Starting phenix.real_space_refine
on Tue Mar 11 17:04:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr4_34045/03_2025/7yr4_34045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr4_34045/03_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_34045/03_2025/7yr4_34045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2025/7yr4_34045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_2025/7yr4_34045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr4_34045/03_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.33, per 1000 atoms: 0.83
  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: 1.71
  Conformation dependent library (CDL) restraints added in 967.7 milliseconds
  

  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: 0.66
  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: 2.05

  Time building geometry restraints manager: 2.10 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:                  0.010
  Normalize map: mean=0, sd=1:             2.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     22.880
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.070
-------------------------------------------------------------------------------
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   6578  Z= 0.427
  Angle     :  1.165  40.904   8938  Z= 0.599
  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 

*********************** 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  : 0.705 
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: 0.2370
  time to fit residues: 80.5466
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  : 0.720 
-------------------------------------------------------------------------------
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   6578  Z= 0.209
  Angle     :  0.686  10.169   8938  Z= 0.351
  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 

*********************** 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  : 0.703 
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: 0.2215
  time to fit residues: 53.5510
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  : 0.720 
-------------------------------------------------------------------------------
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:    0.0980
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A  60 GLN
A 239 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
A 556 ASN
** A 599 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 = 0.3841 r_free = 0.3841 target = 0.090223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.070283 restraints weight = 26944.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.072862 restraints weight = 18875.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.074830 restraints weight = 14314.070|
|-----------------------------------------------------------------------------|
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.4592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6578  Z= 0.159
  Angle     :  0.648   9.530   8938  Z= 0.326
  Chirality :  0.043   0.151    931
  Planarity :  0.005   0.049   1159
  Dihedral  :  5.239  26.871    854
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 13.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  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 : 0.00 %

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: -0.87 (0.29), residues: 783
  helix:  0.25 (0.27), residues: 358
  sheet: -0.76 (0.82), residues: 33
  loop : -1.34 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 473 
 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 

*********************** 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  : 0.839 
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   97 LEU cc_start: 0.9678 (mt) cc_final: 0.9400 (mt)
REVERT: A  105 SER cc_start: 0.7589 (m) cc_final: 0.7295 (p)
REVERT: A  207 TYR cc_start: 0.9301 (m-80) cc_final: 0.8823 (m-80)
REVERT: A  212 VAL cc_start: 0.8762 (m) cc_final: 0.8548 (p)
REVERT: A  215 TYR cc_start: 0.8505 (m-80) cc_final: 0.8288 (m-80)
REVERT: A  277 ASN cc_start: 0.9229 (m110) cc_final: 0.8653 (t0)
REVERT: A  313 LYS cc_start: 0.9179 (pttp) cc_final: 0.8917 (pptt)
REVERT: A  315 PHE cc_start: 0.9445 (m-10) cc_final: 0.8420 (m-10)
REVERT: A  355 ASP cc_start: 0.8100 (t0) cc_final: 0.7797 (t0)
REVERT: A  376 MET cc_start: 0.9375 (tpt) cc_final: 0.8608 (tpt)
REVERT: A  379 ILE cc_start: 0.9589 (mm) cc_final: 0.9265 (mm)
REVERT: A  380 GLN cc_start: 0.9558 (tp40) cc_final: 0.9224 (tp40)
REVERT: A  455 MET cc_start: 0.8437 (ppp) cc_final: 0.7679 (ppp)
REVERT: A  480 MET cc_start: 0.9207 (tpt) cc_final: 0.8760 (tpt)
REVERT: A  505 HIS cc_start: 0.8635 (m90) cc_final: 0.8337 (m90)
REVERT: A  513 ILE cc_start: 0.9546 (mm) cc_final: 0.9316 (mm)
REVERT: A  525 PHE cc_start: 0.9501 (m-80) cc_final: 0.9068 (m-80)
REVERT: A  554 LEU cc_start: 0.9259 (tp) cc_final: 0.8996 (tp)
REVERT: A  564 GLU cc_start: 0.9150 (mp0) cc_final: 0.8738 (mp0)
REVERT: A  587 TYR cc_start: 0.8966 (t80) cc_final: 0.7446 (t80)
REVERT: D  346 ARG cc_start: 0.8821 (tpt90) cc_final: 0.8558 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2176
  time to fit residues: 49.6265
Evaluate side-chains
  144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** A  96 GLN ** 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**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.093424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.073858 restraints weight = 27328.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.076457 restraints weight = 18893.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.078439 restraints weight = 14165.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.5171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6578  Z= 0.174
  Angle     :  0.624   8.968   8938  Z= 0.318
  Chirality :  0.043   0.162    931
  Planarity :  0.005   0.049   1159
  Dihedral  :  4.974  25.199    854
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  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: -0.72 (0.29), residues: 783
  helix:  0.33 (0.27), residues: 360
  sheet: -0.61 (0.82), residues: 33
  loop : -1.23 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 461 
 HIS   0.006   0.001   HIS A 265 
 PHE   0.012   0.001   PHE A 230 
 TYR   0.025   0.001   TYR A 515 
 ARG   0.008   0.001   ARG A 204 

