Starting phenix.real_space_refine
on Tue Mar  3 13:12:56 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjl_23877/03_2026/7mjl_23877.map"
  }
  resolution = 2.95
  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=   0.024
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    3037      2.51       5
     N     793      2.21       5
     O     939      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4788
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1564
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 197, 1564
          Classifications: {'peptide': 197}
          Link IDs: {'PTRANS': 11, 'TRANS': 185}
    Chain: "H"
      Number of atoms: 1585
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1585
          Classifications: {'peptide': 211}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 1625
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1625
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.21, per 1000 atoms: 0.25
  Number of scatterers: 4788
  At special positions: 0
  Unit cell: (75, 62, 129, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     939      8.00
     N     793      7.00
     C    3037      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 144 " - pdb=" SG  CYS H 200 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 134 " - pdb=" SG  CYS L 194 " 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
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
  Time building additional restraints: 0.22
  Conformation dependent library (CDL) restraints added in 220.1 milliseconds
  

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 14 sheets defined
      9.5% alpha, 42.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.873A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 384 through 389
      removed outlier: 4.098A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'H' and resid 28 through 32
      removed outlier: 3.697A  pdb=" N   ASN H  32 " --> pdb=" O   VAL H  29 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 73 through 75
      No H-bonds generated for 'chain 'H' and resid 73 through 75'
    Processing helix  chain 'H' and resid 86 through 90
      removed outlier: 3.734A  pdb=" N   THR H  90 " --> pdb=" O   ALA H  87 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.652A  pdb=" N   ASP L  82 " --> pdb=" O   GLN L  79 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL L  83 " --> pdb=" O   ALA L  80 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'L' and resid 79 through 83'
    Processing helix  chain 'L' and resid 121 through 126
      removed outlier: 3.641A  pdb=" N   LYS L 126 " --> pdb=" O   ASP L 122 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.613A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.594A  pdb=" N   THR H  77 " --> pdb=" O   HIS H  72 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12
      removed outlier: 4.318A  pdb=" N   TYR H  33 " --> pdb=" O   GLY H  98 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.921A  pdb=" N   TYR H 106 " --> pdb=" O   ARG H  97 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.135A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128
      removed outlier: 4.135A  pdb=" N   GLY H 143 " --> pdb=" O   LEU H 128 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   TYR H 180 " --> pdb=" O   ASP H 148 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158
      removed outlier: 4.055A  pdb=" N   TYR H 198 " --> pdb=" O   VAL H 215 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS H 213 " --> pdb=" O   CYS H 200 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.632A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.390A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU L  33 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   TYR L  49 " --> pdb=" O   LEU L  33 " (cutoff:3.500A)
      removed outlier: 6.670A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.390A  pdb=" N   LEU L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118
      removed outlier: 5.437A  pdb=" N   SER L 131 " --> pdb=" O   LEU L 181 " (cutoff:3.500A)
      removed outlier: 7.403A  pdb=" N   LEU L 181 " --> pdb=" O   SER L 131 " (cutoff:3.500A)
      removed outlier: 5.606A  pdb=" N   VAL L 133 " --> pdb=" O   LEU L 179 " (cutoff:3.500A)
      removed outlier: 7.298A  pdb=" N   LEU L 179 " --> pdb=" O   VAL L 133 " (cutoff:3.500A)
      removed outlier: 5.490A  pdb=" N   LEU L 135 " --> pdb=" O   SER L 177 " (cutoff:3.500A)
      removed outlier: 7.289A  pdb=" N   SER L 177 " --> pdb=" O   LEU L 135 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ASN L 137 " --> pdb=" O   LEU L 175 " (cutoff:3.500A)
      removed outlier: 7.248A  pdb=" N   LEU L 175 " --> pdb=" O   ASN L 137 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'L' and resid 145 through 150

    181 hydrogen bonds defined for protein.
