Starting phenix.real_space_refine
on Thu Jul 24 15:20:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.12
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr4_34045/07_2025/7yr4_34045.cif"
  }
  resolution = 4.12
  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=   0.016
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    4103      2.51       5
     N    1064      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 6394
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4832
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4832
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 26, 'TRANS': 565}
    Chain: "D"
      Number of atoms: 1562
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1562
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 12, 'TRANS': 182}
  Time building chain proxies: 5.01, per 1000 atoms: 0.78
  Number of scatterers: 6394
  At special positions: 0
  Unit cell: (84.24, 87.36, 118.56, 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    1190      8.00
     N    1064      7.00
     C    4103      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=2.04
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 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
  Time building additional restraints: 1.73
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1484

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 4 sheets defined
      51.3% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.726A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 82
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.594A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.994A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 3.665A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 4.003A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 219 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.683A  pdb=" N   LEU A 266 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    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
      removed outlier: 3.650A  pdb=" N   MET A 297 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 298 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.564A  pdb=" N   ALA A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 331
      removed outlier: 4.251A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 400 through 412
      removed outlier: 3.800A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 412 " --> pdb=" O   MET A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.663A  pdb=" N   LEU A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.174A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 3.992A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 509
      removed outlier: 4.076A  pdb=" N   SER A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 530
      removed outlier: 3.591A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 600
      Proline residue:  A 590  - end of helix
      removed outlier: 4.403A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 342
      removed outlier: 3.624A  pdb=" N   VAL D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 371
    Processing helix  chain 'D' and resid 405 through 407
      No H-bonds generated for 'chain 'D' and resid 405 through 407'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA2, first strand: chain 'D' and resid 356 through 358
    Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.551A  pdb=" N   TYR D 473 " --> pdb=" O   TYR D 489 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    272 hydrogen bonds defined for protein.
    795 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.97

  Time building geometry restraints manager: 2.15 seconds

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

  Histogram of bond lengths:
        1.09 -     1.23: 406
        1.23 -     1.38: 2252
        1.38 -     1.53: 3633
        1.53 -     1.68: 229
        1.68 -     1.83: 58
  Bond restraints: 6578
  Sorted by residual:
  bond pdb=" CG  PRO D 373 "
       pdb=" CD  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.503  1.085  0.418 3.40e-02 8.65e+02 1.51e+02
  bond pdb=" CB  PRO D 373 "
       pdb=" CG  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.492  1.217  0.275 5.00e-02 4.00e+02 3.03e+01
  bond pdb=" N   PRO D 373 "
       pdb=" CD  PRO D 373 "
    ideal  model  delta    sigma   weight residual
    1.473  1.517 -0.044 1.40e-02 5.10e+03 9.86e+00
  bond pdb=" CB  ASN A 601 "
       pdb=" CG  ASN A 601 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.36e+00
  bond pdb=" CG  LYS D 478 "
       pdb=" CD  LYS D 478 "
    ideal  model  delta    sigma   weight residual
    1.520  1.572 -0.052 3.00e-02 1.11e+03 3.06e+00
  ... (remaining 6573 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.18: 8924
        8.18 -    16.36: 11
       16.36 -    24.54: 1
       24.54 -    32.72: 1
       32.72 -    40.90: 1
  Bond angle restraints: 8938
  Sorted by residual:
  angle pdb=" N   PRO D 373 "
        pdb=" CD  PRO D 373 "
        pdb=" CG  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     103.20   75.60   27.60 1.50e+00 4.44e-01 3.39e+02
  angle pdb=" CB  PRO D 373 "
        pdb=" CG  PRO D 373 "
        pdb=" CD  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     106.10  147.00  -40.90 3.20e+00 9.77e-02 1.63e+02
