Starting phenix.real_space_refine
on Sun Apr  5 00:32:59 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdh_31543/04_2026/7fdh_31543.map"
  }
  resolution = 3.72
  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=   0.002
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      37      5.16       5
     C    4150      2.51       5
     N    1069      2.21       5
     O    1232      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6488
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "E"
      Number of atoms: 1541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1541
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "E"
      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: 2.37, per 1000 atoms: 0.37
  Number of scatterers: 6488
  At special positions: 0
  Unit cell: (122.72, 78, 76.96, 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      37     16.00
     O    1232      8.00
     N    1069      7.00
     C    4150      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 336 " - pdb=" SG  CYS E 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 379 " - pdb=" SG  CYS E 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 391 " - pdb=" SG  CYS E 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 480 " - pdb=" SG  CYS E 488 " 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 A 701 " - " ASN A 546 "
      " NAG A 702 " - " ASN A  90 "
      " NAG A 703 " - " ASN A 322 "
      " NAG A 704 " - " ASN A  53 "
      " NAG E 601 " - " ASN E 343 "
  Time building additional restraints: 0.57
  Conformation dependent library (CDL) restraints added in 401.9 milliseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 6 sheets defined
      57.0% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.872A  pdb=" N   GLN A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
      removed outlier: 3.565A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 102
      removed outlier: 3.609A  pdb=" N   GLN A 102 " --> pdb=" O   GLN A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 3.560A  pdb=" N   SER A 106 " --> pdb=" O   ASN A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.779A  pdb=" N   VAL A 172 " --> pdb=" O   TRP A 168 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.812A  pdb=" N   ASN A 194 " --> pdb=" O   MET A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 218 through 252
      removed outlier: 3.756A  pdb=" N   ILE A 223 " --> pdb=" O   ARG A 219 " (cutoff:3.500A)
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 299
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.588A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 3.974A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.846A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.962A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 448 through 465
      removed outlier: 4.211A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.963A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   LYS A 481 " --> pdb=" O   TRP A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 509
    Processing helix  chain 'A' and resid 513 through 533
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.970A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 575
      removed outlier: 3.808A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 599
      Proline residue:  A 590  - end of helix
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'E' and resid 337 through 343
      removed outlier: 3.955A  pdb=" N   VAL E 341 " --> pdb=" O   PRO E 337 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 349 through 353
    Processing helix  chain 'E' and resid 365 through 370
    Processing helix  chain 'E' and resid 385 through 390
      removed outlier: 3.531A  pdb=" N   LEU E 390 " --> pdb=" O   LEU E 387 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 404 through 410
    Processing helix  chain 'E' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 5.960A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 352
      removed outlier: 5.692A  pdb=" N   ASP A 355 " --> pdb=" O   LEU A 351 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454
    Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474

    320 hydrogen bonds defined for protein.
    893 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: 0.95

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2079
        1.35 -     1.47: 1767
        1.47 -     1.59: 2768
        1.59 -     1.71: 0
        1.71 -     1.84: 58
  Bond restraints: 6672
  Sorted by residual:
  bond pdb=" C1  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.24e+00
  bond pdb=" C1  NAG A 704 "
       pdb=" O5  NAG A 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.90e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.432 -0.026 2.00e-02 2.50e+03 1.74e+00
  bond pdb=" C1  NAG A 702 "
       pdb=" O5  NAG A 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.61e+00
  bond pdb=" C5  NAG E 601 "
