Starting phenix.real_space_refine
on Tue Feb 11 20:17:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_31543.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_31543.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_31543.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_31543.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fdh_31543/02_2025/7fdh_31543.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.51, per 1000 atoms: 1.00
  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: 1.67
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.94
  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: 2.17

  Time building geometry restraints manager: 1.94 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:             1.980
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     22.700
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.010
-------------------------------------------------------------------------------
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   6672  Z= 0.273
  Angle     :  0.735  10.983   9071  Z= 0.425
  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 : 13.20
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.024   0.002   TRP A 473 
 HIS   0.004   0.001   HIS A 540 
 PHE   0.015   0.002   PHE A 314 
 TYR   0.021   0.002   TYR E 453 
 ARG   0.003   0.001   ARG A 169 

*********************** 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  : 0.716 
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: 0.7859 (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: 0.2191
  time to fit residues: 35.2708
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  : 0.706 
-------------------------------------------------------------------------------
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 65 optimal weight:    5.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3705 r_free = 0.3705 target = 0.108425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.082484 restraints weight = 26669.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.086789 restraints weight = 10729.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.088040 restraints weight = 5417.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3367
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3367 r_free = 0.3367    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6672  Z= 0.215
  Angle     :  0.650   9.405   9071  Z= 0.331
  Chirality :  0.046   0.312    962
  Planarity :  0.005   0.063   1170
  Dihedral  :  5.393  33.884    968
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.28), residues: 788
  helix:  0.16 (0.25), residues: 386
  sheet: -0.27 (0.72), residues: 51
  loop : -1.34 (0.32), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 473 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.013   0.001   PHE E 392 
 TYR   0.020   0.002   TYR A 183 
 ARG   0.006   0.001   ARG A 219 

*********************** 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
  116 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8154 (m-40) cc_final: 0.7859 (t0)
REVERT: A  123 MET cc_start: 0.7932 (mtm) cc_final: 0.7566 (mtt)
REVERT: A  165 TRP cc_start: 0.7233 (t60) cc_final: 0.6355 (t60)
REVERT: A  222 LEU cc_start: 0.8529 (tp) cc_final: 0.8306 (tp)
REVERT: A  249 MET cc_start: 0.7991 (mmm) cc_final: 0.7745 (mmm)
REVERT: A  455 MET cc_start: 0.8518 (tmm) cc_final: 0.8218 (tmm)
REVERT: A  497 TYR cc_start: 0.8005 (m-80) cc_final: 0.6821 (m-80)
REVERT: A  505 HIS cc_start: 0.7597 (m90) cc_final: 0.7190 (m-70)
REVERT: A  557 MET cc_start: 0.9188 (tmm) cc_final: 0.8739 (tmm)
REVERT: E  340 GLU cc_start: 0.8078 (pt0) cc_final: 0.7460 (mm-30)
REVERT: E  392 PHE cc_start: 0.8611 (m-80) cc_final: 0.8297 (m-10)
REVERT: E  424 LYS cc_start: 0.7727 (tptt) cc_final: 0.7447 (tppt)
REVERT: E  450 ASN cc_start: 0.8444 (m110) cc_final: 0.8210 (t0)
REVERT: E  507 PRO cc_start: 0.9170 (Cg_exo) cc_final: 0.8906 (Cg_endo)
  outliers start: 8
  outliers final: 6
  residues processed: 113
  average time/residue: 0.2061
  time to fit residues: 30.6722
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.749 
-------------------------------------------------------------------------------
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 61 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 15 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 6 optimal weight:    0.3980
   chunk 70 optimal weight:    2.9990
   chunk 54 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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
E 409 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.110397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.085231 restraints weight = 19231.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.088113 restraints weight = 8617.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.089264 restraints weight = 5350.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    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 = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6672  Z= 0.184
  Angle     :  0.611   8.955   9071  Z= 0.310
  Chirality :  0.044   0.246    962
  Planarity :  0.004   0.040   1170
  Dihedral  :  4.821  29.325    967
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.66 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.29), residues: 788
  helix:  0.79 (0.26), residues: 390
  sheet:  0.10 (0.72), residues: 51
  loop : -0.84 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 168 
 HIS   0.003   0.001   HIS A  34 
 PHE   0.010   0.001   PHE A 230 
 TYR   0.019   0.002   TYR A 183 
 ARG   0.004   0.001   ARG E 466 

