.565 -0.085 2.00e-02 2.50e+03 1.82e+01
  ... (remaining 6010 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     9.18: 8163
        9.18 -    18.36: 2
       18.36 -    27.54: 3
       27.54 -    36.72: 1
       36.72 -    45.90: 4
  Bond angle restraints: 8173
  Sorted by residual:
  angle pdb=" C15 1L3 A 804 "
        pdb=" C16 1L3 A 804 "
        pdb=" C18 1L3 A 804 "
      ideal   model   delta    sigma   weight residual
     119.97  165.87  -45.90 3.00e+00 1.11e-01 2.34e+02
  angle pdb=" C20 1L3 A 804 "
        pdb=" C21 1L3 A 804 "
        pdb=" C22 1L3 A 804 "
      ideal   model   delta    sigma   weight residual
     124.23  167.89  -43.66 3.00e+00 1.11e-01 2.12e+02
  angle pdb=" C25 1L3 A 804 "
        pdb=" C26 1L3 A 804 "
        pdb=" C27 1L3 A 804 "
      ideal   model   delta    sigma   weight residual
     124.55  166.45  -41.90 3.00e+00 1.11e-01 1.95e+02
  angle pdb=" C15 1L3 A 804 "
        pdb=" C16 1L3 A 804 "
        pdb=" C17 1L3 A 804 "
      ideal   model   delta    sigma   weight residual
     125.06   85.84   39.22 3.00e+00 1.11e-01 1.71e+02
  angle pdb=" C17 1L3 A 804 "
        pdb=" C16 1L3 A 804 "
        pdb=" C18 1L3 A 804 "
      ideal   model   delta    sigma   weight residual
     114.97   80.05   34.92 3.00e+00 1.11e-01 1.35e+02
  ... (remaining 8168 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.53: 3237
       19.53 -    39.05: 292
       39.05 -    58.58: 112
       58.58 -    78.10: 29
       78.10 -    97.63: 2
  Dihedral angle restraints: 3672
    sinusoidal: 1622
      harmonic: 2050
  Sorted by residual:
  dihedral pdb=" C26 1L3 A 804 "
           pdb=" C28 1L3 A 804 "
           pdb=" C29 1L3 A 804 "
           pdb=" C30 1L3 A 804 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -69.10   28.53  -97.63     1      3.00e+01 1.11e-03 1.21e+01
  dihedral pdb=" CA  CYS A 134 "
           pdb=" C   CYS A 134 "
           pdb=" N   TYR A 135 "
           pdb=" CA  TYR A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.65  -17.35     0      5.00e+00 4.00e-02 1.20e+01
  dihedral pdb=" CG  ARG A  68 "
           pdb=" CD  ARG A  68 "
           pdb=" NE  ARG A  68 "
           pdb=" CZ  ARG A  68 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.25   42.25     2      1.50e+01 4.44e-03 9.64e+00
  ... (remaining 3669 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 799
       0.066 -    0.131: 84
       0.131 -    0.197: 18
       0.197 -    0.262: 2
       0.262 -    0.328: 2
  Chirality restraints: 905
  Sorted by residual:
  chirality pdb=" CB  VAL A 460 "
            pdb=" CA  VAL A 460 "
            pdb=" CG1 VAL A 460 "
            pdb=" CG2 VAL A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.30   -0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN A 605 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C5  BMA E   3 "
            pdb=" C4  BMA E   3 "
            pdb=" C6  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.50    0.23 2.00e-01 2.50e+01 1.31e+00
  ... (remaining 902 not shown)

  Planarity restraints: 1007
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 455 "    0.033 5.00e-02 4.00e+02   5.03e-02 4.05e+00
        pdb=" N   PRO A 456 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO A 456 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 456 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 437 "   -0.007 2.00e-02 2.50e+03   1.49e-02 2.23e+00
        pdb=" C   TRP A 437 "    0.026 2.00e-02 2.50e+03
        pdb=" O   TRP A 437 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   LYS A 438 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C19 1L3 A 804 "    0.008 2.00e-02 2.50e+03   1.33e-02 2.22e+00
        pdb=" C20 1L3 A 804 "   -0.021 2.00e-02 2.50e+03
        pdb=" C21 1L3 A 804 "    0.017 2.00e-02 2.50e+03
        pdb=" C22 1L3 A 804 "   -0.008 2.00e-02 2.50e+03
        pdb=" C23 1L3 A 804 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1004 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 615
        2.74 -     3.28: 5898
        3.28 -     3.82: 10692
        3.82 -     4.36: 13037
        4.36 -     4.90: 21837
  Nonbonded interactions: 52079
  Sorted by model distance:
  nonbonded pdb=" CE2 PHE A 294 "
            pdb=" C01 1L3 A 804 "
     model   vdw
     2.206 3.760
  nonbonded pdb=" O   ASN A 177 "
            pdb=" OG  SER A 181 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" OD2 ASP A 153 "
            pdb=" OG1 THR A 155 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASP A  60 "
            pdb=" OH  TYR A 200 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" OH  TYR A 211 "
            pdb=" NE2 HIS A 287 "
     model   vdw
     2.327 3.120
  ... (remaining 52074 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 'B'
  selection = chain 'D'
}

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=0.73 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:             0.780
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.710
  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:6.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