*********************** 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
  173 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8264 (ppp) cc_final: 0.7873 (ppp)
REVERT: A   97 LEU cc_start: 0.9673 (mt) cc_final: 0.9416 (mt)
REVERT: A  177 ARG cc_start: 0.8670 (ptp90) cc_final: 0.8161 (ptt90)
REVERT: A  207 TYR cc_start: 0.9311 (m-80) cc_final: 0.8584 (m-80)
REVERT: A  209 VAL cc_start: 0.9121 (t) cc_final: 0.8629 (t)
REVERT: A  227 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8756 (mm-30)
REVERT: A  273 ARG cc_start: 0.7364 (ttt-90) cc_final: 0.6760 (ptp-170)
REVERT: A  277 ASN cc_start: 0.9278 (m110) cc_final: 0.8580 (t0)
REVERT: A  313 LYS cc_start: 0.9190 (pttp) cc_final: 0.8933 (pptt)
REVERT: A  315 PHE cc_start: 0.9480 (m-10) cc_final: 0.8491 (m-10)
REVERT: A  355 ASP cc_start: 0.8553 (t0) cc_final: 0.8160 (t0)
REVERT: A  376 MET cc_start: 0.9340 (tpt) cc_final: 0.8578 (tpt)
REVERT: A  379 ILE cc_start: 0.9522 (mm) cc_final: 0.9213 (mm)
REVERT: A  455 MET cc_start: 0.8484 (ppp) cc_final: 0.7507 (ppp)
REVERT: A  480 MET cc_start: 0.9037 (tpt) cc_final: 0.8633 (tpt)
REVERT: A  505 HIS cc_start: 0.8668 (m90) cc_final: 0.8328 (m90)
REVERT: A  516 TYR cc_start: 0.8637 (t80) cc_final: 0.8096 (t80)
REVERT: A  523 PHE cc_start: 0.9436 (m-80) cc_final: 0.9056 (m-80)
REVERT: A  525 PHE cc_start: 0.9534 (m-80) cc_final: 0.9093 (m-80)
REVERT: A  554 LEU cc_start: 0.9266 (tp) cc_final: 0.9017 (tp)
REVERT: A  564 GLU cc_start: 0.9078 (mp0) cc_final: 0.8673 (mp0)
REVERT: D  346 ARG cc_start: 0.8796 (tpt90) cc_final: 0.8524 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1925
  time to fit residues: 43.2733
Evaluate side-chains
  144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0010
   chunk 42 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 57 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6186

-------------------------------------------------------------------------------
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 429 GLN
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.092445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.073244 restraints weight = 27450.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.075817 restraints weight = 18872.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.077800 restraints weight = 14147.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3580
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.5541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6578  Z= 0.146
  Angle     :  0.618   6.813   8938  Z= 0.314
  Chirality :  0.043   0.146    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.888  23.832    854
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  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: -0.50 (0.29), residues: 783
  helix:  0.54 (0.27), residues: 353
  sheet: -0.44 (0.85), residues: 33
  loop : -1.11 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 459 
 HIS   0.002   0.001   HIS A 378 
 PHE   0.016   0.001   PHE A 588 
 TYR   0.018   0.001   TYR D 495 
 ARG   0.007   0.001   ARG D 457 