  angle pdb=" CA  PRO D 373 "
        pdb=" CB  PRO D 373 "
        pdb=" CG  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     104.50   80.22   24.28 1.90e+00 2.77e-01 1.63e+02
  angle pdb=" CA  PRO D 373 "
        pdb=" N   PRO D 373 "
        pdb=" CD  PRO D 373 "
      ideal   model   delta    sigma   weight residual
     112.00  103.00    9.00 1.40e+00 5.10e-01 4.13e+01
  angle pdb=" C   LYS A 600 "
        pdb=" N   ASN A 601 "
        pdb=" CA  ASN A 601 "
      ideal   model   delta    sigma   weight residual
     123.05  130.49   -7.44 1.57e+00 4.06e-01 2.25e+01
  ... (remaining 8933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3445
       17.77 -    35.55: 354
       35.55 -    53.32: 58
       53.32 -    71.09: 15
       71.09 -    88.86: 10
  Dihedral angle restraints: 3882
    sinusoidal: 1571
      harmonic: 2311
  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   19.27   73.73     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS D 336 "
           pdb=" SG  CYS D 336 "
           pdb=" SG  CYS D 361 "
           pdb=" CB  CYS D 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.50   73.50     1      1.00e+01 1.00e-02 6.87e+01
  dihedral pdb=" CB  CYS D 391 "
           pdb=" SG  CYS D 391 "
           pdb=" SG  CYS D 525 "
           pdb=" CB  CYS D 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.07   60.07     1      1.00e+01 1.00e-02 4.81e+01
  ... (remaining 3879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 741
       0.063 -    0.126: 159
       0.126 -    0.189: 28
       0.189 -    0.252: 2
       0.252 -    0.315: 1
  Chirality restraints: 931
  Sorted by residual:
  chirality pdb=" CB  VAL A 293 "
            pdb=" CA  VAL A 293 "
            pdb=" CG1 VAL A 293 "
            pdb=" CG2 VAL A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.31   -0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CA  ASN A 601 "
            pdb=" N   ASN A 601 "
            pdb=" C   ASN A 601 "
            pdb=" CB  ASN A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  VAL A 364 "
            pdb=" CA  VAL A 364 "
            pdb=" CG1 VAL A 364 "
            pdb=" CG2 VAL A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 928 not shown)

  Planarity restraints: 1159
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 477 "    0.031 2.00e-02 2.50e+03   3.06e-02 2.35e+01
        pdb=" CG  TRP A 477 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 477 "    0.040 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 477 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 477 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 477 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 477 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 477 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 477 "    0.007 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 477 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 288 "    0.062 5.00e-02 4.00e+02   9.48e-02 1.44e+01
        pdb=" N   PRO A 289 "   -0.164 5.00e-02 4.00e+02
        pdb=" CA  PRO A 289 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 289 "    0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 459 "   -0.017 2.00e-02 2.50e+03   2.25e-02 1.26e+01
        pdb=" CG  TRP A 459 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 459 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 459 "   -0.013 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 459 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 459 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 459 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 459 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 459 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1156 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 961
        2.76 -     3.29: 6316
        3.29 -     3.83: 10623
        3.83 -     4.36: 12003
        4.36 -     4.90: 19898
  Nonbonded interactions: 49801
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 278 "
            pdb=" OG1 THR A 282 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR A  83 "
            pdb=" OH  TYR D 489 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   SER A 105 "
            pdb=" OG  SER A 113 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   HIS A 239 "
            pdb=" ND2 ASN A 599 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   THR D 393 "
            pdb=" OG1 THR D 523 "
     model   vdw
     2.322 3.040
  ... (remaining 49796 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     20.630
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5610
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      :  0.008   0.418   6585  Z= 0.282
  Angle     :  1.166  40.904   8952  Z= 0.600
  Chirality :  0.055   0.315    931
  Planarity :  0.007   0.095   1159
  Dihedral  : 14.906  88.862   2377
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.63 %
    Twisted General : 0.40 %

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: -1.79 (0.27), residues: 783
  helix: -0.62 (0.25), residues: 350
  sheet: -1.30 (0.76), residues: 32
  loop : -1.68 (0.28), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.082   0.004   TRP A 477 