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      :  0.006   0.154   6023  Z= 0.352
  Angle     :  1.332  45.897   8196  Z= 0.543
  Chirality :  0.048   0.328    905
  Planarity :  0.004   0.050   1004
  Dihedral  : 17.484  97.626   2347
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.29 %
    Favored  : 80.51 %
  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 are not related in a simple way.
  whole:  1.11 (0.32), residues: 689
  helix:  1.46 (0.28), residues: 343
  sheet: -0.15 (0.53), residues: 74
  loop :  0.22 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 498 
 TYR   0.017   0.002   TYR A 425 
 PHE   0.014   0.001   PHE A  67 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00649 ( 6015)
  covalent geometry    : angle       1.33055 ( 8173)
  SS BOND              : bond        0.00191 (    1)
  SS BOND              : angle       0.37539 (    2)
  hydrogen bonds       : bond        0.12925 (  300)
  hydrogen bonds       : angle       5.83074 (  855)
  link_BETA1-4         : bond        0.00642 (    4)
  link_BETA1-4         : angle       2.27549 (   12)
  link_NAG-ASN         : bond        0.00795 (    3)
  link_NAG-ASN         : angle       1.18037 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 PHE cc_start: 0.8238 (t80) cc_final: 0.8037 (t80)
REVERT: A  422 GLU cc_start: 0.7543 (tt0) cc_final: 0.7249 (tm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 94
  average time/residue: 0.6072
  time to fit residues: 59.4943
Evaluate side-chains
  87 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  343 CYS
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  721 THR
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** 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 = 0.3561 r_free = 0.3561 target = 0.142037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.116871 restraints weight = 6213.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 1.61
r_work: 0.3079 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2932
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.73   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2931 r_free = 0.2931    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2931
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.0802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6023  Z= 0.163
  Angle     :  0.950  41.181   8196  Z= 0.376
  Chirality :  0.040   0.167    905
  Planarity :  0.005   0.043   1004
  Dihedral  : 11.780  85.818   1090
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.10 %
    Favored  : 81.02 %
  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 are not related in a simple way.
  whole:  1.38 (0.32), residues: 689
  helix:  1.60 (0.28), residues: 350
  sheet: -0.10 (0.51), residues: 75
  loop :  0.44 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 498 
 TYR   0.014   0.002   TYR A 425 
 PHE   0.017   0.001   PHE A 299 
 TRP   0.011   0.002   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 6015)
  covalent geometry    : angle       0.94805 ( 8173)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.40225 (    2)
  hydrogen bonds       : bond        0.03903 (  300)
  hydrogen bonds       : angle       5.05575 (  855)
  link_BETA1-4         : bond        0.00661 (    4)
  link_BETA1-4         : angle       1.88015 (   12)
  link_NAG-ASN         : bond        0.00844 (    3)
  link_NAG-ASN         : angle       1.18974 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8104 (tt0)
REVERT: A  281 PHE cc_start: 0.8350 (t80) cc_final: 0.8121 (t80)
REVERT: A  417 ASP cc_start: 0.8009 (t0) cc_final: 0.7691 (t0)
REVERT: A  422 GLU cc_start: 0.7912 (tt0) cc_final: 0.7690 (tm-30)
REVERT: A  459 ASN cc_start: 0.7923 (OUTLIER) cc_final: 0.7714 (t0)
REVERT: A  679 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8087 (mm-30)
REVERT: A  713 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7670 (mm)
  outliers start: 17
  outliers final: 7
  residues processed: 101
  average time/residue: 0.5464
  time to fit residues: 57.6033
Evaluate side-chains
  102 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue   82 GLU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  459 ASN
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.7980
   chunk 52 optimal weight:    2.9990
   chunk 24 optimal weight:    0.1980
   chunk 32 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** 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 = 0.3530 r_free = 0.3530 target = 0.140086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.113373 restraints weight = 6244.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.48
r_work: 0.3085 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2955 r_free = 0.2955    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6023  Z= 0.144
  Angle     :  0.930  40.369   8196  Z= 0.363
  Chirality :  0.039   0.164    905
  Planarity :  0.004   0.044   1004
  Dihedral  : 10.889  86.283   1084
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.46 %
    Favored  : 79.83 %
  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 are not related in a simple way.