*********************** 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
  171 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.122 
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   82 MET cc_start: 0.8360 (ppp) cc_final: 0.8013 (ppp)
REVERT: A  203 TRP cc_start: 0.8008 (m-10) cc_final: 0.6953 (m-10)
REVERT: A  207 TYR cc_start: 0.9338 (m-80) cc_final: 0.8712 (m-80)
REVERT: A  215 TYR cc_start: 0.8473 (m-80) cc_final: 0.8114 (m-80)
REVERT: A  227 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8773 (mm-30)
REVERT: A  270 MET cc_start: 0.8740 (tpt) cc_final: 0.8461 (tpp)
REVERT: A  273 ARG cc_start: 0.7483 (ttt-90) cc_final: 0.6745 (ptp-170)
REVERT: A  313 LYS cc_start: 0.9188 (pttp) cc_final: 0.8940 (pptt)
REVERT: A  315 PHE cc_start: 0.9497 (m-10) cc_final: 0.8239 (m-10)
REVERT: A  355 ASP cc_start: 0.8574 (t0) cc_final: 0.8144 (t0)
REVERT: A  376 MET cc_start: 0.9333 (tpt) cc_final: 0.8518 (tpt)
REVERT: A  379 ILE cc_start: 0.9482 (mm) cc_final: 0.9191 (mm)
REVERT: A  455 MET cc_start: 0.8516 (ppp) cc_final: 0.7598 (ppp)
REVERT: A  480 MET cc_start: 0.8978 (tpt) cc_final: 0.8590 (tpt)
REVERT: A  505 HIS cc_start: 0.8605 (m90) cc_final: 0.8329 (m-70)
REVERT: A  516 TYR cc_start: 0.8630 (t80) cc_final: 0.8290 (t80)
REVERT: A  525 PHE cc_start: 0.9501 (m-80) cc_final: 0.9050 (m-80)
REVERT: A  554 LEU cc_start: 0.9228 (tp) cc_final: 0.8986 (tp)
REVERT: A  564 GLU cc_start: 0.9032 (mp0) cc_final: 0.8617 (mp0)
REVERT: A  588 PHE cc_start: 0.8967 (m-80) cc_final: 0.8759 (m-80)
REVERT: D  346 ARG cc_start: 0.8790 (tpt90) cc_final: 0.8495 (mmm160)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2054
  time to fit residues: 45.2316
Evaluate side-chains
  145 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 47 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 3 optimal weight:   10.0000
   chunk 70 optimal weight:    9.9990
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 9 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 239 HIS
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
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 = 0.3768 r_free = 0.3768 target = 0.089795 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.071548 restraints weight = 28199.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.073929 restraints weight = 19809.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.075756 restraints weight = 15041.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.6246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6578  Z= 0.240
  Angle     :  0.681   8.113   8938  Z= 0.355
  Chirality :  0.044   0.208    931
  Planarity :  0.005   0.057   1159
  Dihedral  :  5.070  24.655    854
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 19.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -0.70 (0.29), residues: 783
  helix:  0.28 (0.27), residues: 374
  sheet: -0.37 (0.83), residues: 33
  loop : -1.21 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 461 
 HIS   0.009   0.002   HIS A 265 
 PHE   0.014   0.002   PHE A 230 
 TYR   0.016   0.002   TYR A 237 
 ARG   0.020   0.001   ARG A 177 