 HIS   0.005   0.001   HIS D 519 
 PHE   0.035   0.003   PHE D 497 
 TYR   0.030   0.003   TYR A 279 
 ARG   0.006   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10658 (  272)
  hydrogen bonds       : angle       6.01419 (  795)
  SS BOND              : bond        0.00516 (    7)
  SS BOND              : angle       1.78588 (   14)
  covalent geometry    : bond        0.00776 ( 6578)
  covalent geometry    : angle       1.16486 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.684 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 LEU cc_start: 0.7503 (mt) cc_final: 0.6836 (mt)
REVERT: A  520 LEU cc_start: 0.6720 (mp) cc_final: 0.6272 (tt)
REVERT: A  523 PHE cc_start: 0.6854 (m-80) cc_final: 0.6493 (m-80)
REVERT: A  543 ASP cc_start: 0.4915 (t0) cc_final: 0.4563 (t0)
REVERT: A  587 TYR cc_start: 0.5147 (t80) cc_final: 0.4703 (t80)
REVERT: A  592 PHE cc_start: 0.4417 (t80) cc_final: 0.3218 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.2132
  time to fit residues: 71.9477
Evaluate side-chains
  150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 20 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    8.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 37 optimal weight:    7.9990
   chunk 45 optimal weight:    0.0050
   chunk 70 optimal weight:    0.4980
   overall best weight:    1.8798

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

Flipped N/Q/H residues before XYZ refinement:
A  58 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.096123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.076405 restraints weight = 26855.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.078887 restraints weight = 19060.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.080807 restraints weight = 14602.091|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6585  Z= 0.159
  Angle     :  0.692  10.169   8952  Z= 0.354
  Chirality :  0.044   0.157    931
  Planarity :  0.006   0.064   1159
  Dihedral  :  5.739  30.730    854
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 15.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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: -1.13 (0.28), residues: 783
  helix: -0.02 (0.26), residues: 361
  sheet: -0.98 (0.76), residues: 33
  loop : -1.41 (0.30), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 459 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.020   0.002   PHE A 525 
 TYR   0.023   0.002   TYR A 385 
 ARG   0.005   0.001   ARG A 115 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04359 (  272)
  hydrogen bonds       : angle       5.13180 (  795)
  SS BOND              : bond        0.00626 (    7)
  SS BOND              : angle       2.37560 (   14)
  covalent geometry    : bond        0.00329 ( 6578)
  covalent geometry    : angle       0.68563 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 ARG cc_start: 0.8756 (ptp90) cc_final: 0.8513 (ptp90)
REVERT: A  277 ASN cc_start: 0.9341 (m110) cc_final: 0.8783 (t0)
REVERT: A  313 LYS cc_start: 0.9149 (pttp) cc_final: 0.8924 (pptt)
REVERT: A  315 PHE cc_start: 0.9490 (m-10) cc_final: 0.8713 (m-10)
REVERT: A  355 ASP cc_start: 0.8629 (t0) cc_final: 0.8090 (t0)
REVERT: A  376 MET cc_start: 0.9446 (tpt) cc_final: 0.8722 (tpt)
REVERT: A  379 ILE cc_start: 0.9549 (mm) cc_final: 0.9304 (mm)
REVERT: A  380 GLN cc_start: 0.9571 (tp40) cc_final: 0.9316 (tp40)
REVERT: A  455 MET cc_start: 0.8718 (ppp) cc_final: 0.8147 (ppp)
REVERT: A  520 LEU cc_start: 0.9381 (mp) cc_final: 0.9145 (tt)
REVERT: A  525 PHE cc_start: 0.9393 (m-80) cc_final: 0.8905 (m-80)
REVERT: A  543 ASP cc_start: 0.7717 (t0) cc_final: 0.7171 (t0)
REVERT: A  554 LEU cc_start: 0.9297 (tp) cc_final: 0.9036 (tp)
REVERT: A  564 GLU cc_start: 0.9148 (mp0) cc_final: 0.8726 (mp0)
REVERT: A  587 TYR cc_start: 0.8946 (t80) cc_final: 0.7354 (t80)
REVERT: D  378 LYS cc_start: 0.9222 (tmtt) cc_final: 0.8726 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.2422
  time to fit residues: 58.0790
Evaluate side-chains
  138 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 71 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 68 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0030
   chunk 52 optimal weight:    9.9990
   overall best weight:    1.2394

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A  63 ASN
A 239 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 535 HIS
A 556 ASN
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.088354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.068815 restraints weight = 27180.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.071303 restraints weight = 19011.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.073231 restraints weight = 14440.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.4755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6585  Z= 0.127
  Angle     :  0.657   9.891   8952  Z= 0.333
  Chirality :  0.043   0.145    931
  Planarity :  0.005   0.049   1159
  Dihedral  :  5.248  27.130    854
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.29), residues: 783
  helix:  0.29 (0.27), residues: 358
  sheet: -0.76 (0.81), residues: 33
  loop : -1.34 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 459 
 HIS   0.005   0.001   HIS A 265 
 PHE   0.017   0.002   PHE A 525 
