Starting phenix.real_space_refine
on Thu Jul 24 01:52:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_23877.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_23877.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_23877.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_23877.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7mjl_23877/07_2025/7mjl_23877.cif"
  }
  resolution = 2.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.82, per 1000 atoms: 0.80
  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: 1.01
  Conformation dependent library (CDL) restraints added in 571.3 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: 0.65
  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: 1.35

  Time building geometry restraints manager: 1.24 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:             3.840
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.610
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:12.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.270
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.002   HIS H  72 
 PHE   0.015   0.002   PHE L  71 
 TYR   0.025   0.002   TYR A 495 
 ARG   0.006   0.001   ARG H  19 

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

*********************** 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  : 0.542 
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: 1.3849
  time to fit residues: 128.9102
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  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 46 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0670
   chunk 24 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 18 optimal weight:    0.0270
   chunk 29 optimal weight:    0.2980
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9980
   overall best weight:    0.3376

-------------------------------------------------------------------------------
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 = 0.3142 r_free = 0.3142 target = 0.065525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2910 r_free = 0.2910 target = 0.054844 restraints weight = 12328.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 2.88
r_work: 0.2781 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.1474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4918  Z= 0.108
  Angle     :  0.532   6.643   6701  Z= 0.277
  Chirality :  0.043   0.138    737
  Planarity :  0.005   0.055    858
  Dihedral  :  4.852  36.343    699
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  9.23 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.33), residues: 613
  helix: -4.70 (0.49), residues: 20
  sheet:  0.65 (0.33), residues: 244
  loop : -0.36 (0.32), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.003   0.001   HIS H  72 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.013   0.001   TYR A 495 
 ARG   0.010   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00140 (    1)
  link_NAG-ASN         : angle       1.00512 (    3)
  hydrogen bonds       : bond        0.03007 (  160)
  hydrogen bonds       : angle       5.92885 (  453)
  SS BOND              : bond        0.00188 (    8)
  SS BOND              : angle       0.45031 (   16)
  covalent geometry    : bond        0.00237 ( 4909)
  covalent geometry    : angle       0.53146 ( 6682)

*********************** 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
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9170 (m-30) cc_final: 0.8800 (m-30)
REVERT: A  516 GLU cc_start: 0.8101 (pp20) cc_final: 0.7648 (pp20)
REVERT: A  528 LYS cc_start: 0.6280 (tttm) cc_final: 0.4896 (pptt)
REVERT: H    3 GLN cc_start: 0.8286 (mm110) cc_final: 0.8051 (mm110)
REVERT: H   88 GLU cc_start: 0.9035 (pm20) cc_final: 0.8800 (pm20)
REVERT: L   17 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: L  158 ASN cc_start: 0.7819 (m110) cc_final: 0.7573 (m110)
REVERT: L  167 ASP cc_start: 0.8937 (t0) cc_final: 0.8418 (t0)
REVERT: L  170 ASP cc_start: 0.8699 (p0) cc_final: 0.8487 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 76
  average time/residue: 1.4256
  time to fit residues: 112.0873
Evaluate side-chains
  63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 41 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
H 109 GLN
L 137 ASN
L 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.060134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.049392 restraints weight = 12813.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.2747 rms_B_bonded: 2.86
r_work: 0.2626 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8540
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.033   4918  Z= 0.316
  Angle     :  0.622   6.984   6701  Z= 0.325
  Chirality :  0.045   0.146    737
  Planarity :  0.005   0.067    858
  Dihedral  :  5.242  34.564    699
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 10.36 %
    Favored  : 87.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.34), residues: 613
  helix: -4.53 (0.65), residues: 26
  sheet:  0.50 (0.33), residues: 244
  loop : -0.27 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.005   0.002   HIS H  72 
 PHE   0.011   0.001   PHE L  71 
 TYR   0.017   0.002   TYR A 495 
 ARG   0.011   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00667 (    1)
  link_NAG-ASN         : angle       1.68739 (    3)
  hydrogen bonds       : bond        0.03430 (  160)
  hydrogen bonds       : angle       6.14233 (  453)
  SS BOND              : bond        0.00291 (    8)
  SS BOND              : angle       0.84105 (   16)
  covalent geometry    : bond        0.00688 ( 4909)
  covalent geometry    : angle       0.62063 ( 6682)