  whole:  1.52 (0.32), residues: 689
  helix:  1.67 (0.28), residues: 351
  sheet:  0.05 (0.52), residues: 75
  loop :  0.55 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.013   0.001   TYR A 425 
 PHE   0.012   0.001   PHE A 299 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 6015)
  covalent geometry    : angle       0.92850 ( 8173)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.34559 (    2)
  hydrogen bonds       : bond        0.03637 (  300)
  hydrogen bonds       : angle       4.75847 (  855)
  link_BETA1-4         : bond        0.00647 (    4)
  link_BETA1-4         : angle       1.74540 (   12)
  link_NAG-ASN         : bond        0.00754 (    3)
  link_NAG-ASN         : angle       1.12053 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: A  260 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8100 (tp)
REVERT: A  422 GLU cc_start: 0.7936 (tt0) cc_final: 0.7696 (tm-30)
REVERT: A  679 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7997 (mm-30)
REVERT: A  683 ARG cc_start: 0.7173 (OUTLIER) cc_final: 0.6726 (mmp80)
REVERT: A  713 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7607 (mm)
  outliers start: 16
  outliers final: 7
  residues processed: 102
  average time/residue: 0.5551
  time to fit residues: 59.1398
Evaluate side-chains
  100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  611 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 0 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0870
   chunk 36 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.167686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.142192 restraints weight = 6279.653|
|-----------------------------------------------------------------------------|
r_work (start): 0.3750 rms_B_bonded: 1.61
r_work: 0.3632 rms_B_bonded: 2.19 restraints_weight: 0.5000
r_work: 0.3512 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3500
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.76   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3500 r_free = 0.3500    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3500
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6023  Z= 0.133
  Angle     :  0.922  41.138   8196  Z= 0.359
  Chirality :  0.039   0.157    905
  Planarity :  0.004   0.044   1004
  Dihedral  : 10.602  85.325   1082
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 18.98 %
    Favored  : 77.97 %
  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 are not related in a simple way.
  whole:  1.63 (0.32), residues: 689
  helix:  1.82 (0.28), residues: 345
  sheet:  0.22 (0.54), residues: 75
  loop :  0.51 (0.41), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.013   0.001   TYR A 162 
 PHE   0.011   0.001   PHE A  67 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6015)
  covalent geometry    : angle       0.92032 ( 8173)
  SS BOND              : bond        0.00215 (    1)
  SS BOND              : angle       0.35593 (    2)
  hydrogen bonds       : bond        0.03440 (  300)
  hydrogen bonds       : angle       4.65992 (  855)
  link_BETA1-4         : bond        0.00621 (    4)
  link_BETA1-4         : angle       1.78207 (   12)
  link_NAG-ASN         : bond        0.00744 (    3)
  link_NAG-ASN         : angle       1.14383 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  422 GLU cc_start: 0.7847 (tt0) cc_final: 0.7608 (tm-30)
REVERT: A  679 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7952 (mm-30)
REVERT: A  683 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6754 (mmp80)
REVERT: A  713 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7559 (mm)
  outliers start: 18
  outliers final: 8
  residues processed: 103
  average time/residue: 0.4640
  time to fit residues: 49.9221
Evaluate side-chains
  100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    6.9990
   chunk 51 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 17 optimal weight:    0.6980
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 170 GLN
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.141222 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.114408 restraints weight = 6291.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.47
r_work: 0.3080 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2943 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2952
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6023  Z= 0.159
  Angle     :  0.936  41.017   8196  Z= 0.365
  Chirality :  0.040   0.161    905
  Planarity :  0.004   0.046   1004
  Dihedral  : 10.551  86.721   1082
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 19.66 %
    Favored  : 76.95 %
  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 are not related in a simple way.