       pdb=" O5  NAG E 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.438 -0.025 2.00e-02 2.50e+03 1.51e+00
  ... (remaining 6667 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 8902
        2.20 -     4.39: 150
        4.39 -     6.59: 15
        6.59 -     8.79: 3
        8.79 -    10.98: 1
  Bond angle restraints: 9071
  Sorted by residual:
  angle pdb=" CA  CYS A 141 "
        pdb=" CB  CYS A 141 "
        pdb=" SG  CYS A 141 "
      ideal   model   delta    sigma   weight residual
     114.40  125.38  -10.98 2.30e+00 1.89e-01 2.28e+01
  angle pdb=" N   CYS A 141 "
        pdb=" CA  CYS A 141 "
        pdb=" C   CYS A 141 "
      ideal   model   delta    sigma   weight residual
     108.96  115.21   -6.25 1.49e+00 4.50e-01 1.76e+01
  angle pdb=" N   CYS E 379 "
        pdb=" CA  CYS E 379 "
        pdb=" C   CYS E 379 "
      ideal   model   delta    sigma   weight residual
     108.60  114.00   -5.40 1.46e+00 4.69e-01 1.37e+01
  angle pdb=" CA  CYS E 379 "
        pdb=" CB  CYS E 379 "
        pdb=" SG  CYS E 379 "
      ideal   model   delta    sigma   weight residual
     114.40  121.73   -7.33 2.30e+00 1.89e-01 1.01e+01
  angle pdb=" CA  CYS A 133 "
        pdb=" CB  CYS A 133 "
        pdb=" SG  CYS A 133 "
      ideal   model   delta    sigma   weight residual
     114.40  121.68   -7.28 2.30e+00 1.89e-01 1.00e+01
  ... (remaining 9066 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3552
       17.59 -    35.19: 350
       35.19 -    52.78: 73
       52.78 -    70.37: 12
       70.37 -    87.96: 10
  Dihedral angle restraints: 3997
    sinusoidal: 1672
      harmonic: 2325
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   11.10   81.90     1      1.00e+01 1.00e-02 8.25e+01
  dihedral pdb=" CA  CYS A 141 "
           pdb=" C   CYS A 141 "
           pdb=" N   LEU A 142 "
           pdb=" CA  LEU A 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.46  -26.54     0      5.00e+00 4.00e-02 2.82e+01
  dihedral pdb=" CB  CYS E 379 "
           pdb=" SG  CYS E 379 "
           pdb=" SG  CYS E 432 "
           pdb=" CB  CYS E 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   51.66   41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 3994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 862
       0.078 -    0.156: 97
       0.156 -    0.234: 1
       0.234 -    0.312: 1
       0.312 -    0.390: 1
  Chirality restraints: 962
  Sorted by residual:
  chirality pdb=" C1  NAG E 601 "
            pdb=" ND2 ASN E 343 "
            pdb=" C2  NAG E 601 "
            pdb=" O5  NAG E 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.81e+00
  chirality pdb=" CA  CYS A 141 "
            pdb=" N   CYS A 141 "
            pdb=" C   CYS A 141 "
            pdb=" CB  CYS A 141 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CA  ASN E 343 "
            pdb=" N   ASN E 343 "
            pdb=" C   ASN E 343 "
            pdb=" CB  ASN E 343 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.59e-01
  ... (remaining 959 not shown)

  Planarity restraints: 1175
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 145 "   -0.034 5.00e-02 4.00e+02   5.10e-02 4.17e+00
        pdb=" N   PRO A 146 "    0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 146 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 146 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A  33 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.07e+00
        pdb=" C   ASN A  33 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASN A  33 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   HIS A  34 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 582 "    0.028 5.00e-02 4.00e+02   4.18e-02 2.80e+00
        pdb=" N   PRO A 583 "   -0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO A 583 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 583 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1172 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 196
        2.70 -     3.25: 6959
        3.25 -     3.80: 10455
        3.80 -     4.35: 13483
        4.35 -     4.90: 22150
  Nonbonded interactions: 53243
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 438 "
            pdb=" OD2 ASP E 442 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" O   VAL E 367 "
            pdb=" OG  SER E 371 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" NE2 GLN A 221 "
            pdb=" OD1 ASP A 225 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" OG  SER A 511 "
            pdb=" NH2 ARG A 514 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OG  SER E 349 "
            pdb=" O   LEU E 452 "
     model   vdw
     2.236 3.040
  ... (remaining 53238 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             1.680
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.650
  Find NCS groups from input model:        0.030
  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:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8064
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6684  Z= 0.206