*********************** 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
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.545 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9166 (m-30) cc_final: 0.8662 (m-30)
REVERT: A  462 LYS cc_start: 0.9105 (OUTLIER) cc_final: 0.8675 (mtmm)
REVERT: A  516 GLU cc_start: 0.8050 (pp20) cc_final: 0.7484 (pp20)
REVERT: H    3 GLN cc_start: 0.8243 (mm110) cc_final: 0.7963 (mp10)
REVERT: H   88 GLU cc_start: 0.9078 (pm20) cc_final: 0.8702 (pm20)
REVERT: H  205 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8613 (tptp)
REVERT: L    4 MET cc_start: 0.8860 (mmm) cc_final: 0.7815 (mmm)
REVERT: L  158 ASN cc_start: 0.7911 (m110) cc_final: 0.7681 (m110)
REVERT: L  165 GLU cc_start: 0.8219 (pp20) cc_final: 0.7975 (pp20)
REVERT: L  167 ASP cc_start: 0.8919 (t0) cc_final: 0.8406 (t0)
  outliers start: 11
  outliers final: 4
  residues processed: 65
  average time/residue: 1.1391
  time to fit residues: 77.3030
Evaluate side-chains
  63 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
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   13 LEU
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 25 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0770
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0870
   chunk 1 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0570
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.3234

-------------------------------------------------------------------------------
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 = 0.3115 r_free = 0.3115 target = 0.064486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.053555 restraints weight = 12574.737|
|-----------------------------------------------------------------------------|
r_work (start): 0.2872 rms_B_bonded: 2.98
r_work: 0.2747 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
moved from start:          0.1967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4918  Z= 0.105
  Angle     :  0.487   6.619   6701  Z= 0.254
  Chirality :  0.042   0.152    737
  Planarity :  0.004   0.059    858
  Dihedral  :  4.305  18.559    699
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 12.24 %
    Favored  : 86.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.34), residues: 613
  helix: -4.50 (0.58), residues: 26
  sheet:  0.75 (0.33), residues: 244
  loop : -0.17 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 158 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE H  67 
 TYR   0.011   0.001   TYR L 192 
 ARG   0.007   0.001   ARG L  24 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.24398 (    3)
  hydrogen bonds       : bond        0.02655 (  160)
  hydrogen bonds       : angle       5.46301 (  453)
  SS BOND              : bond        0.00159 (    8)
  SS BOND              : angle       0.49656 (   16)
  covalent geometry    : bond        0.00229 ( 4909)
  covalent geometry    : angle       0.48632 ( 6682)

*********************** 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
  79 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 73
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9176 (m-30) cc_final: 0.8685 (m-30)
REVERT: A  462 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8677 (mtmm)
REVERT: A  516 GLU cc_start: 0.8191 (pp20) cc_final: 0.7610 (pp20)
REVERT: A  528 LYS cc_start: 0.6544 (tttt) cc_final: 0.4810 (pptt)
REVERT: H    3 GLN cc_start: 0.8384 (mm110) cc_final: 0.8125 (mp10)
REVERT: H   86 ARG cc_start: 0.8388 (mtt-85) cc_final: 0.8102 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9075 (pm20) cc_final: 0.8795 (pm20)
REVERT: H  205 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8910 (mmmt)
REVERT: L   17 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7999 (mt-10)
REVERT: L   81 GLU cc_start: 0.9223 (pm20) cc_final: 0.9005 (pm20)
REVERT: L  142 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8425 (ttp80)
REVERT: L  158 ASN cc_start: 0.7852 (m110) cc_final: 0.7648 (m110)
REVERT: L  167 ASP cc_start: 0.9005 (t0) cc_final: 0.8505 (t0)
REVERT: L  170 ASP cc_start: 0.8714 (p0) cc_final: 0.8463 (p0)
  outliers start: 6
  outliers final: 1
  residues processed: 75
  average time/residue: 1.3458
  time to fit residues: 104.6647
Evaluate side-chains
  64 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  462 LYS
Chi-restraints excluded: chain H residue  145 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 18 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 7 optimal weight:    0.6980
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0670
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    0.5980
   chunk 50 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.063793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.053057 restraints weight = 12600.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.2858 rms_B_bonded: 2.94
r_work: 0.2734 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.2008