    453 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.75

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1500
        1.34 -     1.46: 1168
        1.46 -     1.58: 2219
        1.58 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 4909
  Sorted by residual:
  bond pdb=" N   ASP H 101 "
       pdb=" CA  ASP H 101 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 5.98e+00
  bond pdb=" C1  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.60e+00
  bond pdb=" C   LYS H 205 "
       pdb=" N   PRO H 206 "
    ideal  model  delta    sigma   weight residual
    1.336  1.355 -0.019 1.20e-02 6.94e+03 2.59e+00
  bond pdb=" CB  ASN H  73 "
       pdb=" CG  ASN H  73 "
    ideal  model  delta    sigma   weight residual
    1.516  1.552 -0.036 2.50e-02 1.60e+03 2.05e+00
  bond pdb=" C   SER L  94 "
       pdb=" N   PRO L  95 "
    ideal  model  delta    sigma   weight residual
    1.334  1.366 -0.032 2.34e-02 1.83e+03 1.87e+00
  ... (remaining 4904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 6337
        1.67 -     3.33: 284
        3.33 -     5.00: 44
        5.00 -     6.66: 11
        6.66 -     8.33: 6
  Bond angle restraints: 6682
  Sorted by residual:
  angle pdb=" C   GLY H 100 "
        pdb=" N   ASP H 101 "
        pdb=" CA  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     121.54  129.87   -8.33 1.91e+00 2.74e-01 1.90e+01
  angle pdb=" C   TRP L  50 "
        pdb=" N   ALA L  51 "
        pdb=" CA  ALA L  51 "
      ideal   model   delta    sigma   weight residual
     121.54  128.33   -6.79 1.91e+00 2.74e-01 1.26e+01
  angle pdb=" C   PHE A 515 "
        pdb=" N   GLU A 516 "
        pdb=" CA  GLU A 516 "
      ideal   model   delta    sigma   weight residual
     122.94  117.62    5.32 1.50e+00 4.44e-01 1.26e+01
  angle pdb=" CA  ASP H 101 "
        pdb=" CB  ASP H 101 "
        pdb=" CG  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     112.60  115.97   -3.37 1.00e+00 1.00e+00 1.14e+01
  angle pdb=" CA  LYS H 210 "
        pdb=" CB  LYS H 210 "
        pdb=" CG  LYS H 210 "
      ideal   model   delta    sigma   weight residual
     114.10  120.52   -6.42 2.00e+00 2.50e-01 1.03e+01
  ... (remaining 6677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.53: 2713
       16.53 -    33.06: 151
       33.06 -    49.59: 38
       49.59 -    66.12: 11
       66.12 -    82.65: 8
  Dihedral angle restraints: 2921
    sinusoidal: 1124
      harmonic: 1797
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.49  -74.49     1      1.00e+01 1.00e-02 7.03e+01
  dihedral pdb=" CB  CYS H 144 "
           pdb=" SG  CYS H 144 "
           pdb=" SG  CYS H 200 "
           pdb=" CB  CYS H 200 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.05  -51.05     1      1.00e+01 1.00e-02 3.56e+01
  dihedral pdb=" CA  HIS H  72 "
           pdb=" C   HIS H  72 "
           pdb=" N   ASN H  73 "
           pdb=" CA  ASN H  73 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.47  -22.53     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 2918 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 506
       0.047 -    0.094: 159
       0.094 -    0.142: 61
       0.142 -    0.189: 9
       0.189 -    0.236: 2
  Chirality restraints: 737
  Sorted by residual:
  chirality pdb=" CA  ASP H 101 "
            pdb=" N   ASP H 101 "
            pdb=" C   ASP H 101 "
            pdb=" CB  ASP H 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  ILE A 332 "
            pdb=" CA  ILE A 332 "
            pdb=" CG1 ILE A 332 "
            pdb=" CG2 ILE A 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CB  ILE L 117 "
            pdb=" CA  ILE L 117 "
            pdb=" CG1 ILE L 117 "
            pdb=" CG2 ILE L 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.18 2.00e-01 2.50e+01 8.17e-01
  ... (remaining 734 not shown)

  Planarity restraints: 859
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 478 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.80e+00
        pdb=" N   PRO A 479 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 479 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 479 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 152 "   -0.034 5.00e-02 4.00e+02   5.15e-02 4.24e+00
        pdb=" N   PRO H 153 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO H 153 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO H 153 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP L  60 "    0.009 2.00e-02 2.50e+03   1.86e-02 3.47e+00
        pdb=" CG  ASP L  60 "   -0.032 2.00e-02 2.50e+03
        pdb=" OD1 ASP L  60 "    0.012 2.00e-02 2.50e+03
        pdb=" OD2 ASP L  60 "    0.011 2.00e-02 2.50e+03
  ... (remaining 856 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 1635
        2.86 -     3.37: 3870
        3.37 -     3.88: 8010