  Angle     :  0.751  10.983   9100  Z= 0.430
  Chirality :  0.048   0.390    962
  Planarity :  0.005   0.051   1170
  Dihedral  : 14.493  87.964   2486
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 13.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.88 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -2.91 (0.25), residues: 788
  helix: -1.53 (0.22), residues: 377
  sheet: -0.84 (0.69), residues: 50
  loop : -2.49 (0.27), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 169 
 TYR   0.021   0.002   TYR E 453 
 PHE   0.015   0.002   PHE A 314 
 TRP   0.024   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 540 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6672)
  covalent geometry    : angle       0.73489 ( 9071)
  SS BOND              : bond        0.00425 (    7)
  SS BOND              : angle       3.24811 (   14)
  hydrogen bonds       : bond        0.14443 (  320)
  hydrogen bonds       : angle       6.54927 (  893)
  link_NAG-ASN         : bond        0.00866 (    5)
  link_NAG-ASN         : angle       2.30054 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8102 (m-40) cc_final: 0.7867 (t0)
REVERT: A   98 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7860 (tp-100)
REVERT: A  123 MET cc_start: 0.7787 (mtm) cc_final: 0.7464 (mtt)
REVERT: A  165 TRP cc_start: 0.7254 (t60) cc_final: 0.5965 (t60)
REVERT: A  455 MET cc_start: 0.8600 (tmm) cc_final: 0.8285 (tmm)
REVERT: A  478 TRP cc_start: 0.7962 (m100) cc_final: 0.7587 (m100)
REVERT: A  497 TYR cc_start: 0.7564 (m-80) cc_final: 0.6574 (m-80)
REVERT: A  505 HIS cc_start: 0.7573 (m90) cc_final: 0.7157 (m-70)
REVERT: E  366 SER cc_start: 0.8329 (m) cc_final: 0.8047 (p)
REVERT: E  396 TYR cc_start: 0.7613 (m-80) cc_final: 0.6939 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.0941
  time to fit residues: 15.2418
Evaluate side-chains
  84 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 221 GLN
A 239 HIS
A 290 ASN
** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 GLN
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
E 334 ASN
E 388 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.106916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.082012 restraints weight = 13785.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.084681 restraints weight = 7385.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.086476 restraints weight = 5049.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.087548 restraints weight = 4003.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.087804 restraints weight = 3496.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3372
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3372 r_free = 0.3372    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3371 r_free = 0.3371    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3371
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6684  Z= 0.179
  Angle     :  0.675   9.501   9100  Z= 0.344
  Chirality :  0.047   0.290    962
  Planarity :  0.005   0.068   1170
  Dihedral  :  5.572  34.538    968
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.22 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.02 (0.28), residues: 788
  helix: -0.03 (0.25), residues: 390
  sheet: -0.34 (0.72), residues: 51
  loop : -1.42 (0.32), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 219 
 TYR   0.021   0.002   TYR A 183 
 PHE   0.012   0.001   PHE E 392 
 TRP   0.016   0.002   TRP A 473 
 HIS   0.003   0.001   HIS A 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 6672)
  covalent geometry    : angle       0.66823 ( 9071)
  SS BOND              : bond        0.01106 (    7)
  SS BOND              : angle       1.89582 (   14)
  hydrogen bonds       : bond        0.05315 (  320)
  hydrogen bonds       : angle       5.10643 (  893)
  link_NAG-ASN         : bond        0.00712 (    5)
  link_NAG-ASN         : angle       1.67532 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8137 (m-40) cc_final: 0.7862 (t0)
REVERT: A  114 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8352 (ptpp)
REVERT: A  123 MET cc_start: 0.7974 (mtm) cc_final: 0.7619 (mtt)
REVERT: A  165 TRP cc_start: 0.7227 (t60) cc_final: 0.6377 (t60)
REVERT: A  222 LEU cc_start: 0.8565 (tp) cc_final: 0.8359 (tp)
REVERT: A  249 MET cc_start: 0.7772 (mmm) cc_final: 0.7567 (mmm)
REVERT: A  455 MET cc_start: 0.8588 (tmm) cc_final: 0.8262 (tmm)
REVERT: A  481 LYS cc_start: 0.7736 (mttt) cc_final: 0.7300 (mttt)
REVERT: A  497 TYR cc_start: 0.7880 (m-80) cc_final: 0.6643 (m-80)
REVERT: A  505 HIS cc_start: 0.7590 (m90) cc_final: 0.7222 (m-70)
REVERT: A  557 MET cc_start: 0.9204 (tmm) cc_final: 0.8765 (tmm)
REVERT: E  340 GLU cc_start: 0.7880 (pt0) cc_final: 0.7540 (mm-30)
REVERT: E  392 PHE cc_start: 0.8484 (m-80) cc_final: 0.8203 (m-10)
REVERT: E  424 LYS cc_start: 0.7797 (tptt) cc_final: 0.7530 (tppt)
REVERT: E  450 ASN cc_start: 0.8431 (m110) cc_final: 0.8190 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 105