  whole:  1.58 (0.33), residues: 689
  helix:  1.71 (0.28), residues: 351
  sheet:  0.24 (0.54), residues: 75
  loop :  0.55 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.016   0.002   TYR A 425 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.011   0.001   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 6015)
  covalent geometry    : angle       0.93412 ( 8173)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.46030 (    2)
  hydrogen bonds       : bond        0.03532 (  300)
  hydrogen bonds       : angle       4.62033 (  855)
  link_BETA1-4         : bond        0.00583 (    4)
  link_BETA1-4         : angle       1.74784 (   12)
  link_NAG-ASN         : bond        0.00744 (    3)
  link_NAG-ASN         : angle       1.23883 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
REVERT: A  422 GLU cc_start: 0.7842 (tt0) cc_final: 0.7547 (tm-30)
REVERT: A  679 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7887 (mm-30)
REVERT: A  683 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6675 (mmp80)
REVERT: A  713 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7581 (mm)
  outliers start: 20
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4876
  time to fit residues: 50.4201
Evaluate side-chains
  103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain A residue  713 LEU
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0050
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 15 optimal weight:    0.4980
   chunk 57 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.6396

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN
** C  38 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 = 0.3557 r_free = 0.3557 target = 0.141771 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.115096 restraints weight = 6241.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 1.46
r_work: 0.3101 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.77   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8072
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6023  Z= 0.143
  Angle     :  0.927  40.852   8196  Z= 0.360
  Chirality :  0.039   0.161    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.434  85.005   1082
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 20.00 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.32), residues: 689
  helix:  1.72 (0.28), residues: 351
  sheet:  0.35 (0.56), residues: 75
  loop :  0.40 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 108 
 TYR   0.016   0.001   TYR A 425 
 PHE   0.022   0.001   PHE A 281 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6015)
  covalent geometry    : angle       0.92498 ( 8173)
  SS BOND              : bond        0.00213 (    1)
  SS BOND              : angle       0.45267 (    2)
  hydrogen bonds       : bond        0.03421 (  300)
  hydrogen bonds       : angle       4.57781 (  855)
  link_BETA1-4         : bond        0.00600 (    4)
  link_BETA1-4         : angle       1.74982 (   12)
  link_NAG-ASN         : bond        0.00738 (    3)
  link_NAG-ASN         : angle       1.21264 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  108 ARG cc_start: 0.8032 (mtp85) cc_final: 0.7503 (mtp85)
REVERT: A  273 ASP cc_start: 0.8100 (m-30) cc_final: 0.7774 (m-30)
REVERT: A  422 GLU cc_start: 0.7818 (tt0) cc_final: 0.7468 (tm-30)
REVERT: A  679 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7885 (mm-30)
REVERT: A  683 ARG cc_start: 0.7200 (OUTLIER) cc_final: 0.6744 (mmp80)
  outliers start: 19
  outliers final: 12
  residues processed: 99
  average time/residue: 0.5533
  time to fit residues: 57.2139
Evaluate side-chains
  103 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 18 optimal weight:    0.2980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  81 GLN
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
C  34 HIS
C  36 ASN
C  38 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.142793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.117719 restraints weight = 6157.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3201 rms_B_bonded: 1.60
r_work: 0.3065 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6023  Z= 0.166
  Angle     :  0.937  40.933   8196  Z= 0.365
  Chirality :  0.040   0.163    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.462  85.119   1082
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 21.19 %
    Favored  : 76.10 %
  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 are not related in a simple way.