        3.88 -     4.39: 9038
        4.39 -     4.90: 15985
  Nonbonded interactions: 38538
  Sorted by model distance:
  nonbonded pdb=" O   TRP A 353 "
            pdb=" NH1 ARG A 466 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" OG  SER A 366 "
            pdb=" OD1 ASN A 388 "
     model   vdw
     2.354 3.040
  nonbonded pdb=" OD2 ASP A 420 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" OH  TYR A 453 "
            pdb=" OH  TYR H 102 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" OG  SER H 207 "
            pdb=" OG1 THR H 209 "
     model   vdw
     2.404 3.040
  ... (remaining 38533 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.520
  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:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     6.120
  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:6.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
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      :  0.005   0.046   4918  Z= 0.230
  Angle     :  0.819   8.326   6701  Z= 0.444
  Chirality :  0.054   0.236    737
  Planarity :  0.006   0.055    858
  Dihedral  : 12.247  82.651   1757
  Min Nonbonded Distance : 2.351

Molprobity Statistics.
  All-atom Clashscore : 2.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.92 %
    Favored  : 96.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.32), residues: 613
  helix: -4.72 (0.22), residues: 37
  sheet:  0.46 (0.32), residues: 243
  loop : -0.82 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  19 
 TYR   0.025   0.002   TYR A 495 
 PHE   0.015   0.002   PHE L  71 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.002   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 ( 4909)
  covalent geometry    : angle       0.81755 ( 6682)
  SS BOND              : bond        0.00228 (    8)
  SS BOND              : angle       1.11351 (   16)
  hydrogen bonds       : bond        0.14625 (  160)
  hydrogen bonds       : angle       7.89792 (  453)
  link_NAG-ASN         : bond        0.00349 (    1)
  link_NAG-ASN         : angle       1.41317 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  516 GLU cc_start: 0.8034 (pp20) cc_final: 0.7555 (pp20)
REVERT: A  528 LYS cc_start: 0.5794 (tttm) cc_final: 0.4720 (pptt)
REVERT: L  158 ASN cc_start: 0.7795 (m110) cc_final: 0.7591 (m110)
REVERT: L  167 ASP cc_start: 0.8609 (t0) cc_final: 0.8273 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.6864
  time to fit residues: 63.6950
Evaluate side-chains
  61 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 58 optimal weight:    0.6980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
H 201 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.063182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.052201 restraints weight = 12639.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.94
r_work: 0.2716 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8614
moved from start:          0.1450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4918  Z= 0.190
  Angle     :  0.569   6.768   6701  Z= 0.297
  Chirality :  0.043   0.133    737
  Planarity :  0.005   0.060    858
  Dihedral  :  5.224  41.985    699
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  9.79 %
    Favored  : 89.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.33), residues: 613
  helix: -4.72 (0.51), residues: 20
  sheet:  0.58 (0.33), residues: 244
  loop : -0.36 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG L  24 
 TYR   0.016   0.001   TYR A 495 
 PHE   0.008   0.001   PHE L  71 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.004   0.001   HIS H  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 4909)
  covalent geometry    : angle       0.56891 ( 6682)
  SS BOND              : bond        0.00188 (    8)
  SS BOND              : angle       0.53806 (   16)
  hydrogen bonds       : bond        0.03288 (  160)
  hydrogen bonds       : angle       6.15397 (  453)
  link_NAG-ASN         : bond        0.00177 (    1)
  link_NAG-ASN         : angle       1.24748 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9150 (m-30) cc_final: 0.8782 (m-30)
REVERT: A  516 GLU cc_start: 0.8129 (pp20) cc_final: 0.7625 (pp20)
REVERT: A  528 LYS cc_start: 0.6014 (tttm) cc_final: 0.5015 (pptt)
REVERT: H    3 GLN cc_start: 0.8315 (mm110) cc_final: 0.8098 (mm110)
REVERT: H   88 GLU cc_start: 0.9060 (pm20) cc_final: 0.8835 (pm20)
REVERT: L  158 ASN cc_start: 0.7834 (m110) cc_final: 0.7621 (m110)
REVERT: L  167 ASP cc_start: 0.8984 (t0) cc_final: 0.8488 (t0)
  outliers start: 4
  outliers final: 1
  residues processed: 67
  average time/residue: 0.6595
  time to fit residues: 45.5765
Evaluate side-chains
  61 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 24 optimal weight:    0.7980
   chunk 41 optimal weight:    7.9990