*********************** 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
  162 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.699 
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: A  203 TRP cc_start: 0.8340 (m-10) cc_final: 0.7485 (m-10)
REVERT: A  204 ARG cc_start: 0.7849 (mtm-85) cc_final: 0.7641 (mtp85)
REVERT: A  207 TYR cc_start: 0.9388 (m-80) cc_final: 0.8788 (m-80)
REVERT: A  215 TYR cc_start: 0.8502 (m-80) cc_final: 0.8039 (m-80)
REVERT: A  225 ASP cc_start: 0.9026 (t0) cc_final: 0.8365 (t0)
REVERT: A  227 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8799 (mm-30)
REVERT: A  237 TYR cc_start: 0.8615 (t80) cc_final: 0.8367 (t80)
REVERT: A  239 HIS cc_start: 0.8261 (m90) cc_final: 0.7920 (m-70)
REVERT: A  313 LYS cc_start: 0.9186 (pttp) cc_final: 0.8937 (pptt)
REVERT: A  315 PHE cc_start: 0.9555 (m-10) cc_final: 0.8599 (m-10)
REVERT: A  323 MET cc_start: 0.6469 (tmm) cc_final: 0.6242 (tmm)
REVERT: A  355 ASP cc_start: 0.9004 (t0) cc_final: 0.8449 (t0)
REVERT: A  376 MET cc_start: 0.9452 (tpt) cc_final: 0.8727 (tpt)
REVERT: A  379 ILE cc_start: 0.9445 (mm) cc_final: 0.9224 (mm)
REVERT: A  407 ILE cc_start: 0.8993 (mt) cc_final: 0.8792 (mt)
REVERT: A  455 MET cc_start: 0.8731 (ppp) cc_final: 0.7823 (ppp)
REVERT: A  464 PHE cc_start: 0.9129 (m-80) cc_final: 0.8883 (m-80)
REVERT: A  478 TRP cc_start: 0.8402 (m100) cc_final: 0.7566 (m100)
REVERT: A  480 MET cc_start: 0.9070 (tpt) cc_final: 0.8622 (tpt)
REVERT: A  505 HIS cc_start: 0.8785 (m90) cc_final: 0.8377 (m90)
REVERT: A  516 TYR cc_start: 0.8714 (t80) cc_final: 0.8322 (t80)
REVERT: A  519 THR cc_start: 0.9710 (p) cc_final: 0.9505 (p)
REVERT: A  523 PHE cc_start: 0.9571 (m-80) cc_final: 0.9071 (m-80)
REVERT: A  525 PHE cc_start: 0.9565 (m-80) cc_final: 0.9123 (m-80)
REVERT: A  544 ILE cc_start: 0.9388 (pt) cc_final: 0.9091 (tp)
REVERT: A  554 LEU cc_start: 0.9257 (tp) cc_final: 0.8971 (tp)
REVERT: A  564 GLU cc_start: 0.9067 (mp0) cc_final: 0.8595 (mp0)
REVERT: A  579 MET cc_start: 0.7419 (mtp) cc_final: 0.5362 (mtp)
REVERT: A  587 TYR cc_start: 0.9356 (t80) cc_final: 0.8421 (t80)
REVERT: A  588 PHE cc_start: 0.8985 (m-80) cc_final: 0.8155 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1913
  time to fit residues: 40.3790
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 23 optimal weight:    0.4980
   chunk 44 optimal weight:    0.6980
   chunk 45 optimal weight:    0.4980
   chunk 17 optimal weight:    0.9980
   chunk 33 optimal weight:    8.9990
   chunk 57 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 69 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 300 GLN
** 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.093328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.074504 restraints weight = 27580.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.077016 restraints weight = 19156.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.078960 restraints weight = 14474.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.6420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6578  Z= 0.161
  Angle     :  0.634   7.023   8938  Z= 0.324
  Chirality :  0.044   0.176    931
  Planarity :  0.005   0.073   1159
  Dihedral  :  4.825  23.602    854
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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: -0.42 (0.30), residues: 783
  helix:  0.48 (0.27), residues: 369
  sheet: -0.24 (0.82), residues: 34
  loop : -1.01 (0.32), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.002   TRP A 163 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.013   0.001   PHE A 230 
 TYR   0.013   0.001   TYR A 516 
 ARG   0.013   0.001   ARG A 177 