 TYR   0.019   0.002   TYR A 515 
 ARG   0.005   0.001   ARG A 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04180 (  272)
  hydrogen bonds       : angle       4.92379 (  795)
  SS BOND              : bond        0.00384 (    7)
  SS BOND              : angle       2.39447 (   14)
  covalent geometry    : bond        0.00266 ( 6578)
  covalent geometry    : angle       0.65028 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 SER cc_start: 0.7564 (m) cc_final: 0.7289 (p)
REVERT: A  207 TYR cc_start: 0.9307 (m-80) cc_final: 0.8860 (m-80)
REVERT: A  277 ASN cc_start: 0.9210 (m110) cc_final: 0.8629 (t0)
REVERT: A  313 LYS cc_start: 0.9225 (pttp) cc_final: 0.8969 (pptt)
REVERT: A  315 PHE cc_start: 0.9463 (m-10) cc_final: 0.8443 (m-10)
REVERT: A  355 ASP cc_start: 0.8097 (t0) cc_final: 0.7799 (t0)
REVERT: A  376 MET cc_start: 0.9371 (tpt) cc_final: 0.8589 (tpt)
REVERT: A  379 ILE cc_start: 0.9609 (mm) cc_final: 0.9286 (mm)
REVERT: A  380 GLN cc_start: 0.9555 (tp40) cc_final: 0.9235 (tp40)
REVERT: A  455 MET cc_start: 0.8446 (ppp) cc_final: 0.7648 (ppp)
REVERT: A  480 MET cc_start: 0.9188 (tpt) cc_final: 0.8736 (tpt)
REVERT: A  505 HIS cc_start: 0.8654 (m90) cc_final: 0.8329 (m90)
REVERT: A  513 ILE cc_start: 0.9554 (mm) cc_final: 0.9236 (mm)
REVERT: A  516 TYR cc_start: 0.8524 (t80) cc_final: 0.8100 (t80)
REVERT: A  519 THR cc_start: 0.9694 (p) cc_final: 0.9381 (p)
REVERT: A  525 PHE cc_start: 0.9511 (m-80) cc_final: 0.9079 (m-80)
REVERT: A  554 LEU cc_start: 0.9260 (tp) cc_final: 0.8982 (tp)
REVERT: A  564 GLU cc_start: 0.9129 (mp0) cc_final: 0.8703 (mp0)
REVERT: A  587 TYR cc_start: 0.9016 (t80) cc_final: 0.7500 (t80)
REVERT: D  346 ARG cc_start: 0.8838 (tpt90) cc_final: 0.8560 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2522
  time to fit residues: 57.6023
Evaluate side-chains
  142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:   30.0000
   chunk 55 optimal weight:    6.9990
   chunk 18 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 437 ASN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.089168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.069877 restraints weight = 28043.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.072425 restraints weight = 19355.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.074364 restraints weight = 14533.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7612
moved from start:          0.5158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6585  Z= 0.118
  Angle     :  0.619   8.633   8952  Z= 0.313
  Chirality :  0.043   0.145    931
  Planarity :  0.004   0.050   1159
  Dihedral  :  4.946  25.115    854
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 14.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.63 (0.29), residues: 783
  helix:  0.40 (0.27), residues: 358
  sheet: -0.61 (0.83), residues: 33
  loop : -1.16 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 265 
 PHE   0.011   0.001   PHE A 525 
 TYR   0.023   0.001   TYR A 515 
 ARG   0.005   0.000   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03976 (  272)
  hydrogen bonds       : angle       4.90352 (  795)
  SS BOND              : bond        0.00588 (    7)
  SS BOND              : angle       1.62332 (   14)
  covalent geometry    : bond        0.00250 ( 6578)
  covalent geometry    : angle       0.61644 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.770 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8277 (ppp) cc_final: 0.7878 (ppp)
REVERT: A   97 LEU cc_start: 0.9677 (mt) cc_final: 0.9424 (mt)
REVERT: A  207 TYR cc_start: 0.9287 (m-80) cc_final: 0.8496 (m-80)
REVERT: A  227 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8733 (mm-30)
REVERT: A  273 ARG cc_start: 0.7284 (ttt-90) cc_final: 0.6599 (ptp-170)
REVERT: A  277 ASN cc_start: 0.9234 (m110) cc_final: 0.8522 (t0)
REVERT: A  313 LYS cc_start: 0.9208 (pttp) cc_final: 0.8955 (pptt)
REVERT: A  315 PHE cc_start: 0.9442 (m-10) cc_final: 0.8428 (m-10)
REVERT: A  355 ASP cc_start: 0.8380 (t0) cc_final: 0.8056 (t0)
REVERT: A  376 MET cc_start: 0.9318 (tpt) cc_final: 0.8549 (tpt)
REVERT: A  379 ILE cc_start: 0.9522 (mm) cc_final: 0.9206 (mm)
REVERT: A  455 MET cc_start: 0.8429 (ppp) cc_final: 0.7672 (ppp)
REVERT: A  461 TRP cc_start: 0.8184 (m-10) cc_final: 0.7849 (m-10)
REVERT: A  480 MET cc_start: 0.9021 (tpt) cc_final: 0.8661 (tpt)
REVERT: A  512 PHE cc_start: 0.8275 (m-10) cc_final: 0.7680 (m-10)
REVERT: A  516 TYR cc_start: 0.8615 (t80) cc_final: 0.8252 (t80)
REVERT: A  525 PHE cc_start: 0.9482 (m-80) cc_final: 0.9057 (m-80)
REVERT: A  554 LEU cc_start: 0.9271 (tp) cc_final: 0.9020 (tp)
REVERT: A  564 GLU cc_start: 0.9056 (mp0) cc_final: 0.8651 (mp0)
REVERT: D  346 ARG cc_start: 0.8739 (tpt90) cc_final: 0.8463 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 170
  average time/residue: 0.2023
  time to fit residues: 44.3490
Evaluate side-chains
  139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   chunk 65 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 42 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 58 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 343 ASN
D 370 ASN
** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.093552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.074249 restraints weight = 27596.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.076745 restraints weight = 19178.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.078646 restraints weight = 14546.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6585  Z= 0.124
  Angle     :  0.623   7.128   8952  Z= 0.318
  Chirality :  0.043   0.145    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.931  23.850    854
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 14.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.56 (0.29), residues: 783
  helix:  0.43 (0.27), residues: 361
  sheet: -0.44 (0.85), residues: 33
  loop : -1.11 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 459 
 HIS   0.006   0.001   HIS A 265 
 PHE   0.015   0.001   PHE A 588 
 TYR   0.022   0.002   TYR D 495 
 ARG   0.006   0.001   ARG D 498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  272)
  hydrogen bonds       : angle       4.90422 (  795)
  SS BOND              : bond        0.00332 (    7)
  SS BOND              : angle       1.90548 (   14)
  covalent geometry    : bond        0.00255 ( 6578)
  covalent geometry    : angle       0.61873 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8342 (ppp) cc_final: 0.7960 (ppp)
REVERT: A  203 TRP cc_start: 0.8049 (m-10) cc_final: 0.7025 (m-10)
REVERT: A  207 TYR cc_start: 0.9303 (m-80) cc_final: 0.8708 (m-80)
REVERT: A  227 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8754 (mm-30)
REVERT: A  273 ARG cc_start: 0.7630 (ttt-90) cc_final: 0.6800 (ptp-170)
REVERT: A  313 LYS cc_start: 0.9169 (pttp) cc_final: 0.8946 (pptt)
REVERT: A  315 PHE cc_start: 0.9565 (m-10) cc_final: 0.8509 (m-10)
REVERT: A  355 ASP cc_start: 0.8734 (t0) cc_final: 0.8258 (t70)
REVERT: A  376 MET cc_start: 0.9397 (tpt) cc_final: 0.8666 (tpt)
REVERT: A  379 ILE cc_start: 0.9481 (mm) cc_final: 0.9207 (mm)
REVERT: A  455 MET cc_start: 0.8451 (ppp) cc_final: 0.7665 (ppp)
REVERT: A  480 MET cc_start: 0.9048 (tpt) cc_final: 0.8697 (tpt)
REVERT: A  512 PHE cc_start: 0.8403 (m-10) cc_final: 0.7676 (m-10)
REVERT: A  515 TYR cc_start: 0.8223 (m-10) cc_final: 0.7960 (m-80)
REVERT: A  516 TYR cc_start: 0.8683 (t80) cc_final: 0.8339 (t80)
REVERT: A  525 PHE cc_start: 0.9530 (m-80) cc_final: 0.9075 (m-80)
REVERT: A  554 LEU cc_start: 0.9239 (tp) cc_final: 0.8979 (tp)
REVERT: A  564 GLU cc_start: 0.9050 (mp0) cc_final: 0.8627 (mp0)
REVERT: D  346 ARG cc_start: 0.8734 (tpt90) cc_final: 0.8440 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1940
  time to fit residues: 41.4748
Evaluate side-chains
  142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:    9.9990
   chunk 70 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.087178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.069433 restraints weight = 28598.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.071749 restraints weight = 19910.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.073572 restraints weight = 15087.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.6590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6585  Z= 0.200
  Angle     :  0.696   7.544   8952  Z= 0.365
  Chirality :  0.044   0.148    931
  Planarity :  0.005   0.064   1159
  Dihedral  :  5.207  26.847    854
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 20.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.78 (0.29), residues: 783
  helix:  0.23 (0.27), residues: 371
  sheet: -0.41 (0.84), residues: 33
  loop : -1.25 (0.30), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.002   TRP A 163 
 HIS   0.008   0.002   HIS A 241 
 PHE   0.021   0.002   PHE A 523 
 TYR   0.034   0.002   TYR D 495 
 ARG   0.008   0.001   ARG A 582 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04269 (  272)
  hydrogen bonds       : angle       5.21533 (  795)
  SS BOND              : bond        0.00618 (    7)
  SS BOND              : angle       1.38656 (   14)
  covalent geometry    : bond        0.00415 ( 6578)
  covalent geometry    : angle       0.69415 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9553 (t80) cc_final: 0.9343 (t80)
REVERT: A   82 MET cc_start: 0.8196 (ppp) cc_final: 0.7955 (ppp)
REVERT: A  203 TRP cc_start: 0.8282 (m-10) cc_final: 0.7526 (m-10)
REVERT: A  207 TYR cc_start: 0.9279 (m-80) cc_final: 0.8692 (m-80)
REVERT: A  227 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8697 (mm-30)
REVERT: A  237 TYR cc_start: 0.8756 (t80) cc_final: 0.8466 (t80)
REVERT: A  239 HIS cc_start: 0.8485 (m90) cc_final: 0.8154 (m-70)
REVERT: A  313 LYS cc_start: 0.9259 (pttp) cc_final: 0.8991 (pptt)
REVERT: A  315 PHE cc_start: 0.9577 (m-10) cc_final: 0.8582 (m-10)
REVERT: A  323 MET cc_start: 0.6614 (tmm) cc_final: 0.6401 (tmm)
REVERT: A  355 ASP cc_start: 0.8866 (t0) cc_final: 0.8368 (t0)
REVERT: A  376 MET cc_start: 0.9365 (tpt) cc_final: 0.8675 (tpt)
REVERT: A  379 ILE cc_start: 0.9384 (mm) cc_final: 0.9147 (mm)
REVERT: A  455 MET cc_start: 0.8487 (ppp) cc_final: 0.7602 (ppp)
REVERT: A  461 TRP cc_start: 0.8537 (m-10) cc_final: 0.7921 (m-10)
REVERT: A  480 MET cc_start: 0.9026 (tpt) cc_final: 0.8653 (tpt)
REVERT: A  505 HIS cc_start: 0.8719 (m90) cc_final: 0.8448 (m90)
REVERT: A  516 TYR cc_start: 0.8654 (t80) cc_final: 0.8176 (t80)
REVERT: A  523 PHE cc_start: 0.9523 (m-80) cc_final: 0.9184 (m-80)