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= 0.124
  Angle     :  0.490   6.589   6701  Z= 0.255
  Chirality :  0.042   0.148    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.198  19.791    699
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.75 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.34), residues: 613
  helix: -4.46 (0.58), residues: 26
  sheet:  0.88 (0.33), residues: 244
  loop : -0.11 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS H  72 
 PHE   0.006   0.001   PHE L  98 
 TYR   0.016   0.001   TYR H  79 
 ARG   0.008   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00081 (    1)
  link_NAG-ASN         : angle       1.28510 (    3)
  hydrogen bonds       : bond        0.02650 (  160)
  hydrogen bonds       : angle       5.32349 (  453)
  SS BOND              : bond        0.00147 (    8)
  SS BOND              : angle       0.47255 (   16)
  covalent geometry    : bond        0.00274 ( 4909)
  covalent geometry    : angle       0.48896 ( 6682)

*********************** 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
  78 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  420 ASP cc_start: 0.9189 (m-30) cc_final: 0.8663 (m-30)
REVERT: A  462 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8643 (mtmm)
REVERT: A  516 GLU cc_start: 0.8184 (pp20) cc_final: 0.7580 (pp20)
REVERT: A  518 LEU cc_start: 0.8974 (mt) cc_final: 0.8714 (mp)
REVERT: A  528 LYS cc_start: 0.6443 (tttt) cc_final: 0.4920 (pptt)
REVERT: H    3 GLN cc_start: 0.8384 (mm110) cc_final: 0.8112 (mp10)
REVERT: H   86 ARG cc_start: 0.8396 (mtt-85) cc_final: 0.8092 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9081 (pm20) cc_final: 0.8795 (pm20)
REVERT: H  205 LYS cc_start: 0.9135 (mmmm) cc_final: 0.8887 (mmmt)
REVERT: L   17 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8118 (mt-10)
REVERT: L   81 GLU cc_start: 0.9167 (pm20) cc_final: 0.8922 (pm20)
REVERT: L  142 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8763 (ttt-90)
REVERT: L  147 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.6041 (mt0)
REVERT: L  158 ASN cc_start: 0.7833 (m110) cc_final: 0.7613 (m110)
REVERT: L  167 ASP cc_start: 0.8976 (t0) cc_final: 0.8440 (t0)
  outliers start: 8
  outliers final: 3
  residues processed: 73
  average time/residue: 1.3799
  time to fit residues: 104.3628
Evaluate side-chains
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.553 
-------------------------------------------------------------------------------
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   10 THR
Chi-restraints excluded: chain L residue  147 GLN
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 0 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0970
   chunk 23 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   overall best weight:    0.5378

-------------------------------------------------------------------------------
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 = 0.3105 r_free = 0.3105 target = 0.063904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.053149 restraints weight = 12596.475|
|-----------------------------------------------------------------------------|
r_work (start): 0.2861 rms_B_bonded: 2.93
r_work: 0.2736 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4918  Z= 0.124
  Angle     :  0.495   6.750   6701  Z= 0.255
  Chirality :  0.042   0.143    737
  Planarity :  0.004   0.060    858
  Dihedral  :  4.097  19.636    699
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 14.88 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.35), residues: 613
  helix: -4.41 (0.60), residues: 26
  sheet:  0.96 (0.33), residues: 244
  loop : -0.09 (0.34), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  98 
 TYR   0.015   0.001   TYR H  79 
 ARG   0.007   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00050 (    1)
  link_NAG-ASN         : angle       1.23780 (    3)
  hydrogen bonds       : bond        0.02623 (  160)
  hydrogen bonds       : angle       5.19370 (  453)
  SS BOND              : bond        0.00147 (    8)
  SS BOND              : angle       0.43501 (   16)
  covalent geometry    : bond        0.00274 ( 4909)
  covalent geometry    : angle       0.49468 ( 6682)