   chunk 60 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
L 137 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.061142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.050417 restraints weight = 12679.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.2789 rms_B_bonded: 2.89
r_work: 0.2665 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8618
moved from start:          0.1848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.029   4918  Z= 0.277
  Angle     :  0.591   6.946   6701  Z= 0.309
  Chirality :  0.044   0.154    737
  Planarity :  0.005   0.066    858
  Dihedral  :  5.162  35.150    699
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 4.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.55 %
    Favored  : 87.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.34), residues: 613
  helix: -4.52 (0.65), residues: 26
  sheet:  0.62 (0.33), residues: 243
  loop : -0.24 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG L  24 
 TYR   0.017   0.002   TYR A 495 
 PHE   0.010   0.001   PHE L  71 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00606 ( 4909)
  covalent geometry    : angle       0.58969 ( 6682)
  SS BOND              : bond        0.00216 (    8)
  SS BOND              : angle       0.67924 (   16)
  hydrogen bonds       : bond        0.03306 (  160)
  hydrogen bonds       : angle       6.08053 (  453)
  link_NAG-ASN         : bond        0.00536 (    1)
  link_NAG-ASN         : angle       1.61266 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9170 (m-30) cc_final: 0.8689 (m-30)
REVERT: A  516 GLU cc_start: 0.8127 (pp20) cc_final: 0.7513 (pp20)
REVERT: A  518 LEU cc_start: 0.9030 (mt) cc_final: 0.8797 (mp)
REVERT: A  528 LYS cc_start: 0.6045 (tttm) cc_final: 0.4963 (pptt)
REVERT: H    3 GLN cc_start: 0.8337 (mm110) cc_final: 0.8057 (mp10)
REVERT: H   88 GLU cc_start: 0.9077 (pm20) cc_final: 0.8720 (pm20)
REVERT: H  205 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8554 (tptp)
REVERT: L  165 GLU cc_start: 0.8201 (pp20) cc_final: 0.7990 (pp20)
REVERT: L  167 ASP cc_start: 0.8979 (t0) cc_final: 0.8465 (t0)
REVERT: L  170 ASP cc_start: 0.8600 (p0) cc_final: 0.8373 (p0)
  outliers start: 8
  outliers final: 3
  residues processed: 64
  average time/residue: 0.5910
  time to fit residues: 39.2442
Evaluate side-chains
  60 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 37 optimal weight:    8.9990
   chunk 30 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0970
   chunk 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
L 155 GLN
L 158 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.063188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.052451 restraints weight = 12493.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.92
r_work: 0.2715 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4918  Z= 0.136
  Angle     :  0.497   6.698   6701  Z= 0.260
  Chirality :  0.043   0.149    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.477  20.575    699
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 12.62 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.34), residues: 613
  helix: -4.51 (0.61), residues: 26
  sheet:  0.79 (0.33), residues: 243
  loop : -0.14 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG L  24 
 TYR   0.012   0.001   TYR A 495 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4909)
  covalent geometry    : angle       0.49602 ( 6682)
  SS BOND              : bond        0.00156 (    8)
  SS BOND              : angle       0.46827 (   16)
  hydrogen bonds       : bond        0.02788 (  160)
  hydrogen bonds       : angle       5.59892 (  453)
  link_NAG-ASN         : bond        0.00132 (    1)
  link_NAG-ASN         : angle       1.35951 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 71
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9181 (m-30) cc_final: 0.8663 (m-30)
REVERT: A  462 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8738 (mtmm)
REVERT: A  516 GLU cc_start: 0.8176 (pp20) cc_final: 0.7524 (pp20)
REVERT: A  518 LEU cc_start: 0.8992 (mt) cc_final: 0.8749 (mp)
REVERT: A  528 LYS cc_start: 0.6094 (tttm) cc_final: 0.5097 (pptt)
REVERT: H    3 GLN cc_start: 0.8391 (mm110) cc_final: 0.8117 (mp10)
REVERT: H   86 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8211 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9091 (pm20) cc_final: 0.8766 (pm20)
REVERT: H  205 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8911 (mmmt)
REVERT: L   17 GLU cc_start: 0.8549 (mt-10) cc_final: 0.8169 (mt-10)
REVERT: L   81 GLU cc_start: 0.9136 (pm20) cc_final: 0.8930 (pm20)
REVERT: L  167 ASP cc_start: 0.9017 (t0) cc_final: 0.8530 (t0)
  outliers start: 7
  outliers final: 3
  residues processed: 74
  average time/residue: 0.6733