*********************** 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
  167 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.377 
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: A   82 MET cc_start: 0.8265 (ppp) cc_final: 0.8012 (ppp)
REVERT: A   85 LEU cc_start: 0.9335 (pt) cc_final: 0.9134 (tp)
REVERT: A  154 ASN cc_start: 0.8684 (m-40) cc_final: 0.8397 (m110)
REVERT: A  176 LEU cc_start: 0.8062 (mm) cc_final: 0.7444 (mm)
REVERT: A  203 TRP cc_start: 0.8164 (m-10) cc_final: 0.7301 (m-10)
REVERT: A  207 TYR cc_start: 0.9378 (m-80) cc_final: 0.9000 (m-80)
REVERT: A  215 TYR cc_start: 0.8618 (m-80) cc_final: 0.8089 (m-80)
REVERT: A  225 ASP cc_start: 0.8854 (t0) cc_final: 0.8262 (t0)
REVERT: A  227 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8780 (mm-30)
REVERT: A  237 TYR cc_start: 0.8464 (t80) cc_final: 0.8250 (t80)
REVERT: A  239 HIS cc_start: 0.8299 (m90) cc_final: 0.8009 (m-70)
REVERT: A  270 MET cc_start: 0.8926 (tpt) cc_final: 0.8594 (tpp)
REVERT: A  313 LYS cc_start: 0.9165 (pttp) cc_final: 0.8921 (pptt)
REVERT: A  315 PHE cc_start: 0.9499 (m-10) cc_final: 0.8313 (m-10)
REVERT: A  323 MET cc_start: 0.6313 (tmm) cc_final: 0.6054 (tmm)
REVERT: A  355 ASP cc_start: 0.8878 (t0) cc_final: 0.8402 (t0)
REVERT: A  376 MET cc_start: 0.9389 (tpt) cc_final: 0.8757 (tpt)
REVERT: A  379 ILE cc_start: 0.9323 (mm) cc_final: 0.9090 (mm)
REVERT: A  455 MET cc_start: 0.8641 (ppp) cc_final: 0.7671 (ppp)
REVERT: A  478 TRP cc_start: 0.8343 (m100) cc_final: 0.7393 (m100)
REVERT: A  480 MET cc_start: 0.9021 (tpt) cc_final: 0.8545 (tpt)
REVERT: A  505 HIS cc_start: 0.8713 (m90) cc_final: 0.8066 (m90)
REVERT: A  516 TYR cc_start: 0.8663 (t80) cc_final: 0.8277 (t80)
REVERT: A  525 PHE cc_start: 0.9517 (m-80) cc_final: 0.9095 (m-80)
REVERT: A  544 ILE cc_start: 0.9308 (pt) cc_final: 0.9015 (tp)
REVERT: A  554 LEU cc_start: 0.9184 (tp) cc_final: 0.8895 (tp)
REVERT: A  564 GLU cc_start: 0.8973 (mp0) cc_final: 0.8687 (mp0)
REVERT: A  577 LYS cc_start: 0.8626 (mtmm) cc_final: 0.8284 (tptp)
REVERT: A  579 MET cc_start: 0.7202 (mtp) cc_final: 0.5464 (mtp)
REVERT: A  587 TYR cc_start: 0.9257 (t80) cc_final: 0.8246 (t80)
REVERT: A  588 PHE cc_start: 0.8910 (m-80) cc_final: 0.8037 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.2189
  time to fit residues: 47.3303
Evaluate side-chains
  149 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 34 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0270
   chunk 10 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    6.9990
   overall best weight:    2.0046

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** 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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.089405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.070931 restraints weight = 28434.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.073337 restraints weight = 19669.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.075203 restraints weight = 14896.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.6781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6578  Z= 0.197
  Angle     :  0.662  10.612   8938  Z= 0.339
  Chirality :  0.044   0.219    931
  Planarity :  0.005   0.049   1159
  Dihedral  :  4.898  24.123    854
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 16.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.16 %
    Favored  : 98.70 %
  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: -0.49 (0.30), residues: 783
  helix:  0.37 (0.27), residues: 375
  sheet: -0.26 (0.81), residues: 34
  loop : -1.01 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 461 
 HIS   0.009   0.001   HIS A 265 
 PHE   0.025   0.001   PHE A 356 
 TYR   0.016   0.002   TYR A 202 
 ARG   0.008   0.001   ARG A 177 