REVERT: A  525 PHE cc_start: 0.9497 (m-80) cc_final: 0.9027 (m-80)
REVERT: A  544 ILE cc_start: 0.9352 (pt) cc_final: 0.9095 (tp)
REVERT: A  554 LEU cc_start: 0.9266 (tp) cc_final: 0.8969 (tp)
REVERT: A  564 GLU cc_start: 0.9100 (mp0) cc_final: 0.8669 (mp0)
REVERT: D  365 TYR cc_start: 0.7997 (m-80) cc_final: 0.7647 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1968
  time to fit residues: 42.8788
Evaluate side-chains
  141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.760 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 9 optimal weight:    4.9990
   chunk 23 optimal weight:    9.9990
   chunk 44 optimal weight:    0.6980
   chunk 45 optimal weight:    6.9990
   chunk 17 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 69 optimal weight:    9.9990
   chunk 40 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 330 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.089183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.071223 restraints weight = 28375.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.073640 restraints weight = 19844.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.075481 restraints weight = 15059.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.6780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6585  Z= 0.138
  Angle     :  0.645   6.163   8952  Z= 0.330
  Chirality :  0.045   0.184    931
  Planarity :  0.004   0.037   1159
  Dihedral  :  5.008  26.417    854
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.38 (0.30), residues: 783
  helix:  0.57 (0.27), residues: 360
  sheet: -0.37 (0.83), residues: 34
  loop : -1.00 (0.31), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 606 
 HIS   0.008   0.001   HIS A 265 
 PHE   0.016   0.001   PHE A 523 
 TYR   0.013   0.001   TYR A 252 
 ARG   0.004   0.001   ARG A 192 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04021 (  272)
  hydrogen bonds       : angle       5.01719 (  795)
  SS BOND              : bond        0.00321 (    7)
  SS BOND              : angle       0.99227 (   14)
  covalent geometry    : bond        0.00298 ( 6578)
  covalent geometry    : angle       0.64434 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.690 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9535 (ppp) cc_final: 0.9317 (ppp)
REVERT: A   82 MET cc_start: 0.8250 (ppp) cc_final: 0.8012 (ppp)
REVERT: A  154 ASN cc_start: 0.8804 (m-40) cc_final: 0.8479 (m110)
REVERT: A  203 TRP cc_start: 0.8214 (m-10) cc_final: 0.7477 (m-10)
REVERT: A  207 TYR cc_start: 0.9359 (m-80) cc_final: 0.8982 (m-80)
REVERT: A  227 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8568 (mm-30)
REVERT: A  237 TYR cc_start: 0.8675 (t80) cc_final: 0.8395 (t80)
REVERT: A  239 HIS cc_start: 0.8445 (m90) cc_final: 0.8105 (m-70)
REVERT: A  313 LYS cc_start: 0.9221 (pttp) cc_final: 0.8977 (pptt)
REVERT: A  315 PHE cc_start: 0.9547 (m-10) cc_final: 0.8365 (m-10)
REVERT: A  323 MET cc_start: 0.6542 (tmm) cc_final: 0.6289 (tmm)
REVERT: A  355 ASP cc_start: 0.8967 (t0) cc_final: 0.8554 (t0)
REVERT: A  376 MET cc_start: 0.9386 (tpt) cc_final: 0.8768 (tpt)
REVERT: A  379 ILE cc_start: 0.9325 (mm) cc_final: 0.9081 (mm)
REVERT: A  440 LEU cc_start: 0.9802 (tp) cc_final: 0.9591 (mt)
REVERT: A  455 MET cc_start: 0.8406 (ppp) cc_final: 0.7440 (ppp)
REVERT: A  480 MET cc_start: 0.8936 (tpt) cc_final: 0.8534 (tpt)
REVERT: A  505 HIS cc_start: 0.8842 (m90) cc_final: 0.8401 (m90)
REVERT: A  516 TYR cc_start: 0.8612 (t80) cc_final: 0.8242 (t80)
REVERT: A  523 PHE cc_start: 0.9541 (m-80) cc_final: 0.9144 (m-80)
REVERT: A  525 PHE cc_start: 0.9495 (m-80) cc_final: 0.9084 (m-80)
REVERT: A  544 ILE cc_start: 0.9342 (pt) cc_final: 0.9068 (tp)
REVERT: A  554 LEU cc_start: 0.9229 (tp) cc_final: 0.8945 (tp)
REVERT: A  564 GLU cc_start: 0.9052 (mp0) cc_final: 0.8775 (mp0)
REVERT: A  588 PHE cc_start: 0.9064 (m-80) cc_final: 0.8779 (m-80)
REVERT: D  365 TYR cc_start: 0.7974 (m-80) cc_final: 0.7774 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.1791
  time to fit residues: 38.5854
Evaluate side-chains
  141 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 141
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.2980
   chunk 10 optimal weight:    9.9990
   chunk 23 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    8.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 241 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.090109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.071664 restraints weight = 27963.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.074168 restraints weight = 19241.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.076112 restraints weight = 14357.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.6881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6585  Z= 0.124
  Angle     :  0.647   6.837   8952  Z= 0.327
  Chirality :  0.044   0.154    931
  Planarity :  0.004   0.036   1159
  Dihedral  :  4.831  24.229    854
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.27 (0.30), residues: 783
  helix:  0.59 (0.27), residues: 365
  sheet: -0.16 (0.83), residues: 34
  loop : -0.90 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 165 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.012   0.001   PHE A 523 
 TYR   0.013   0.001   TYR D 495 