  average time/residue: 0.0907
  time to fit residues: 12.4292
Evaluate side-chains
  85 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 40 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 65 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.2980
   chunk 62 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 ASN
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.109714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.084597 restraints weight = 20275.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.087625 restraints weight = 8731.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.088738 restraints weight = 5450.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.089456 restraints weight = 4458.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.090270 restraints weight = 4112.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3411
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3411 r_free = 0.3411    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3411
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6684  Z= 0.132
  Angle     :  0.616   8.813   9100  Z= 0.312
  Chirality :  0.044   0.250    962
  Planarity :  0.005   0.045   1170
  Dihedral  :  4.947  30.044    967
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.23 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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: -0.11 (0.29), residues: 788
  helix:  0.71 (0.26), residues: 391
  sheet: -0.03 (0.71), residues: 51
  loop : -0.94 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 466 
 TYR   0.018   0.002   TYR A 183 
 PHE   0.010   0.001   PHE A 230 
 TRP   0.017   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6672)
  covalent geometry    : angle       0.61161 ( 9071)
  SS BOND              : bond        0.00366 (    7)
  SS BOND              : angle       1.12196 (   14)
  hydrogen bonds       : bond        0.04592 (  320)
  hydrogen bonds       : angle       4.65609 (  893)
  link_NAG-ASN         : bond        0.00588 (    5)
  link_NAG-ASN         : angle       1.56651 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 105
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8153 (m-40) cc_final: 0.7868 (t0)
REVERT: A  123 MET cc_start: 0.7809 (mtm) cc_final: 0.7607 (mtt)
REVERT: A  165 TRP cc_start: 0.7204 (t60) cc_final: 0.6598 (t60)
REVERT: A  455 MET cc_start: 0.8431 (tmm) cc_final: 0.8149 (tmm)
REVERT: A  481 LYS cc_start: 0.7605 (mttt) cc_final: 0.7327 (mttt)
REVERT: A  489 GLU cc_start: 0.8781 (pm20) cc_final: 0.8537 (pm20)
REVERT: A  497 TYR cc_start: 0.7929 (m-80) cc_final: 0.6758 (m-80)
REVERT: A  505 HIS cc_start: 0.7680 (m90) cc_final: 0.7209 (m-70)
REVERT: A  557 MET cc_start: 0.9154 (tmm) cc_final: 0.8677 (tmm)
REVERT: E  340 GLU cc_start: 0.8083 (pt0) cc_final: 0.7420 (mm-30)
REVERT: E  392 PHE cc_start: 0.8617 (m-80) cc_final: 0.8242 (m-10)
REVERT: E  396 TYR cc_start: 0.7812 (m-10) cc_final: 0.7077 (m-10)
  outliers start: 9
  outliers final: 5
  residues processed: 109
  average time/residue: 0.0921
  time to fit residues: 13.3152
Evaluate side-chains
  90 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 85
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 28 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   overall best weight:    1.3182

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.108050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.080145 restraints weight = 27024.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.083818 restraints weight = 11102.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.086250 restraints weight = 6469.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.087813 restraints weight = 4652.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.088802 restraints weight = 3814.388|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3393
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3393 r_free = 0.3393    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3393
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.2465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6684  Z= 0.170
  Angle     :  0.654  10.329   9100  Z= 0.324
  Chirality :  0.044   0.228    962
  Planarity :  0.004   0.037   1170
  Dihedral  :  4.881  27.078    967
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.09 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.16 (0.30), residues: 788
  helix:  0.88 (0.26), residues: 389
  sheet:  0.08 (0.71), residues: 51
  loop : -0.73 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 357 
 TYR   0.019   0.002   TYR E 453 
 PHE   0.015   0.001   PHE A 603 
 TRP   0.050   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6672)
  covalent geometry    : angle       0.64894 ( 9071)
  SS BOND              : bond        0.00603 (    7)
  SS BOND              : angle       1.47364 (   14)
  hydrogen bonds       : bond        0.04767 (  320)
  hydrogen bonds       : angle       4.64342 (  893)