*********************** 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
  173 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.702 
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: A   62 MET cc_start: 0.9542 (ppp) cc_final: 0.9327 (ppp)
REVERT: A  154 ASN cc_start: 0.8798 (m-40) cc_final: 0.8502 (m110)
REVERT: A  176 LEU cc_start: 0.8300 (mm) cc_final: 0.7688 (mm)
REVERT: A  203 TRP cc_start: 0.8298 (m-10) cc_final: 0.7451 (m-10)
REVERT: A  204 ARG cc_start: 0.8347 (mtp180) cc_final: 0.7900 (mtp-110)
REVERT: A  207 TYR cc_start: 0.9386 (m-80) cc_final: 0.8916 (m-80)
REVERT: A  215 TYR cc_start: 0.8634 (m-80) cc_final: 0.8116 (m-80)
REVERT: A  225 ASP cc_start: 0.8917 (t0) cc_final: 0.8408 (t0)
REVERT: A  227 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8794 (mm-30)
REVERT: A  237 TYR cc_start: 0.8533 (t80) cc_final: 0.8165 (t80)
REVERT: A  239 HIS cc_start: 0.8393 (m90) cc_final: 0.8006 (m-70)
REVERT: A  313 LYS cc_start: 0.9188 (pttp) cc_final: 0.8925 (pptt)
REVERT: A  315 PHE cc_start: 0.9460 (m-10) cc_final: 0.8537 (m-10)
REVERT: A  355 ASP cc_start: 0.8469 (t0) cc_final: 0.8009 (t0)
REVERT: A  376 MET cc_start: 0.9417 (tpt) cc_final: 0.8779 (tpt)
REVERT: A  379 ILE cc_start: 0.9494 (mm) cc_final: 0.9259 (mm)
REVERT: A  440 LEU cc_start: 0.9811 (tp) cc_final: 0.9595 (mt)
REVERT: A  455 MET cc_start: 0.8763 (ppp) cc_final: 0.7809 (ppp)
REVERT: A  474 MET cc_start: 0.7359 (mpp) cc_final: 0.7053 (mpp)
REVERT: A  478 TRP cc_start: 0.8311 (m100) cc_final: 0.7395 (m100)
REVERT: A  480 MET cc_start: 0.8964 (tpt) cc_final: 0.8561 (tpt)
REVERT: A  495 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7692 (mm-30)
REVERT: A  505 HIS cc_start: 0.8746 (m90) cc_final: 0.8157 (m-70)
REVERT: A  515 TYR cc_start: 0.8305 (m-80) cc_final: 0.8056 (m-80)
REVERT: A  516 TYR cc_start: 0.8616 (t80) cc_final: 0.8233 (t80)
REVERT: A  523 PHE cc_start: 0.9582 (m-80) cc_final: 0.9107 (m-80)
REVERT: A  525 PHE cc_start: 0.9526 (m-80) cc_final: 0.9102 (m-80)
REVERT: A  544 ILE cc_start: 0.9295 (pt) cc_final: 0.9044 (tp)
REVERT: A  554 LEU cc_start: 0.9203 (tp) cc_final: 0.8927 (tp)
REVERT: A  564 GLU cc_start: 0.9021 (mp0) cc_final: 0.8640 (mp0)
REVERT: A  577 LYS cc_start: 0.8668 (mtmm) cc_final: 0.8362 (tptp)
REVERT: A  579 MET cc_start: 0.7338 (mtp) cc_final: 0.5205 (mtp)
REVERT: A  588 PHE cc_start: 0.8979 (m-80) cc_final: 0.8727 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 173
  average time/residue: 0.1945
  time to fit residues: 43.5170
Evaluate side-chains
  143 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 69 optimal weight:    0.0970
   chunk 38 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0040
   chunk 37 optimal weight:    0.7980
   chunk 72 optimal weight:    6.9990
   chunk 39 optimal weight:    6.9990
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4990