 ARG   0.004   0.000   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03993 (  272)
  hydrogen bonds       : angle       4.98024 (  795)
  SS BOND              : bond        0.00277 (    7)
  SS BOND              : angle       0.88893 (   14)
  covalent geometry    : bond        0.00263 ( 6578)
  covalent geometry    : angle       0.64608 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   32 PHE cc_start: 0.9630 (t80) cc_final: 0.9424 (t80)
REVERT: A   82 MET cc_start: 0.8262 (ppp) cc_final: 0.7993 (ppp)
REVERT: A   85 LEU cc_start: 0.9344 (pt) cc_final: 0.9068 (tp)
REVERT: A  154 ASN cc_start: 0.8799 (m-40) cc_final: 0.8485 (m110)
REVERT: A  203 TRP cc_start: 0.8255 (m-10) cc_final: 0.7439 (m-10)
REVERT: A  207 TYR cc_start: 0.9381 (m-80) cc_final: 0.9159 (m-80)
REVERT: A  227 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8649 (mm-30)
REVERT: A  237 TYR cc_start: 0.8741 (t80) cc_final: 0.8494 (t80)
REVERT: A  270 MET cc_start: 0.9161 (tpp) cc_final: 0.8213 (tpp)
REVERT: A  313 LYS cc_start: 0.9175 (pttp) cc_final: 0.8938 (pptt)
REVERT: A  315 PHE cc_start: 0.9544 (m-10) cc_final: 0.8316 (m-10)
REVERT: A  355 ASP cc_start: 0.8951 (t0) cc_final: 0.8551 (t0)
REVERT: A  376 MET cc_start: 0.9439 (tpt) cc_final: 0.8784 (tpt)
REVERT: A  455 MET cc_start: 0.8436 (ppp) cc_final: 0.7553 (ppp)
REVERT: A  480 MET cc_start: 0.8969 (tpt) cc_final: 0.8525 (tpt)
REVERT: A  505 HIS cc_start: 0.8868 (m90) cc_final: 0.8420 (m90)
REVERT: A  516 TYR cc_start: 0.8679 (t80) cc_final: 0.8230 (t80)
REVERT: A  523 PHE cc_start: 0.9567 (m-80) cc_final: 0.9139 (m-80)
REVERT: A  525 PHE cc_start: 0.9537 (m-80) cc_final: 0.9121 (m-80)
REVERT: A  544 ILE cc_start: 0.9375 (pt) cc_final: 0.9084 (tp)
REVERT: A  554 LEU cc_start: 0.9186 (tp) cc_final: 0.8903 (tp)
REVERT: A  564 GLU cc_start: 0.9055 (mp0) cc_final: 0.8725 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1849
  time to fit residues: 39.9459
Evaluate side-chains
  142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 69 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 72 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 6 optimal weight:   20.0000
   overall best weight:    0.7740

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.092068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.073720 restraints weight = 28652.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.076143 restraints weight = 20172.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.078057 restraints weight = 15378.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.7053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6585  Z= 0.130
  Angle     :  0.684   9.109   8952  Z= 0.350
  Chirality :  0.045   0.193    931
  Planarity :  0.004   0.037   1159
  Dihedral  :  4.769  21.223    854
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.32 (0.30), residues: 783
  helix:  0.47 (0.27), residues: 371
  sheet: -0.14 (0.80), residues: 34
  loop : -0.85 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 275 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.015   0.001   PHE A 230 
 TYR   0.013   0.001   TYR D 495 
 ARG   0.003   0.001   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04042 (  272)
  hydrogen bonds       : angle       5.21917 (  795)
  SS BOND              : bond        0.00252 (    7)
  SS BOND              : angle       1.32485 (   14)
  covalent geometry    : bond        0.00273 ( 6578)
  covalent geometry    : angle       0.68289 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 161
  time to evaluate  : 0.700 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9501 (ppp) cc_final: 0.9300 (ppp)
REVERT: A   82 MET cc_start: 0.8287 (ppp) cc_final: 0.8031 (ppp)
REVERT: A   85 LEU cc_start: 0.9398 (pt) cc_final: 0.9144 (tp)
REVERT: A   97 LEU cc_start: 0.9619 (mt) cc_final: 0.9418 (mt)
REVERT: A  154 ASN cc_start: 0.8816 (m-40) cc_final: 0.8481 (m110)
REVERT: A  203 TRP cc_start: 0.8174 (m-10) cc_final: 0.7382 (m-10)
REVERT: A  207 TYR cc_start: 0.9333 (m-80) cc_final: 0.9127 (m-80)
REVERT: A  227 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8722 (mm-30)
REVERT: A  237 TYR cc_start: 0.8801 (t80) cc_final: 0.8501 (t80)
REVERT: A  270 MET cc_start: 0.9069 (tpp) cc_final: 0.8138 (tpp)
REVERT: A  313 LYS cc_start: 0.9194 (pttp) cc_final: 0.8942 (pptt)
REVERT: A  315 PHE cc_start: 0.9508 (m-10) cc_final: 0.9167 (m-10)
REVERT: A  323 MET cc_start: 0.6098 (tmm) cc_final: 0.5874 (tmm)
REVERT: A  355 ASP cc_start: 0.8920 (t0) cc_final: 0.8543 (t0)
REVERT: A  455 MET cc_start: 0.8407 (ppp) cc_final: 0.7551 (ppp)
REVERT: A  480 MET cc_start: 0.8928 (tpt) cc_final: 0.8519 (tpt)
REVERT: A  505 HIS cc_start: 0.8761 (m90) cc_final: 0.8270 (m90)
REVERT: A  516 TYR cc_start: 0.8593 (t80) cc_final: 0.8229 (t80)
REVERT: A  519 THR cc_start: 0.9664 (p) cc_final: 0.9462 (p)
REVERT: A  523 PHE cc_start: 0.9443 (m-80) cc_final: 0.9009 (m-80)
REVERT: A  525 PHE cc_start: 0.9490 (m-80) cc_final: 0.9086 (m-80)
REVERT: A  544 ILE cc_start: 0.9306 (pt) cc_final: 0.9053 (tp)
REVERT: A  554 LEU cc_start: 0.9185 (tp) cc_final: 0.8908 (tp)
REVERT: A  564 GLU cc_start: 0.9035 (mp0) cc_final: 0.8716 (mp0)
  outliers start: 1
  outliers final: 1
  residues processed: 162
  average time/residue: 0.1842
  time to fit residues: 39.1812