*********************** 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: 8
    poor density    : 70
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8637 (mtmm)
REVERT: A  516 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7558 (pp20)
REVERT: A  528 LYS cc_start: 0.6473 (tttt) cc_final: 0.4949 (pptt)
REVERT: H    3 GLN cc_start: 0.8401 (mm110) cc_final: 0.8116 (mp10)
REVERT: H   86 ARG cc_start: 0.8391 (mtt-85) cc_final: 0.8067 (mtt-85)
REVERT: H   88 GLU cc_start: 0.9081 (pm20) cc_final: 0.8781 (pm20)
REVERT: H  205 LYS cc_start: 0.9128 (mmmm) cc_final: 0.8867 (mmmt)
REVERT: L   17 GLU cc_start: 0.8443 (mt-10) cc_final: 0.7988 (mt-10)
REVERT: L   81 GLU cc_start: 0.9127 (pm20) cc_final: 0.8919 (pm20)
REVERT: L  142 ARG cc_start: 0.9100 (tpp80) cc_final: 0.8740 (ttt-90)
REVERT: L  158 ASN cc_start: 0.7828 (m110) cc_final: 0.7622 (m110)
REVERT: L  167 ASP cc_start: 0.8934 (t0) cc_final: 0.8188 (t0)
REVERT: L  170 ASP cc_start: 0.8689 (p0) cc_final: 0.8402 (p0)
  outliers start: 8
  outliers final: 5
  residues processed: 72
  average time/residue: 1.6974
  time to fit residues: 126.7368
Evaluate side-chains
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
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  161 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 6 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9990
   chunk 60 optimal weight:    0.3980
   chunk 11 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 57 optimal weight:    5.9990
   overall best weight:    0.9584

-------------------------------------------------------------------------------
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 = 0.3078 r_free = 0.3078 target = 0.062644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.051708 restraints weight = 12597.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.2828 rms_B_bonded: 2.94
r_work: 0.2704 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8626
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4918  Z= 0.188
  Angle     :  0.529   6.664   6701  Z= 0.271
  Chirality :  0.043   0.140    737
  Planarity :  0.004   0.063    858
  Dihedral  :  4.356  20.739    699
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 15.44 %
    Favored  : 82.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.35), residues: 613
  helix: -4.40 (0.64), residues: 26
  sheet:  0.99 (0.33), residues: 241
  loop : -0.03 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A 519 
 PHE   0.007   0.001   PHE L  71 
 TYR   0.018   0.001   TYR H  79 
 ARG   0.008   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00280 (    1)
  link_NAG-ASN         : angle       1.40163 (    3)
  hydrogen bonds       : bond        0.02845 (  160)
  hydrogen bonds       : angle       5.36005 (  453)
  SS BOND              : bond        0.00151 (    8)
  SS BOND              : angle       0.46217 (   16)
  covalent geometry    : bond        0.00410 ( 4909)
  covalent geometry    : angle       0.52885 ( 6682)

*********************** 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
  74 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8655 (mtmm)
REVERT: A  516 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7942 (pp20)
REVERT: A  528 LYS cc_start: 0.6486 (tttt) cc_final: 0.4886 (pptt)
REVERT: H    3 GLN cc_start: 0.8382 (mm110) cc_final: 0.8053 (mp10)
REVERT: H   88 GLU cc_start: 0.9104 (pm20) cc_final: 0.8731 (pm20)
REVERT: H  205 LYS cc_start: 0.9153 (mmmm) cc_final: 0.8881 (mmmt)
REVERT: L  142 ARG cc_start: 0.9127 (tpp80) cc_final: 0.8345 (ttp80)
REVERT: L  147 GLN cc_start: 0.6490 (OUTLIER) cc_final: 0.6022 (mt0)
REVERT: L  167 ASP cc_start: 0.8929 (t0) cc_final: 0.8449 (t0)
REVERT: L  170 ASP cc_start: 0.8637 (p0) cc_final: 0.8391 (p0)
  outliers start: 10
  outliers final: 5
  residues processed: 68
  average time/residue: 2.2321
  time to fit residues: 158.3286
Evaluate side-chains
  70 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 49 optimal weight:    0.7980
   chunk 44 optimal weight:    0.6980
   chunk 50 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 0 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.063131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.052189 restraints weight = 12593.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2839 rms_B_bonded: 2.95
r_work: 0.2713 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8622
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4918  Z= 0.155
  Angle     :  0.527   8.462   6701  Z= 0.271
  Chirality :  0.043   0.137    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.247  20.125    699
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 16.20 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.35), residues: 613
  helix: -4.38 (0.62), residues: 26
  sheet:  1.00 (0.33), residues: 241
  loop : -0.03 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.006   0.001   PHE L  71 
 TYR   0.018   0.001   TYR H  79 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       1.35130 (    3)
  hydrogen bonds       : bond        0.02722 (  160)
  hydrogen bonds       : angle       5.27515 (  453)
  SS BOND              : bond        0.00154 (    8)
  SS BOND              : angle       0.40308 (   16)
  covalent geometry    : bond        0.00345 ( 4909)
  covalent geometry    : angle       0.52637 ( 6682)