  link_NAG-ASN         : bond        0.00682 (    5)
  link_NAG-ASN         : angle       1.58418 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8115 (m-40) cc_final: 0.7858 (t0)
REVERT: A  123 MET cc_start: 0.7828 (mtm) cc_final: 0.7475 (mtt)
REVERT: A  152 MET cc_start: 0.7757 (tpp) cc_final: 0.7304 (tpp)
REVERT: A  161 ARG cc_start: 0.6903 (mtp85) cc_final: 0.6141 (mtp180)
REVERT: A  455 MET cc_start: 0.8395 (tmm) cc_final: 0.8100 (tmm)
REVERT: A  481 LYS cc_start: 0.7588 (mttt) cc_final: 0.7355 (mttt)
REVERT: A  497 TYR cc_start: 0.7963 (m-80) cc_final: 0.6746 (m-80)
REVERT: A  505 HIS cc_start: 0.7648 (m90) cc_final: 0.7165 (m-70)
REVERT: A  557 MET cc_start: 0.9151 (tmm) cc_final: 0.8694 (tmm)
REVERT: E  340 GLU cc_start: 0.7797 (pt0) cc_final: 0.7414 (mm-30)
REVERT: E  355 ARG cc_start: 0.8487 (ttt90) cc_final: 0.7621 (ttm-80)
  outliers start: 14
  outliers final: 13
  residues processed: 106
  average time/residue: 0.0882
  time to fit residues: 12.2351
Evaluate side-chains
  103 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  366 SER
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0030
   chunk 31 optimal weight:    0.0570
   chunk 60 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 46 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 11 optimal weight:    0.6980
   chunk 41 optimal weight:    5.9990
   overall best weight:    0.5108

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.111912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.084507 restraints weight = 24346.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.088213 restraints weight = 10131.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.090631 restraints weight = 5920.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.092204 restraints weight = 4266.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.093101 restraints weight = 3499.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3463
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3463 r_free = 0.3463    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3463
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6684  Z= 0.119
  Angle     :  0.620   9.642   9100  Z= 0.306
  Chirality :  0.043   0.237    962
  Planarity :  0.004   0.037   1170
  Dihedral  :  4.487  22.959    967
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 14.96 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.47 (0.30), residues: 788
  helix:  1.14 (0.26), residues: 387
  sheet:  0.19 (0.71), residues: 51
  loop : -0.55 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 357 
 TYR   0.019   0.001   TYR E 421 
 PHE   0.012   0.001   PHE A 603 
 TRP   0.047   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6672)
  covalent geometry    : angle       0.61569 ( 9071)
  SS BOND              : bond        0.00394 (    7)
  SS BOND              : angle       1.36847 (   14)
  hydrogen bonds       : bond        0.04199 (  320)
  hydrogen bonds       : angle       4.40105 (  893)
  link_NAG-ASN         : bond        0.00477 (    5)
  link_NAG-ASN         : angle       1.52323 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8152 (m-40) cc_final: 0.7914 (t0)
REVERT: A  152 MET cc_start: 0.7780 (tpp) cc_final: 0.7529 (tpp)
REVERT: A  161 ARG cc_start: 0.6859 (mtp85) cc_final: 0.6657 (mtp85)
REVERT: A  165 TRP cc_start: 0.7120 (t60) cc_final: 0.6035 (t60)
REVERT: A  249 MET cc_start: 0.7883 (mmm) cc_final: 0.7649 (mmm)
REVERT: A  478 TRP cc_start: 0.7894 (m100) cc_final: 0.7501 (m100)
REVERT: A  505 HIS cc_start: 0.7724 (m90) cc_final: 0.7215 (m-70)
REVERT: A  557 MET cc_start: 0.9111 (tmm) cc_final: 0.8611 (tmm)
REVERT: E  340 GLU cc_start: 0.7686 (pt0) cc_final: 0.7318 (mm-30)
REVERT: E  392 PHE cc_start: 0.8292 (m-10) cc_final: 0.8053 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0855
  time to fit residues: 12.7995
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  440 ASN
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   chunk 47 optimal weight:    7.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.107561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.082402 restraints weight = 13686.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.085111 restraints weight = 7367.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.086841 restraints weight = 5037.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.087980 restraints weight = 4012.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.088560 restraints weight = 3491.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6684  Z= 0.208
  Angle     :  0.720  11.942   9100  Z= 0.359
  Chirality :  0.047   0.263    962
  Planarity :  0.004   0.038   1170
  Dihedral  :  4.828  25.401    967
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.40 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.35 (0.30), residues: 788
  helix:  0.95 (0.26), residues: 387
  sheet:  0.19 (0.72), residues: 51
  loop : -0.50 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 357 