Evaluate side-chains
  139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.694 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 52 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 18 optimal weight:    8.9990
   chunk 10 optimal weight:    1.9990
   chunk 75 optimal weight:    7.9990
   chunk 16 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 26 optimal weight:    0.5980
   chunk 12 optimal weight:    5.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.089455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.071571 restraints weight = 29469.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.073894 restraints weight = 20793.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.075700 restraints weight = 15869.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.7313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6585  Z= 0.144
  Angle     :  0.676   8.615   8952  Z= 0.350
  Chirality :  0.045   0.158    931
  Planarity :  0.004   0.038   1159
  Dihedral  :  4.837  24.240    854
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.30), residues: 783
  helix:  0.57 (0.27), residues: 361
  sheet: -0.16 (0.77), residues: 34
  loop : -0.82 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 459 
 HIS   0.008   0.001   HIS A 265 
 PHE   0.020   0.001   PHE A  32 
 TYR   0.018   0.001   TYR A 497 
 ARG   0.004   0.001   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04030 (  272)
  hydrogen bonds       : angle       5.26346 (  795)
  SS BOND              : bond        0.00247 (    7)
  SS BOND              : angle       1.02164 (   14)
  covalent geometry    : bond        0.00301 ( 6578)
  covalent geometry    : angle       0.67574 ( 8938)

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

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

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1566 Ramachandran restraints generated.
    783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.837 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9518 (ppp) cc_final: 0.9305 (ppp)
REVERT: A  154 ASN cc_start: 0.8930 (m-40) cc_final: 0.8634 (m110)
REVERT: A  203 TRP cc_start: 0.8176 (m-10) cc_final: 0.7450 (m-10)
REVERT: A  227 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8690 (mm-30)
REVERT: A  237 TYR cc_start: 0.8805 (t80) cc_final: 0.8544 (t80)
REVERT: A  270 MET cc_start: 0.9202 (tpp) cc_final: 0.8320 (tpp)
REVERT: A  313 LYS cc_start: 0.9196 (pttp) cc_final: 0.8936 (pptt)
REVERT: A  315 PHE cc_start: 0.9479 (m-10) cc_final: 0.8312 (m-10)
REVERT: A  355 ASP cc_start: 0.8408 (t0) cc_final: 0.8104 (m-30)
REVERT: A  376 MET cc_start: 0.9341 (tpt) cc_final: 0.8713 (tpt)
REVERT: A  379 ILE cc_start: 0.9484 (mm) cc_final: 0.9267 (mm)
REVERT: A  455 MET cc_start: 0.8426 (ppp) cc_final: 0.7576 (ppp)
REVERT: A  461 TRP cc_start: 0.8567 (m-10) cc_final: 0.8085 (m-10)
REVERT: A  478 TRP cc_start: 0.8190 (m100) cc_final: 0.7260 (m100)
REVERT: A  480 MET cc_start: 0.8833 (tpt) cc_final: 0.8461 (tpt)
REVERT: A  505 HIS cc_start: 0.8796 (m90) cc_final: 0.8331 (m90)
REVERT: A  516 TYR cc_start: 0.8501 (t80) cc_final: 0.8077 (t80)
REVERT: A  523 PHE cc_start: 0.9430 (m-80) cc_final: 0.9024 (m-80)
REVERT: A  525 PHE cc_start: 0.9451 (m-80) cc_final: 0.9040 (m-80)
REVERT: A  544 ILE cc_start: 0.9296 (pt) cc_final: 0.9074 (tp)
REVERT: A  554 LEU cc_start: 0.9197 (tp) cc_final: 0.8910 (tp)
REVERT: A  564 GLU cc_start: 0.9002 (mp0) cc_final: 0.8659 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2037
  time to fit residues: 43.1357
Evaluate side-chains
  134 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    9.9990
   chunk 58 optimal weight:    0.6980
   chunk 61 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 21 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0980
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
A 599 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.085140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.067364 restraints weight = 30075.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.069811 restraints weight = 20993.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.071673 restraints weight = 15860.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.7379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6585  Z= 0.126
  Angle     :  0.672   8.419   8952  Z= 0.344
  Chirality :  0.045   0.159    931
  Planarity :  0.004   0.039   1159
  Dihedral  :  4.751  23.752    854
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.20 (0.30), residues: 783
  helix:  0.58 (0.27), residues: 365
  sheet: -0.11 (0.77), residues: 34
  loop : -0.78 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 275 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.031   0.002   PHE A 356 
 TYR   0.012   0.001   TYR D 495 
 ARG   0.003   0.000   ARG A 460 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03980 (  272)
  hydrogen bonds       : angle       5.11049 (  795)
  SS BOND              : bond        0.00201 (    7)
  SS BOND              : angle       0.81106 (   14)
  covalent geometry    : bond        0.00260 ( 6578)
  covalent geometry    : angle       0.67151 ( 8938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2818.76 seconds
wall clock time: 50 minutes 18.73 seconds (3018.73 seconds total)