*********************** 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
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8170 (m-40) cc_final: 0.7865 (t0)
REVERT: A  123 MET cc_start: 0.7812 (mtm) cc_final: 0.7603 (mtt)
REVERT: A  165 TRP cc_start: 0.7178 (t60) cc_final: 0.6288 (t60)
REVERT: A  455 MET cc_start: 0.8473 (tmm) cc_final: 0.8174 (tmm)
REVERT: A  481 LYS cc_start: 0.7602 (mttt) cc_final: 0.7250 (mttt)
REVERT: A  489 GLU cc_start: 0.8847 (pm20) cc_final: 0.8584 (pm20)
REVERT: A  497 TYR cc_start: 0.7934 (m-80) cc_final: 0.6732 (m-80)
REVERT: A  505 HIS cc_start: 0.7539 (m90) cc_final: 0.7115 (m-70)
REVERT: A  557 MET cc_start: 0.9167 (tmm) cc_final: 0.8708 (tmm)
REVERT: E  340 GLU cc_start: 0.8104 (pt0) cc_final: 0.7480 (mm-30)
REVERT: E  392 PHE cc_start: 0.8586 (m-80) cc_final: 0.8249 (m-10)
REVERT: E  450 ASN cc_start: 0.8396 (m110) cc_final: 0.8150 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 113
  average time/residue: 0.2085
  time to fit residues: 30.6388
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 90
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
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  366 SER
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 46 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0670
   chunk 69 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 42 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   chunk 45 optimal weight:    7.9990
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3759 r_free = 0.3759 target = 0.111481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.083750 restraints weight = 26203.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087525 restraints weight = 10601.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.090040 restraints weight = 6089.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3415
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3415 r_free = 0.3415    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 = 0.3415 r_free = 0.3415    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3415
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6672  Z= 0.174
  Angle     :  0.615  10.327   9071  Z= 0.304
  Chirality :  0.043   0.231    962
  Planarity :  0.004   0.036   1170
  Dihedral  :  4.602  25.147    967
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.96 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.30), residues: 788
  helix:  1.12 (0.26), residues: 384
  sheet:  0.40 (0.72), residues: 50
  loop : -0.59 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.009   0.001   PHE E 429 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.007   0.001   ARG A 161 

*********************** 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
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8185 (m-40) cc_final: 0.7917 (t0)
REVERT: A  123 MET cc_start: 0.7819 (mtm) cc_final: 0.7615 (mtt)
REVERT: A  165 TRP cc_start: 0.7144 (t60) cc_final: 0.6142 (t60)
REVERT: A  249 MET cc_start: 0.8216 (mmm) cc_final: 0.7907 (mmm)
REVERT: A  455 MET cc_start: 0.8251 (tmm) cc_final: 0.7883 (tmm)
REVERT: A  478 TRP cc_start: 0.8006 (m100) cc_final: 0.7604 (m100)
REVERT: A  481 LYS cc_start: 0.7320 (mttt) cc_final: 0.7112 (mttt)
REVERT: A  505 HIS cc_start: 0.7531 (m90) cc_final: 0.7046 (m-70)
REVERT: E  340 GLU cc_start: 0.7975 (pt0) cc_final: 0.7367 (mm-30)
  outliers start: 13
  outliers final: 13
  residues processed: 105
  average time/residue: 0.1985
  time to fit residues: 27.7497
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  : 0.847 
-------------------------------------------------------------------------------
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  116 LEU
Chi-restraints excluded: chain A residue  190 MET
Chi-restraints excluded: chain A residue  233 ILE
Chi-restraints excluded: chain A residue  360 MET
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  366 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:    0.6980
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0010
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 210 ASN
** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.112437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.087247 restraints weight = 17087.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.089682 restraints weight = 8243.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.091795 restraints weight = 5471.026|
|-----------------------------------------------------------------------------|
r_work (final): 0.3439
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3438
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3438 r_free = 0.3438    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 = 0.3438 r_free = 0.3438    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3438
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6672  Z= 0.178
  Angle     :  0.633  11.123   9071  Z= 0.315
  Chirality :  0.044   0.225    962
  Planarity :  0.005   0.053   1170
  Dihedral  :  4.474  23.207    967
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 8.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.97 %
    Favored  : 81.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.61 (0.30), residues: 788
  helix:  1.25 (0.26), residues: 385
  sheet:  0.18 (0.71), residues: 51
  loop : -0.46 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.014   0.001   PHE E 429 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.007   0.001   ARG E 357 