 TYR   0.022   0.002   TYR E 453 
 PHE   0.018   0.002   PHE A 603 
 TRP   0.038   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 ( 6672)
  covalent geometry    : angle       0.70335 ( 9071)
  SS BOND              : bond        0.00438 (    7)
  SS BOND              : angle       3.60853 (   14)
  hydrogen bonds       : bond        0.04956 (  320)
  hydrogen bonds       : angle       4.63944 (  893)
  link_NAG-ASN         : bond        0.00778 (    5)
  link_NAG-ASN         : angle       1.75882 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8102 (m-40) cc_final: 0.7863 (t0)
REVERT: A  161 ARG cc_start: 0.7064 (mtp85) cc_final: 0.6545 (mtp85)
REVERT: A  455 MET cc_start: 0.8119 (tmm) cc_final: 0.7894 (ttp)
REVERT: A  478 TRP cc_start: 0.8025 (m100) cc_final: 0.7598 (m100)
REVERT: A  505 HIS cc_start: 0.7667 (m90) cc_final: 0.7181 (m-70)
REVERT: A  557 MET cc_start: 0.9176 (tmm) cc_final: 0.8648 (tmm)
REVERT: E  340 GLU cc_start: 0.7803 (pt0) cc_final: 0.7489 (mm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0878
  time to fit residues: 11.9163
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 44 optimal weight:    0.4980
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0870
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.0560

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.109965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.084526 restraints weight = 13741.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.087287 restraints weight = 7397.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.089143 restraints weight = 5055.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.090376 restraints weight = 3997.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.090943 restraints weight = 3456.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3426
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3426 r_free = 0.3426    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3426
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6684  Z= 0.153
  Angle     :  0.685  12.413   9100  Z= 0.343
  Chirality :  0.044   0.220    962
  Planarity :  0.004   0.039   1170
  Dihedral  :  4.619  24.383    967
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.98 %
    Favored  : 80.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.58 (0.30), residues: 788
  helix:  1.08 (0.26), residues: 386
  sheet:  0.46 (0.72), residues: 49
  loop : -0.32 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 219 
 TYR   0.018   0.002   TYR A 183 
 PHE   0.016   0.001   PHE A 603 
 TRP   0.039   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6672)
  covalent geometry    : angle       0.66964 ( 9071)
  SS BOND              : bond        0.00365 (    7)
  SS BOND              : angle       3.47791 (   14)
  hydrogen bonds       : bond        0.04551 (  320)
  hydrogen bonds       : angle       4.49834 (  893)
  link_NAG-ASN         : bond        0.00585 (    5)
  link_NAG-ASN         : angle       1.49552 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8147 (m-40) cc_final: 0.7892 (t0)
REVERT: A  376 MET cc_start: 0.9008 (mmm) cc_final: 0.8784 (mmm)
REVERT: A  455 MET cc_start: 0.8098 (tmm) cc_final: 0.7813 (ttp)
REVERT: A  505 HIS cc_start: 0.7723 (m90) cc_final: 0.7214 (m-70)
REVERT: A  557 MET cc_start: 0.9102 (tmm) cc_final: 0.8580 (tmm)
REVERT: E  340 GLU cc_start: 0.7699 (pt0) cc_final: 0.7390 (mm-30)
REVERT: E  392 PHE cc_start: 0.8255 (m-10) cc_final: 0.8010 (m-10)
  outliers start: 16
  outliers final: 14
  residues processed: 101
  average time/residue: 0.0900
  time to fit residues: 11.9829
Evaluate side-chains
  97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  440 ASN
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 32 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 77 optimal weight:    0.7980
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.107215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.081434 restraints weight = 20932.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.084237 restraints weight = 9206.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.085143 restraints weight = 6064.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.085751 restraints weight = 5199.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.085995 restraints weight = 4560.170|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3329
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3329 r_free = 0.3329    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3329
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6684  Z= 0.223
  Angle     :  0.744  12.273   9100  Z= 0.374
  Chirality :  0.047   0.227    962
  Planarity :  0.005   0.040   1170
  Dihedral  :  4.958  25.861    967
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 16.98 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.36 (0.30), residues: 788
  helix:  0.81 (0.26), residues: 389
  sheet:  0.33 (0.72), residues: 49