  time to fit residues: 51.5058
Evaluate side-chains
  63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 59
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 1 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.6980
   chunk 11 optimal weight:    0.4980
   chunk 52 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 7 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.063755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.053127 restraints weight = 12537.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.93
r_work: 0.2729 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.2035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4918  Z= 0.120
  Angle     :  0.484   6.606   6701  Z= 0.253
  Chirality :  0.042   0.150    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.221  19.902    699
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 15.63 %
    Favored  : 82.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.35), residues: 613
  helix: -4.47 (0.59), residues: 26
  sheet:  0.89 (0.33), residues: 244
  loop : -0.09 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L  24 
 TYR   0.014   0.001   TYR H  79 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4909)
  covalent geometry    : angle       0.48302 ( 6682)
  SS BOND              : bond        0.00163 (    8)
  SS BOND              : angle       0.49167 (   16)
  hydrogen bonds       : bond        0.02649 (  160)
  hydrogen bonds       : angle       5.33970 (  453)
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       1.29681 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9189 (m-30) cc_final: 0.8639 (m-30)
REVERT: A  462 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8724 (mtmm)
REVERT: A  516 GLU cc_start: 0.8160 (pp20) cc_final: 0.7548 (pp20)
REVERT: A  528 LYS cc_start: 0.6031 (tttm) cc_final: 0.5045 (pptt)
REVERT: H    3 GLN cc_start: 0.8362 (mm110) cc_final: 0.8086 (mp10)
REVERT: H   86 ARG cc_start: 0.8404 (mtt-85) cc_final: 0.8082 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9082 (pm20) cc_final: 0.8759 (pm20)
REVERT: H  205 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8875 (mmmt)
REVERT: L   17 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8077 (mt-10)
REVERT: L   81 GLU cc_start: 0.9109 (pm20) cc_final: 0.8894 (pm20)
REVERT: L  167 ASP cc_start: 0.8990 (t0) cc_final: 0.8462 (t0)
REVERT: L  170 ASP cc_start: 0.8692 (p0) cc_final: 0.8425 (p0)
  outliers start: 8
  outliers final: 4
  residues processed: 72
  average time/residue: 0.6589
  time to fit residues: 49.0562
Evaluate side-chains
  68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue  105 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 3 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 56 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.063811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.052942 restraints weight = 12783.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.00
r_work: 0.2722 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4918  Z= 0.133
  Angle     :  0.501   7.081   6701  Z= 0.257
  Chirality :  0.042   0.144    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.186  20.073    699
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.25 %
    Favored  : 83.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.35), residues: 613
  helix: -4.39 (0.61), residues: 26
  sheet:  1.04 (0.34), residues: 242
  loop : -0.06 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  86 
 TYR   0.014   0.001   TYR H  79 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 4909)
  covalent geometry    : angle       0.50063 ( 6682)
  SS BOND              : bond        0.00136 (    8)
  SS BOND              : angle       0.40789 (   16)
  hydrogen bonds       : bond        0.02661 (  160)
  hydrogen bonds       : angle       5.25208 (  453)
  link_NAG-ASN         : bond        0.00094 (    1)
  link_NAG-ASN         : angle       1.28769 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8746 (mtmm)
REVERT: A  516 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7888 (pp20)
REVERT: A  528 LYS cc_start: 0.6079 (tttm) cc_final: 0.5106 (pptt)
REVERT: H    3 GLN cc_start: 0.8394 (mm110) cc_final: 0.8094 (mp10)
REVERT: H   86 ARG cc_start: 0.8425 (mtt-85) cc_final: 0.8141 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9084 (pm20) cc_final: 0.8762 (pm20)
REVERT: H  205 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8876 (mmmt)
REVERT: L   17 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8021 (mt-10)
REVERT: L   81 GLU cc_start: 0.9108 (pm20) cc_final: 0.8877 (pm20)
REVERT: L  142 ARG cc_start: 0.9123 (tpp80) cc_final: 0.8757 (ttt-90)
REVERT: L  147 GLN cc_start: 0.6436 (OUTLIER) cc_final: 0.6056 (mt0)
REVERT: L  167 ASP cc_start: 0.8964 (t0) cc_final: 0.8209 (t0)