  whole:  1.48 (0.32), residues: 689
  helix:  1.68 (0.28), residues: 351
  sheet:  0.30 (0.55), residues: 75
  loop :  0.38 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.018   0.002   TYR A 425 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.011   0.002   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6015)
  covalent geometry    : angle       0.93501 ( 8173)
  SS BOND              : bond        0.00234 (    1)
  SS BOND              : angle       0.45661 (    2)
  hydrogen bonds       : bond        0.03504 (  300)
  hydrogen bonds       : angle       4.59244 (  855)
  link_BETA1-4         : bond        0.00565 (    4)
  link_BETA1-4         : angle       1.73023 (   12)
  link_NAG-ASN         : bond        0.00746 (    3)
  link_NAG-ASN         : angle       1.28979 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.8102 (m-30) cc_final: 0.7797 (OUTLIER)
REVERT: A  422 GLU cc_start: 0.7822 (tt0) cc_final: 0.7463 (tm-30)
REVERT: A  679 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7872 (mm-30)
REVERT: A  683 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6711 (mmp80)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.5547
  time to fit residues: 55.0541
Evaluate side-chains
  100 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 60 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 15 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.141581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.116229 restraints weight = 6117.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 1.61
r_work: 0.3095 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6023  Z= 0.166
  Angle     :  0.941  40.855   8196  Z= 0.368
  Chirality :  0.040   0.166    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.508  82.745   1082
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 20.85 %
    Favored  : 76.27 %
  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 are not related in a simple way.
  whole:  1.47 (0.32), residues: 689
  helix:  1.67 (0.28), residues: 351
  sheet:  0.31 (0.56), residues: 75
  loop :  0.38 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 108 
 TYR   0.019   0.002   TYR A 425 
 PHE   0.012   0.001   PHE A 286 
 TRP   0.011   0.002   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 6015)
  covalent geometry    : angle       0.93884 ( 8173)
  SS BOND              : bond        0.00235 (    1)
  SS BOND              : angle       0.44267 (    2)
  hydrogen bonds       : bond        0.03519 (  300)
  hydrogen bonds       : angle       4.59236 (  855)
  link_BETA1-4         : bond        0.00551 (    4)
  link_BETA1-4         : angle       1.73504 (   12)
  link_NAG-ASN         : bond        0.00744 (    3)
  link_NAG-ASN         : angle       1.30738 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.8095 (m-30) cc_final: 0.7782 (OUTLIER)
REVERT: A  281 PHE cc_start: 0.8405 (t80) cc_final: 0.8123 (t80)
REVERT: A  422 GLU cc_start: 0.7838 (tt0) cc_final: 0.7504 (tm-30)
REVERT: A  679 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7881 (mm-30)
REVERT: A  683 ARG cc_start: 0.7214 (OUTLIER) cc_final: 0.6785 (mmp80)
  outliers start: 17
  outliers final: 12
  residues processed: 92
  average time/residue: 0.5273
  time to fit residues: 50.6998
Evaluate side-chains
  98 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  520 LYS
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0370
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.134644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.107171 restraints weight = 6738.281|
|-----------------------------------------------------------------------------|
r_work (start): 0.3143 rms_B_bonded: 1.57
r_work: 0.3047 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.78   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.1609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6023  Z= 0.162
  Angle     :  0.941  40.924   8196  Z= 0.367
  Chirality :  0.040   0.160    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.495  85.654   1082
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.02 %
    Favored  : 75.93 %
  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 are not related in a simple way.
  whole:  1.51 (0.32), residues: 689
  helix:  1.67 (0.28), residues: 351
  sheet:  0.32 (0.55), residues: 75
  loop :  0.44 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.021   0.002   TYR A 425 
 PHE   0.011   0.001   PHE A  67 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.006   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6015)
  covalent geometry    : angle       0.93888 ( 8173)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       0.43708 (    2)
  hydrogen bonds       : bond        0.03483 (  300)
  hydrogen bonds       : angle       4.57983 (  855)
  link_BETA1-4         : bond        0.00547 (    4)
  link_BETA1-4         : angle       1.71967 (   12)
  link_NAG-ASN         : bond        0.00727 (    3)
  link_NAG-ASN         : angle       1.33715 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  273 ASP cc_start: 0.8077 (m-30) cc_final: 0.7806 (OUTLIER)
REVERT: A  281 PHE cc_start: 0.8342 (t80) cc_final: 0.8043 (t80)
REVERT: A  422 GLU cc_start: 0.7782 (tt0) cc_final: 0.7441 (tm-30)
REVERT: A  679 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7846 (mm-30)
REVERT: A  683 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.6759 (mmp80)
REVERT: A  715 GLN cc_start: 0.6898 (tt0) cc_final: 0.6608 (tp-100)
REVERT: C   30 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7940 (t)
  outliers start: 18
  outliers final: 11
  residues processed: 94
  average time/residue: 0.4739
  time to fit residues: 46.6842
Evaluate side-chains
  98 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 1 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
C  36 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.135381 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.107994 restraints weight = 6700.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3149 rms_B_bonded: 1.57
r_work: 0.3053 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.79   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3033 r_free = 0.3033    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3033
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6023  Z= 0.151
  Angle     :  0.939  40.777   8196  Z= 0.367
  Chirality :  0.040   0.161    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.463  86.951   1082
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 21.86 %
    Favored  : 75.76 %
  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 are not related in a simple way.