  loop : -0.32 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 219 
 TYR   0.024   0.002   TYR E 369 
 PHE   0.018   0.002   PHE A 603 
 TRP   0.034   0.002   TRP A 478 
 HIS   0.004   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 ( 6672)
  covalent geometry    : angle       0.72764 ( 9071)
  SS BOND              : bond        0.00471 (    7)
  SS BOND              : angle       3.65124 (   14)
  hydrogen bonds       : bond        0.05028 (  320)
  hydrogen bonds       : angle       4.72661 (  893)
  link_NAG-ASN         : bond        0.00818 (    5)
  link_NAG-ASN         : angle       1.84173 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8200 (m-40) cc_final: 0.7891 (t0)
REVERT: A  376 MET cc_start: 0.9053 (mmm) cc_final: 0.8790 (mmm)
REVERT: A  455 MET cc_start: 0.8069 (tmm) cc_final: 0.7833 (ttp)
REVERT: A  505 HIS cc_start: 0.7687 (m90) cc_final: 0.7188 (m-70)
REVERT: A  557 MET cc_start: 0.9116 (tmm) cc_final: 0.8619 (tmm)
REVERT: A  572 ASN cc_start: 0.8617 (OUTLIER) cc_final: 0.8284 (m-40)
REVERT: E  340 GLU cc_start: 0.8004 (pt0) cc_final: 0.7605 (mm-30)
REVERT: E  392 PHE cc_start: 0.8361 (m-10) cc_final: 0.8015 (m-10)
  outliers start: 20
  outliers final: 15
  residues processed: 104
  average time/residue: 0.0859
  time to fit residues: 11.8801
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain A residue  579 MET
Chi-restraints excluded: chain A residue  601 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  415 THR
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 30 optimal weight:    2.9990
   chunk 45 optimal weight:    0.6980
   chunk 41 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 4 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 28 optimal weight:    0.1980
   chunk 59 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.111701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.085665 restraints weight = 24658.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.090010 restraints weight = 10005.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.091239 restraints weight = 5239.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.091632 restraints weight = 4335.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.092014 restraints weight = 3920.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3440
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3440 r_free = 0.3440    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3440
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6684  Z= 0.130
  Angle     :  0.695  11.827   9100  Z= 0.345
  Chirality :  0.044   0.207    962
  Planarity :  0.004   0.040   1170
  Dihedral  :  4.572  24.106    967
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.42 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.70 (0.31), residues: 788
  helix:  1.11 (0.27), residues: 386
  sheet:  0.36 (0.71), residues: 49
  loop : -0.13 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 161 
 TYR   0.018   0.001   TYR A 183 
 PHE   0.018   0.001   PHE A 603 
 TRP   0.030   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 6672)
  covalent geometry    : angle       0.68116 ( 9071)
  SS BOND              : bond        0.00303 (    7)
  SS BOND              : angle       3.38569 (   14)
  hydrogen bonds       : bond        0.04306 (  320)
  hydrogen bonds       : angle       4.51159 (  893)
  link_NAG-ASN         : bond        0.00484 (    5)
  link_NAG-ASN         : angle       1.44210 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 96
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8182 (m-40) cc_final: 0.7887 (t0)
REVERT: A  152 MET cc_start: 0.7815 (tpp) cc_final: 0.7105 (tpt)
REVERT: A  376 MET cc_start: 0.8864 (mmm) cc_final: 0.8637 (mmm)
REVERT: A  455 MET cc_start: 0.8112 (tmm) cc_final: 0.7877 (ttp)
REVERT: A  505 HIS cc_start: 0.7736 (m90) cc_final: 0.7232 (m-70)
REVERT: A  557 MET cc_start: 0.9045 (tmm) cc_final: 0.8588 (tmm)
REVERT: A  572 ASN cc_start: 0.8601 (OUTLIER) cc_final: 0.8294 (m-40)
REVERT: E  340 GLU cc_start: 0.7891 (pt0) cc_final: 0.7445 (mm-30)
REVERT: E  392 PHE cc_start: 0.8300 (m-10) cc_final: 0.8007 (m-10)
REVERT: E  414 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8171 (mp10)
  outliers start: 14
  outliers final: 11
  residues processed: 106
  average time/residue: 0.0877
  time to fit residues: 12.3305
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 LEU
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  383 SER
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 54 optimal weight:    0.0670
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0270
   chunk 74 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0470
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.3476

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.113272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.087983 restraints weight = 20247.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090763 restraints weight = 8919.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.092183 restraints weight = 5569.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.093159 restraints weight = 4440.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.093440 restraints weight = 4075.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3465