-------------------------------------------------------------------------------
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 388 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.091678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.072604 restraints weight = 27111.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.075133 restraints weight = 18750.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.077050 restraints weight = 14127.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.6880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6578  Z= 0.164
  Angle     :  0.669   8.824   8938  Z= 0.340
  Chirality :  0.045   0.176    931
  Planarity :  0.004   0.041   1159
  Dihedral  :  4.791  22.662    854
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  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: -0.43 (0.30), residues: 783
  helix:  0.38 (0.27), residues: 376
  sheet: -0.11 (0.83), residues: 34
  loop : -0.94 (0.32), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 461 
 HIS   0.007   0.001   HIS A 265 
 PHE   0.033   0.002   PHE A 464 
 TYR   0.016   0.001   TYR A 497 
 ARG   0.005   0.001   ARG A 177 

*********************** 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
  168 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.708 
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   32 PHE cc_start: 0.9641 (t80) cc_final: 0.9440 (t80)
REVERT: A   62 MET cc_start: 0.9517 (ppp) cc_final: 0.9308 (ppp)
REVERT: A   75 GLU cc_start: 0.9570 (mm-30) cc_final: 0.9358 (pt0)
REVERT: A   82 MET cc_start: 0.8257 (ppp) cc_final: 0.8043 (ppp)
REVERT: A   85 LEU cc_start: 0.9373 (pt) cc_final: 0.9154 (tp)
REVERT: A  154 ASN cc_start: 0.8888 (m-40) cc_final: 0.8589 (m110)
REVERT: A  203 TRP cc_start: 0.8244 (m-10) cc_final: 0.7379 (m-10)
REVERT: A  204 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7237 (mtm110)
REVERT: A  215 TYR cc_start: 0.8575 (m-80) cc_final: 0.7994 (m-80)
REVERT: A  227 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8815 (mm-30)
REVERT: A  237 TYR cc_start: 0.8425 (t80) cc_final: 0.8135 (t80)
REVERT: A  239 HIS cc_start: 0.8388 (m90) cc_final: 0.8046 (m-70)
REVERT: A  270 MET cc_start: 0.8839 (tpt) cc_final: 0.8004 (tpp)
REVERT: A  313 LYS cc_start: 0.9131 (pttp) cc_final: 0.8894 (pptt)
REVERT: A  315 PHE cc_start: 0.9511 (m-10) cc_final: 0.9180 (m-10)
REVERT: A  323 MET cc_start: 0.6174 (tmm) cc_final: 0.5927 (tmm)
REVERT: A  355 ASP cc_start: 0.8608 (t0) cc_final: 0.8186 (t0)
REVERT: A  379 ILE cc_start: 0.9455 (mm) cc_final: 0.9156 (mm)
REVERT: A  455 MET cc_start: 0.8675 (ppp) cc_final: 0.7749 (ppp)
REVERT: A  474 MET cc_start: 0.7215 (mpp) cc_final: 0.6911 (mpp)
REVERT: A  478 TRP cc_start: 0.8276 (m100) cc_final: 0.7358 (m100)
REVERT: A  480 MET cc_start: 0.9017 (tpt) cc_final: 0.8547 (tpt)
REVERT: A  495 GLU cc_start: 0.7294 (mm-30) cc_final: 0.6768 (mm-30)
REVERT: A  505 HIS cc_start: 0.8716 (m90) cc_final: 0.8299 (m90)
REVERT: A  516 TYR cc_start: 0.8665 (t80) cc_final: 0.8266 (t80)
REVERT: A  525 PHE cc_start: 0.9526 (m-80) cc_final: 0.9113 (m-80)
REVERT: A  544 ILE cc_start: 0.9313 (pt) cc_final: 0.9028 (tp)
REVERT: A  554 LEU cc_start: 0.9173 (tp) cc_final: 0.8905 (tp)
REVERT: A  560 LEU cc_start: 0.9129 (mm) cc_final: 0.8398 (tp)
REVERT: A  564 GLU cc_start: 0.8960 (mp0) cc_final: 0.8255 (mp0)
REVERT: A  577 LYS cc_start: 0.8700 (mtmm) cc_final: 0.8345 (tptp)
REVERT: A  588 PHE cc_start: 0.8957 (m-80) cc_final: 0.8658 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.1958
  time to fit residues: 42.5089
Evaluate side-chains
  144 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  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:    9.9990
   chunk 46 optimal weight:    1.9990
   chunk 52 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    9.9990
   chunk 10 optimal weight:    0.7980
   chunk 75 optimal weight:    9.9990
   chunk 16 optimal weight:    0.9980
   chunk 68 optimal weight:   40.0000
   chunk 26 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   overall best weight:    2.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.087007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.068859 restraints weight = 28427.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.071245 restraints weight = 19615.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.073109 restraints weight = 14807.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.7411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6578  Z= 0.239
  Angle     :  0.718   8.227   8938  Z= 0.370
  Chirality :  0.045   0.171    931
  Planarity :  0.005   0.047   1159
  Dihedral  :  4.981  25.215    854
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  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: -0.61 (0.29), residues: 783
  helix:  0.26 (0.27), residues: 378
  sheet: -0.24 (0.82), residues: 37
  loop : -1.08 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP A 461 
 HIS   0.008   0.002   HIS A 265 
 PHE   0.033   0.002   PHE A 356 
 TYR   0.016   0.002   TYR A 158 
 ARG   0.005   0.001   ARG A 177 