*********************** 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
  77 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9302 (OUTLIER) cc_final: 0.8979 (p)
REVERT: A  462 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8639 (mtmm)
REVERT: A  516 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7674 (pp20)
REVERT: A  528 LYS cc_start: 0.6491 (tttt) cc_final: 0.4919 (pptt)
REVERT: H    3 GLN cc_start: 0.8383 (mm110) cc_final: 0.8052 (mp10)
REVERT: H   88 GLU cc_start: 0.9113 (pm20) cc_final: 0.8834 (pm20)
REVERT: H  205 LYS cc_start: 0.9144 (mmmm) cc_final: 0.8876 (mmmt)
REVERT: L   17 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: L   81 GLU cc_start: 0.9135 (pm20) cc_final: 0.8920 (pm20)
REVERT: L  142 ARG cc_start: 0.9116 (tpp80) cc_final: 0.8746 (ttt-90)
REVERT: L  167 ASP cc_start: 0.8988 (t0) cc_final: 0.8251 (t0)
REVERT: L  170 ASP cc_start: 0.8620 (p0) cc_final: 0.8378 (p0)
  outliers start: 10
  outliers final: 6
  residues processed: 71
  average time/residue: 1.2687
  time to fit residues: 93.7001
Evaluate side-chains
  67 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 58
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
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  105 GLU
Chi-restraints excluded: chain L residue  106 ILE
Chi-restraints excluded: chain L residue  161 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 16 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3094 r_free = 0.3094 target = 0.063296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.052687 restraints weight = 12601.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 2.92
r_work: 0.2726 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.2224

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= 0.148
  Angle     :  0.522   7.054   6701  Z= 0.266
  Chirality :  0.043   0.137    737
  Planarity :  0.004   0.061    858
  Dihedral  :  4.220  20.154    699
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.82 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.35), residues: 613
  helix: -4.35 (0.62), residues: 26
  sheet:  0.99 (0.33), residues: 241
  loop : -0.00 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.005   0.001   PHE L  71 
 TYR   0.018   0.001   TYR H  79 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00153 (    1)
  link_NAG-ASN         : angle       1.33736 (    3)
  hydrogen bonds       : bond        0.02692 (  160)
  hydrogen bonds       : angle       5.20510 (  453)
  SS BOND              : bond        0.00145 (    8)
  SS BOND              : angle       0.40656 (   16)
  covalent geometry    : bond        0.00327 ( 4909)
  covalent geometry    : angle       0.52169 ( 6682)

*********************** 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
  72 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9280 (OUTLIER) cc_final: 0.8957 (p)
REVERT: A  462 LYS cc_start: 0.9138 (OUTLIER) cc_final: 0.8645 (mtmm)
REVERT: A  528 LYS cc_start: 0.6552 (tttt) cc_final: 0.4947 (pptt)
REVERT: H    3 GLN cc_start: 0.8367 (mm110) cc_final: 0.8032 (mp10)
REVERT: H   88 GLU cc_start: 0.9094 (pm20) cc_final: 0.8752 (pm20)
REVERT: H  152 GLU cc_start: 0.8945 (mp0) cc_final: 0.8645 (mp0)
REVERT: H  205 LYS cc_start: 0.9134 (mmmm) cc_final: 0.8858 (mmmt)
REVERT: L  142 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8350 (ttp80)
REVERT: L  147 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.6000 (mt0)
REVERT: L  165 GLU cc_start: 0.8905 (mm-30) cc_final: 0.8642 (pm20)
REVERT: L  167 ASP cc_start: 0.8882 (t0) cc_final: 0.8237 (t0)
REVERT: L  170 ASP cc_start: 0.8554 (p0) cc_final: 0.8353 (p0)
  outliers start: 11
  outliers final: 5
  residues processed: 67
  average time/residue: 2.1883
  time to fit residues: 153.3460
Evaluate side-chains
  67 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 1.497 
-------------------------------------------------------------------------------
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  106 ILE
Chi-restraints excluded: chain L residue  147 GLN
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 60 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 16 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.5118