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3465 r_free = 0.3465    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3465
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.3599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6684  Z= 0.125
  Angle     :  0.713  11.527   9100  Z= 0.351
  Chirality :  0.044   0.213    962
  Planarity :  0.004   0.039   1170
  Dihedral  :  4.381  22.288    967
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.56 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.79 (0.31), residues: 788
  helix:  1.11 (0.27), residues: 385
  sheet:  0.29 (0.71), residues: 49
  loop :  0.04 (0.36), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 161 
 TYR   0.028   0.001   TYR A  50 
 PHE   0.018   0.001   PHE A 603 
 TRP   0.028   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6672)
  covalent geometry    : angle       0.70039 ( 9071)
  SS BOND              : bond        0.00338 (    7)
  SS BOND              : angle       3.30133 (   14)
  hydrogen bonds       : bond        0.04080 (  320)
  hydrogen bonds       : angle       4.43793 (  893)
  link_NAG-ASN         : bond        0.00463 (    5)
  link_NAG-ASN         : angle       1.37513 (   15)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8246 (m-40) cc_final: 0.7948 (t0)
REVERT: A   98 GLN cc_start: 0.8139 (pt0) cc_final: 0.7932 (tm-30)
REVERT: A  455 MET cc_start: 0.8141 (tmm) cc_final: 0.7915 (ttp)
REVERT: A  497 TYR cc_start: 0.7911 (m-80) cc_final: 0.6524 (m-80)
REVERT: A  505 HIS cc_start: 0.7753 (m90) cc_final: 0.7253 (m-70)
REVERT: A  572 ASN cc_start: 0.8554 (OUTLIER) cc_final: 0.8235 (m-40)
REVERT: E  340 GLU cc_start: 0.7817 (pt0) cc_final: 0.7380 (mm-30)
REVERT: E  357 ARG cc_start: 0.7755 (ttm-80) cc_final: 0.7057 (tpt170)
REVERT: E  392 PHE cc_start: 0.8290 (m-10) cc_final: 0.8002 (m-10)
REVERT: E  469 SER cc_start: 0.8883 (t) cc_final: 0.8670 (p)
REVERT: E  511 VAL cc_start: 0.9078 (t) cc_final: 0.8830 (p)
  outliers start: 13
  outliers final: 11
  residues processed: 116
  average time/residue: 0.0773
  time to fit residues: 12.0697
Evaluate side-chains
  110 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 98
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  133 CYS
Chi-restraints excluded: chain A residue  149 ASN
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  572 ASN
Chi-restraints excluded: chain E residue  350 VAL
Chi-restraints excluded: chain E residue  362 VAL
Chi-restraints excluded: chain E residue  379 CYS
Chi-restraints excluded: chain E residue  380 TYR
Chi-restraints excluded: chain E residue  432 CYS
Chi-restraints excluded: chain E residue  440 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 13 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 40 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.111436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.086091 restraints weight = 19913.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.089105 restraints weight = 8677.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.090187 restraints weight = 5556.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.091100 restraints weight = 4559.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.091356 restraints weight = 3974.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3432
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3432 r_free = 0.3432    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3432
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.3573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6684  Z= 0.151
  Angle     :  0.717  11.344   9100  Z= 0.354
  Chirality :  0.045   0.228    962
  Planarity :  0.004   0.040   1170
  Dihedral  :  4.444  22.660    967
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 19.28 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    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:  0.83 (0.31), residues: 788
  helix:  1.09 (0.27), residues: 384
  sheet:  0.41 (0.72), residues: 49
  loop :  0.10 (0.36), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 161 
 TYR   0.018   0.001   TYR A  50 
 PHE   0.017   0.001   PHE A 603 
 TRP   0.026   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 ( 6672)
  covalent geometry    : angle       0.70307 ( 9071)
  SS BOND              : bond        0.00242 (    7)
  SS BOND              : angle       3.32700 (   14)
  hydrogen bonds       : bond        0.04260 (  320)
  hydrogen bonds       : angle       4.47400 (  893)
  link_NAG-ASN         : bond        0.00566 (    5)
  link_NAG-ASN         : angle       1.57420 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1421.41 seconds
wall clock time: 25 minutes 10.87 seconds (1510.87 seconds total)