*********************** 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
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8220 (m-40) cc_final: 0.7936 (t0)
REVERT: A  249 MET cc_start: 0.8242 (mmm) cc_final: 0.7887 (mmm)
REVERT: A  455 MET cc_start: 0.8239 (tmm) cc_final: 0.7937 (tmm)
REVERT: A  481 LYS cc_start: 0.7155 (mttt) cc_final: 0.6925 (mttt)
REVERT: A  505 HIS cc_start: 0.7612 (m90) cc_final: 0.7135 (m-70)
REVERT: E  340 GLU cc_start: 0.7987 (pt0) cc_final: 0.7350 (mm-30)
REVERT: E  392 PHE cc_start: 0.8319 (m-10) cc_final: 0.8037 (m-10)
REVERT: E  396 TYR cc_start: 0.7307 (m-10) cc_final: 0.6987 (m-10)
  outliers start: 14
  outliers final: 12
  residues processed: 108
  average time/residue: 0.1973
  time to fit residues: 28.1409
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.2980
   chunk 76 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 8 optimal weight:    5.9990
   chunk 44 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 56 optimal weight:    0.5980
   chunk 30 optimal weight:    0.2980
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.113491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.087788 restraints weight = 20238.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.092074 restraints weight = 9010.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.092941 restraints weight = 4955.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3455
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3453
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3453 r_free = 0.3453    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3453
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6672  Z= 0.166
  Angle     :  0.616  11.258   9071  Z= 0.305
  Chirality :  0.043   0.216    962
  Planarity :  0.004   0.038   1170
  Dihedral  :  4.310  22.870    967
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 15.83 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.30), residues: 788
  helix:  1.23 (0.26), residues: 388
  sheet:  0.41 (0.71), residues: 49
  loop : -0.27 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.010   0.001   PHE E 429 
 TYR   0.019   0.001   TYR A 183 
 ARG   0.006   0.001   ARG A 161 

*********************** 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
  119 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8216 (m-40) cc_final: 0.7937 (t0)
REVERT: A  249 MET cc_start: 0.8165 (mmm) cc_final: 0.7753 (mmm)
REVERT: A  455 MET cc_start: 0.8238 (tmm) cc_final: 0.7842 (tmm)
REVERT: A  481 LYS cc_start: 0.7102 (mttt) cc_final: 0.6881 (mttt)
REVERT: A  505 HIS cc_start: 0.7724 (m90) cc_final: 0.7258 (m-70)
REVERT: E  340 GLU cc_start: 0.7909 (pt0) cc_final: 0.7345 (mm-30)
REVERT: E  392 PHE cc_start: 0.8314 (m-10) cc_final: 0.8032 (m-10)
  outliers start: 17
  outliers final: 15
  residues processed: 113
  average time/residue: 0.2051
  time to fit residues: 30.9146
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
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  116 LEU
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  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  432 CYS
Chi-restraints excluded: chain E residue  434 ILE
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 32 optimal weight:    7.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 55 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0770
   chunk 27 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   chunk 24 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   overall best weight:    0.5940

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.113368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.087249 restraints weight = 24271.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.091502 restraints weight = 9966.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.092746 restraints weight = 5311.000|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3455
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3455 r_free = 0.3455    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3455
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6672  Z= 0.175
  Angle     :  0.640  11.325   9071  Z= 0.315
  Chirality :  0.043   0.215    962
  Planarity :  0.004   0.042   1170
  Dihedral  :  4.207  21.560    967
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 15.54 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.83 (0.30), residues: 788
  helix:  1.27 (0.26), residues: 384
  sheet:  0.46 (0.71), residues: 49
  loop : -0.15 (0.35), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.008   0.001   PHE E 429 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.006   0.001   ARG E 357 