REVERT: L  170 ASP cc_start: 0.8595 (p0) cc_final: 0.8389 (p0)
  outliers start: 9
  outliers final: 4
  residues processed: 72
  average time/residue: 0.6684
  time to fit residues: 49.7833
Evaluate side-chains
  76 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 69
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  147 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0670
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0470
   chunk 56 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5216

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.063904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.053131 restraints weight = 12706.138|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 2.96
r_work: 0.2727 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4918  Z= 0.124
  Angle     :  0.503   7.622   6701  Z= 0.259
  Chirality :  0.042   0.140    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.096  19.843    699
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.63 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.35), residues: 613
  helix: -4.30 (0.62), residues: 26
  sheet:  1.10 (0.34), residues: 242
  loop : -0.04 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG H  19 
 TYR   0.013   0.001   TYR L 192 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4909)
  covalent geometry    : angle       0.50257 ( 6682)
  SS BOND              : bond        0.00127 (    8)
  SS BOND              : angle       0.42184 (   16)
  hydrogen bonds       : bond        0.02593 (  160)
  hydrogen bonds       : angle       5.15620 (  453)
  link_NAG-ASN         : bond        0.00045 (    1)
  link_NAG-ASN         : angle       1.25201 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.8955 (p)
REVERT: A  462 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8724 (mtmm)
REVERT: A  516 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7585 (pp20)
REVERT: A  528 LYS cc_start: 0.6063 (tttm) cc_final: 0.5088 (pptt)
REVERT: H    3 GLN cc_start: 0.8386 (mm110) cc_final: 0.8074 (mp10)
REVERT: H   86 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.8118 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9078 (pm20) cc_final: 0.8757 (pm20)
REVERT: H  205 LYS cc_start: 0.9152 (mmmm) cc_final: 0.8859 (mmmt)
REVERT: L   17 GLU cc_start: 0.8399 (mt-10) cc_final: 0.7974 (mt-10)
REVERT: L   81 GLU cc_start: 0.9120 (pm20) cc_final: 0.8899 (pm20)
REVERT: L  142 ARG cc_start: 0.9131 (tpp80) cc_final: 0.8770 (ttt-90)
REVERT: L  165 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8682 (pm20)
REVERT: L  167 ASP cc_start: 0.8884 (t0) cc_final: 0.8235 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 73
  average time/residue: 0.6135
  time to fit residues: 46.3892
Evaluate side-chains
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 61
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.063326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.052473 restraints weight = 12813.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 2.99
r_work: 0.2710 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4918  Z= 0.157
  Angle     :  0.518   6.887   6701  Z= 0.266
  Chirality :  0.043   0.135    737
  Planarity :  0.004   0.062    858
  Dihedral  :  4.240  20.537    699
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.38 %
    Favored  : 81.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.35), residues: 613
  helix: -4.33 (0.62), residues: 26
  sheet:  1.05 (0.34), residues: 241
  loop :  0.01 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.018   0.001   TYR H  79 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.005   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 4909)
  covalent geometry    : angle       0.51705 ( 6682)
  SS BOND              : bond        0.00169 (    8)
  SS BOND              : angle       0.45323 (   16)
  hydrogen bonds       : bond        0.02715 (  160)
  hydrogen bonds       : angle       5.24381 (  453)
  link_NAG-ASN         : bond        0.00180 (    1)
  link_NAG-ASN         : angle       1.34522 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9287 (OUTLIER) cc_final: 0.8969 (p)
REVERT: A  462 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8690 (mtmm)
REVERT: A  528 LYS cc_start: 0.6076 (tttm) cc_final: 0.5060 (pptt)
REVERT: H    3 GLN cc_start: 0.8380 (mm110) cc_final: 0.8067 (mp10)
REVERT: H   86 ARG cc_start: 0.8420 (mtt-85) cc_final: 0.8089 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9107 (pm20) cc_final: 0.8747 (pm20)
REVERT: H  205 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8869 (mmmt)
REVERT: L  142 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8347 (ttp80)
REVERT: L  165 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8649 (pm20)
REVERT: L  167 ASP cc_start: 0.8918 (t0) cc_final: 0.8268 (t0)