-------------------------------------------------------------------------------
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 = 0.3108 r_free = 0.3108 target = 0.064008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.053414 restraints weight = 12509.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 2.93
r_work: 0.2743 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.2305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4918  Z= 0.122
  Angle     :  0.514   7.039   6701  Z= 0.263
  Chirality :  0.043   0.137    737
  Planarity :  0.004   0.060    858
  Dihedral  :  4.089  19.756    699
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.20 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.76 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.35), residues: 613
  helix: -4.30 (0.60), residues: 26
  sheet:  1.04 (0.33), residues: 242
  loop : -0.00 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.005   0.001   PHE L  98 
 TYR   0.018   0.001   TYR H  79 
 ARG   0.005   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00059 (    1)
  link_NAG-ASN         : angle       1.26995 (    3)
  hydrogen bonds       : bond        0.02599 (  160)
  hydrogen bonds       : angle       5.04490 (  453)
  SS BOND              : bond        0.00154 (    8)
  SS BOND              : angle       0.39786 (   16)
  covalent geometry    : bond        0.00272 ( 4909)
  covalent geometry    : angle       0.51371 ( 6682)

********************** 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
  68 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  430 THR cc_start: 0.9266 (OUTLIER) cc_final: 0.8943 (p)
REVERT: A  462 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8632 (mtmm)
REVERT: A  516 GLU cc_start: 0.8167 (pp20) cc_final: 0.7617 (pp20)
REVERT: A  528 LYS cc_start: 0.6545 (tttt) cc_final: 0.4973 (pptt)
REVERT: H    3 GLN cc_start: 0.8373 (mm110) cc_final: 0.8038 (mp10)
REVERT: H   88 GLU cc_start: 0.9093 (pm20) cc_final: 0.8762 (pm20)
REVERT: H  205 LYS cc_start: 0.9131 (mmmm) cc_final: 0.8846 (mmmt)
REVERT: L  142 ARG cc_start: 0.9144 (tpp80) cc_final: 0.8382 (ttp80)
REVERT: L  165 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8650 (pm20)
REVERT: L  167 ASP cc_start: 0.8865 (t0) cc_final: 0.8227 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 65
  average time/residue: 2.2940
  time to fit residues: 155.5079
Evaluate side-chains
  66 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 2.352 
-------------------------------------------------------------------------------
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  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 52 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0670
   chunk 9 optimal weight:    0.5980
   chunk 13 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0870
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.3094

-------------------------------------------------------------------------------
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 = 0.3140 r_free = 0.3140 target = 0.065435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.054830 restraints weight = 12647.963|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 2.96
r_work: 0.2782 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4918  Z= 0.100
  Angle     :  0.514   8.261   6701  Z= 0.262
  Chirality :  0.042   0.137    737
  Planarity :  0.004   0.060    858
  Dihedral  :  3.893  19.297    699
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.37 (0.35), residues: 613
  helix: -3.97 (0.52), residues: 33
  sheet:  1.25 (0.34), residues: 232
  loop :  0.04 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 436 
 HIS   0.002   0.000   HIS A 519 
 PHE   0.006   0.001   PHE A 377 
 TYR   0.016   0.001   TYR H  79 
 ARG   0.008   0.001   ARG H  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00061 (    1)
  link_NAG-ASN         : angle       1.14412 (    3)
  hydrogen bonds       : bond        0.02433 (  160)
  hydrogen bonds       : angle       4.81741 (  453)
  SS BOND              : bond        0.00170 (    8)
  SS BOND              : angle       0.41936 (   16)
  covalent geometry    : bond        0.00227 ( 4909)
  covalent geometry    : angle       0.51408 ( 6682)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4346.54 seconds
wall clock time: 80 minutes 40.81 seconds (4840.81 seconds total)