*********************** 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
  121 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8230 (m-40) cc_final: 0.7946 (t0)
REVERT: A  152 MET cc_start: 0.8062 (tpp) cc_final: 0.7324 (tpt)
REVERT: A  249 MET cc_start: 0.8245 (mmm) cc_final: 0.7840 (mmm)
REVERT: A  455 MET cc_start: 0.8210 (tmm) cc_final: 0.7894 (tmm)
REVERT: A  505 HIS cc_start: 0.7726 (m90) cc_final: 0.7260 (m-70)
REVERT: E  340 GLU cc_start: 0.7869 (pt0) cc_final: 0.7311 (mm-30)
REVERT: E  392 PHE cc_start: 0.8321 (m-80) cc_final: 0.8040 (m-10)
REVERT: E  414 GLN cc_start: 0.8628 (mm-40) cc_final: 0.8351 (mp10)
  outliers start: 20
  outliers final: 17
  residues processed: 116
  average time/residue: 0.2044
  time to fit residues: 31.5037
Evaluate side-chains
  111 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 94
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  116 LEU
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  601 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  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 17 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0870
   chunk 21 optimal weight:    0.7980
   chunk 14 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.6958

-------------------------------------------------------------------------------
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**
E 409 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.112888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.086875 restraints weight = 19349.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.089937 restraints weight = 9025.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.091795 restraints weight = 5691.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3437 r_free = 0.3437    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 = 0.3437 r_free = 0.3437    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.3523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6672  Z= 0.189
  Angle     :  0.652  11.121   9071  Z= 0.322
  Chirality :  0.044   0.210    962
  Planarity :  0.004   0.041   1170
  Dihedral  :  4.210  20.948    967
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.83 %
    Favored  : 80.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.30), residues: 788
  helix:  1.22 (0.26), residues: 387
  sheet:  0.46 (0.71), residues: 49
  loop :  0.00 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.009   0.001   PHE A 315 
 TYR   0.019   0.001   TYR E 421 
 ARG   0.007   0.001   ARG E 357 

*********************** 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
  115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.847 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8237 (m-40) cc_final: 0.7952 (t0)
REVERT: A  152 MET cc_start: 0.8132 (tpp) cc_final: 0.7381 (tpt)
REVERT: A  249 MET cc_start: 0.8260 (mmm) cc_final: 0.7833 (mmm)
REVERT: A  376 MET cc_start: 0.8962 (mmm) cc_final: 0.8733 (mmm)
REVERT: A  455 MET cc_start: 0.8267 (tmm) cc_final: 0.8019 (tmm)
REVERT: A  497 TYR cc_start: 0.7840 (m-80) cc_final: 0.6561 (m-80)
REVERT: A  505 HIS cc_start: 0.7710 (m90) cc_final: 0.7268 (m-70)
REVERT: E  340 GLU cc_start: 0.7885 (pt0) cc_final: 0.7363 (mm-30)
REVERT: E  392 PHE cc_start: 0.8462 (m-80) cc_final: 0.8173 (m-10)
REVERT: E  469 SER cc_start: 0.8818 (t) cc_final: 0.8568 (p)
  outliers start: 16
  outliers final: 15
  residues processed: 111
  average time/residue: 0.1914
  time to fit residues: 28.3019
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
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 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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 4 optimal weight:    6.9990
   chunk 8 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0020
   chunk 29 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 59 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 472 GLN
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.113125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.084488 restraints weight = 27034.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.088359 restraints weight = 11122.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.090926 restraints weight = 6463.506|
|-----------------------------------------------------------------------------|
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) = 0.090         |
| 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) = 0.090         |
| 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: 0.7928
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6672  Z= 0.192
  Angle     :  0.666  10.932   9071  Z= 0.328
  Chirality :  0.043   0.209    962
  Planarity :  0.004   0.039   1170
  Dihedral  :  4.210  20.652    967
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.27 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.31), residues: 788
  helix:  1.25 (0.27), residues: 385
  sheet:  0.41 (0.71), residues: 49
  loop :  0.08 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 478 
 HIS   0.003   0.001   HIS A 505 
 PHE   0.008   0.001   PHE A 315 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.007   0.001   ARG E 357 