REVERT: L  170 ASP cc_start: 0.8673 (p0) cc_final: 0.8378 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 69
  average time/residue: 0.5837
  time to fit residues: 41.8047
Evaluate side-chains
  71 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   10 THR
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 29 optimal weight:    0.3980
   chunk 55 optimal weight:    0.9980
   chunk 50 optimal weight:    0.8980
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.2980
   chunk 38 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0770
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.5138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.063870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.053311 restraints weight = 12503.323|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 2.91
r_work: 0.2738 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.2201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4918  Z= 0.122
  Angle     :  0.499   6.554   6701  Z= 0.259
  Chirality :  0.042   0.137    737
  Planarity :  0.004   0.060    858
  Dihedral  :  4.088  19.815    699
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 16.20 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.35), residues: 613
  helix: -4.30 (0.60), residues: 26
  sheet:  1.26 (0.35), residues: 232
  loop : -0.02 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.016   0.001   TYR H  79 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 4909)
  covalent geometry    : angle       0.49825 ( 6682)
  SS BOND              : bond        0.00149 (    8)
  SS BOND              : angle       0.43519 (   16)
  hydrogen bonds       : bond        0.02605 (  160)
  hydrogen bonds       : angle       5.09524 (  453)
  link_NAG-ASN         : bond        0.00054 (    1)
  link_NAG-ASN         : angle       1.26093 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8945 (p)
REVERT: A  462 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8687 (mtmm)
REVERT: A  516 GLU cc_start: 0.8145 (pp20) cc_final: 0.7581 (pp20)
REVERT: A  528 LYS cc_start: 0.6072 (tttm) cc_final: 0.5092 (pptt)
REVERT: H    3 GLN cc_start: 0.8383 (mm110) cc_final: 0.8071 (mp10)
REVERT: H   86 ARG cc_start: 0.8379 (mtt-85) cc_final: 0.8067 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9086 (pm20) cc_final: 0.8745 (pm20)
REVERT: H  205 LYS cc_start: 0.9155 (mmmm) cc_final: 0.8854 (mmmt)
REVERT: L   17 GLU cc_start: 0.8366 (mt-10) cc_final: 0.7958 (mt-10)
REVERT: L   81 GLU cc_start: 0.9101 (pm20) cc_final: 0.8886 (pm20)
REVERT: L  142 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8363 (ttp80)
REVERT: L  165 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8654 (pm20)
REVERT: L  167 ASP cc_start: 0.8905 (t0) cc_final: 0.8261 (t0)
REVERT: L  170 ASP cc_start: 0.8654 (p0) cc_final: 0.8371 (p0)
  outliers start: 9
  outliers final: 4
  residues processed: 75
  average time/residue: 0.5885
  time to fit residues: 45.7192
Evaluate side-chains
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 68
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 50 optimal weight:    0.8980
   chunk 1 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0170
   chunk 58 optimal weight:    0.6980
   chunk 59 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 13 optimal weight:    0.2980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5218

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.064062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.053278 restraints weight = 12654.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 2.97
r_work: 0.2730 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4918  Z= 0.124
  Angle     :  0.501   6.545   6701  Z= 0.260
  Chirality :  0.043   0.136    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.068  20.057    699
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.57 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.35), residues: 613
  helix: -4.29 (0.61), residues: 26
  sheet:  1.31 (0.35), residues: 232
  loop : -0.02 (0.34), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 346 
 TYR   0.015   0.001   TYR H  79 
 PHE   0.006   0.001   PHE L  98 
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 4909)
  covalent geometry    : angle       0.50024 ( 6682)
  SS BOND              : bond        0.00144 (    8)
  SS BOND              : angle       0.42872 (   16)
  hydrogen bonds       : bond        0.02589 (  160)
  hydrogen bonds       : angle       5.03656 (  453)
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       1.24171 (    3)

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

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

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1226 Ramachandran restraints generated.