  whole:  1.53 (0.32), residues: 689
  helix:  1.69 (0.28), residues: 351
  sheet:  0.34 (0.55), residues: 75
  loop :  0.45 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 108 
 TYR   0.020   0.002   TYR A 425 
 PHE   0.010   0.001   PHE A  67 
 TRP   0.012   0.001   TRP A 198 
 HIS   0.005   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6015)
  covalent geometry    : angle       0.93719 ( 8173)
  SS BOND              : bond        0.00216 (    1)
  SS BOND              : angle       0.41556 (    2)
  hydrogen bonds       : bond        0.03429 (  300)
  hydrogen bonds       : angle       4.56679 (  855)
  link_BETA1-4         : bond        0.00545 (    4)
  link_BETA1-4         : angle       1.69650 (   12)
  link_NAG-ASN         : bond        0.00697 (    3)
  link_NAG-ASN         : angle       1.33820 (    9)

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

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

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1378 Ramachandran restraints generated.
    689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.208 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 PHE cc_start: 0.8335 (t80) cc_final: 0.8053 (t80)
REVERT: A  422 GLU cc_start: 0.7771 (tt0) cc_final: 0.7436 (tm-30)
REVERT: A  679 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7786 (mm-30)
REVERT: A  683 ARG cc_start: 0.7199 (OUTLIER) cc_final: 0.6742 (mmp80)
REVERT: A  715 GLN cc_start: 0.6845 (tt0) cc_final: 0.6545 (tp-100)
REVERT: C   30 VAL cc_start: 0.8107 (p) cc_final: 0.7819 (t)
  outliers start: 14
  outliers final: 10
  residues processed: 93
  average time/residue: 0.5195
  time to fit residues: 50.6966
Evaluate side-chains
  99 residues out of total 631 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  277 SER
Chi-restraints excluded: chain A residue  472 SER
Chi-restraints excluded: chain A residue  473 ILE
Chi-restraints excluded: chain A residue  524 ASP
Chi-restraints excluded: chain A residue  578 LYS
Chi-restraints excluded: chain A residue  615 LEU
Chi-restraints excluded: chain A residue  679 GLU
Chi-restraints excluded: chain A residue  683 ARG
Chi-restraints excluded: chain C residue   51 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 4 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 58 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.134305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.106858 restraints weight = 6674.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3128 rms_B_bonded: 1.57
r_work: 0.3033 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2910 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8039
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6023  Z= 0.174
  Angle     :  0.949  40.815   8196  Z= 0.372
  Chirality :  0.041   0.158    905
  Planarity :  0.004   0.047   1004
  Dihedral  : 10.556  89.211   1082
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 22.03 %
    Favored  : 75.76 %
  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 are not related in a simple way.
  whole:  1.47 (0.32), residues: 689
  helix:  1.64 (0.28), residues: 351
  sheet:  0.28 (0.55), residues: 75
  loop :  0.43 (0.40), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 108 
 TYR   0.024   0.002   TYR A 425 
 PHE   0.012   0.001   PHE A  67 
 TRP   0.011   0.002   TRP A 198 
 HIS   0.007   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 ( 6015)
  covalent geometry    : angle       0.94747 ( 8173)
  SS BOND              : bond        0.00242 (    1)
  SS BOND              : angle       0.47263 (    2)
  hydrogen bonds       : bond        0.03539 (  300)
  hydrogen bonds       : angle       4.59867 (  855)
  link_BETA1-4         : bond        0.00528 (    4)
  link_BETA1-4         : angle       1.69179 (   12)
  link_NAG-ASN         : bond        0.00695 (    3)
  link_NAG-ASN         : angle       1.38680 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2203.41 seconds
wall clock time: 38 minutes 15.56 seconds (2295.56 seconds total)