*********************** 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
  115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8208 (m-40) cc_final: 0.7949 (t0)
REVERT: A  152 MET cc_start: 0.8126 (tpp) cc_final: 0.7466 (tpt)
REVERT: A  249 MET cc_start: 0.8190 (mmm) cc_final: 0.7753 (mmm)
REVERT: A  376 MET cc_start: 0.8937 (mmm) cc_final: 0.8723 (mmm)
REVERT: A  505 HIS cc_start: 0.7746 (m90) cc_final: 0.7362 (m-70)
REVERT: E  340 GLU cc_start: 0.7771 (pt0) cc_final: 0.7324 (mm-30)
REVERT: E  392 PHE cc_start: 0.8459 (m-80) cc_final: 0.8229 (m-10)
REVERT: E  403 ARG cc_start: 0.7950 (ttp-170) cc_final: 0.7572 (ttp-170)
REVERT: E  469 SER cc_start: 0.8820 (t) cc_final: 0.8582 (p)
  outliers start: 16
  outliers final: 14
  residues processed: 110
  average time/residue: 0.2173
  time to fit residues: 32.0158
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
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  601 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
Chi-restraints excluded: chain E residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 12 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 47 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 58 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.8988

-------------------------------------------------------------------------------
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**
E 498 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.108900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.080607 restraints weight = 27299.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.084251 restraints weight = 11358.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.086684 restraints weight = 6668.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8022
moved from start:          0.3480

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   6672  Z= 0.321
  Angle     :  0.741  11.184   9071  Z= 0.370
  Chirality :  0.047   0.239    962
  Planarity :  0.005   0.064   1170
  Dihedral  :  4.716  22.842    967
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 17.99 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.30), residues: 788
  helix:  1.00 (0.26), residues: 392
  sheet:  0.28 (0.71), residues: 49
  loop : -0.06 (0.35), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 478 
 HIS   0.003   0.001   HIS A 401 
 PHE   0.013   0.002   PHE E 342 
 TYR   0.022   0.002   TYR E 453 
 ARG   0.007   0.001   ARG E 357 

********************** 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
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   64 ASN cc_start: 0.8208 (m-40) cc_final: 0.7954 (t0)
REVERT: A  249 MET cc_start: 0.8175 (mmm) cc_final: 0.7721 (mmm)
REVERT: A  376 MET cc_start: 0.9031 (mmm) cc_final: 0.8670 (mmm)
REVERT: A  497 TYR cc_start: 0.8009 (m-80) cc_final: 0.6684 (m-80)
REVERT: A  505 HIS cc_start: 0.7613 (m90) cc_final: 0.7228 (m-70)
REVERT: E  340 GLU cc_start: 0.7892 (pt0) cc_final: 0.7454 (mm-30)
REVERT: E  392 PHE cc_start: 0.8429 (m-80) cc_final: 0.8153 (m-10)
REVERT: E  469 SER cc_start: 0.8970 (t) cc_final: 0.8658 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1978
  time to fit residues: 26.6146
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
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  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 52 optimal weight:    0.1980
   chunk 77 optimal weight:    0.0270
   chunk 32 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 45 optimal weight:    0.0670
   chunk 61 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 27 optimal weight:    4.9990
   chunk 76 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A  98 GLN
** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.113985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.088768 restraints weight = 17392.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.091318 restraints weight = 8409.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.092989 restraints weight = 5614.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3459
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3459 r_free = 0.3459    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.3459
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6672  Z= 0.188
  Angle     :  0.700  10.878   9071  Z= 0.347
  Chirality :  0.044   0.207    962
  Planarity :  0.004   0.053   1170
  Dihedral  :  4.445  21.304    967
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 18.85 %
    Favored  : 79.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.31), residues: 788
  helix:  1.12 (0.27), residues: 387
  sheet:  0.28 (0.71), residues: 48
  loop :  0.08 (0.36), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 478 
 HIS   0.004   0.001   HIS A 505 
 PHE   0.010   0.001   PHE A 327 
 TYR   0.018   0.001   TYR A 183 
 ARG   0.009   0.001   ARG E 357 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2735.91 seconds
wall clock time: 49 minutes 47.58 seconds (2987.58 seconds total)