    613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.8931 (p)
REVERT: A  462 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8672 (mtmm)
REVERT: A  516 GLU cc_start: 0.8137 (pp20) cc_final: 0.7632 (pp20)
REVERT: A  528 LYS cc_start: 0.6062 (tttm) cc_final: 0.5106 (pptt)
REVERT: H    3 GLN cc_start: 0.8387 (mm110) cc_final: 0.8071 (mp10)
REVERT: H   86 ARG cc_start: 0.8398 (mtt-85) cc_final: 0.8052 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9088 (pm20) cc_final: 0.8744 (pm20)
REVERT: H  205 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8851 (mmmt)
REVERT: L   17 GLU cc_start: 0.8375 (mt-10) cc_final: 0.7972 (mt-10)
REVERT: L   81 GLU cc_start: 0.9102 (pm20) cc_final: 0.8889 (pm20)
REVERT: L  142 ARG cc_start: 0.9149 (tpp80) cc_final: 0.8366 (ttp80)
REVERT: L  165 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8648 (pm20)
REVERT: L  167 ASP cc_start: 0.8890 (t0) cc_final: 0.8246 (t0)
REVERT: L  170 ASP cc_start: 0.8644 (p0) cc_final: 0.8366 (p0)
  outliers start: 7
  outliers final: 5
  residues processed: 72
  average time/residue: 0.6011
  time to fit residues: 44.7478
Evaluate side-chains
  75 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 68
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue   72 HIS
Chi-restraints excluded: chain L residue   13 LEU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 49 optimal weight:    0.0170
   chunk 5 optimal weight:    0.0980
   chunk 55 optimal weight:    0.0030
   chunk 6 optimal weight:    0.0870
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    0.2980
   chunk 58 optimal weight:    0.7980
   chunk 15 optimal weight:    0.0870
   overall best weight:    0.0584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.067094 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.056572 restraints weight = 12438.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.2945 rms_B_bonded: 2.96
r_work: 0.2821 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.2821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   4918  Z= 0.087
  Angle     :  0.484   6.434   6701  Z= 0.250
  Chirality :  0.042   0.139    737
  Planarity :  0.004   0.058    858
  Dihedral  :  3.709  18.520    699
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 17.14 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.35), residues: 613
  helix: -3.80 (0.55), residues: 33
  sheet:  1.40 (0.35), residues: 232
  loop :  0.06 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  19 
 TYR   0.016   0.001   TYR H  79 
 PHE   0.007   0.001   PHE A 377 
 TRP   0.009   0.001   TRP A 436 
 HIS   0.001   0.000   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00197 ( 4909)
  covalent geometry    : angle       0.48345 ( 6682)
  SS BOND              : bond        0.00198 (    8)
  SS BOND              : angle       0.55428 (   16)
  hydrogen bonds       : bond        0.02252 (  160)
  hydrogen bonds       : angle       4.63617 (  453)
  link_NAG-ASN         : bond        0.00219 (    1)
  link_NAG-ASN         : angle       1.01076 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1649.00 seconds
wall clock time: 28 minutes 52.99 seconds (1732.99 seconds total)