********************** 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  : 0.786 
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   62 MET cc_start: 0.9551 (ppp) cc_final: 0.9318 (ppp)
REVERT: A   82 MET cc_start: 0.8190 (ppp) cc_final: 0.7967 (ppp)
REVERT: A  154 ASN cc_start: 0.8921 (m-40) cc_final: 0.8642 (m110)
REVERT: A  203 TRP cc_start: 0.8316 (m-10) cc_final: 0.7518 (m-10)
REVERT: A  204 ARG cc_start: 0.8384 (mtp180) cc_final: 0.7537 (ttm110)
REVERT: A  207 TYR cc_start: 0.9374 (m-80) cc_final: 0.9142 (m-80)
REVERT: A  227 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8750 (mm-30)
REVERT: A  313 LYS cc_start: 0.9204 (pttp) cc_final: 0.8938 (pptt)
REVERT: A  315 PHE cc_start: 0.9577 (m-10) cc_final: 0.8416 (m-10)
REVERT: A  355 ASP cc_start: 0.8503 (t0) cc_final: 0.8261 (t0)
REVERT: A  376 MET cc_start: 0.9364 (tpt) cc_final: 0.8768 (tpt)
REVERT: A  379 ILE cc_start: 0.9395 (mm) cc_final: 0.9152 (mm)
REVERT: A  455 MET cc_start: 0.8777 (ppp) cc_final: 0.7873 (ppp)
REVERT: A  480 MET cc_start: 0.8878 (tpt) cc_final: 0.8506 (tpt)
REVERT: A  505 HIS cc_start: 0.8786 (m90) cc_final: 0.8173 (m90)
REVERT: A  515 TYR cc_start: 0.8413 (m-80) cc_final: 0.8146 (m-80)
REVERT: A  516 TYR cc_start: 0.8664 (t80) cc_final: 0.8283 (t80)
REVERT: A  523 PHE cc_start: 0.9499 (m-80) cc_final: 0.9086 (m-80)
REVERT: A  525 PHE cc_start: 0.9484 (m-80) cc_final: 0.9130 (m-80)
REVERT: A  544 ILE cc_start: 0.9388 (pt) cc_final: 0.9156 (tp)
REVERT: A  554 LEU cc_start: 0.9248 (tp) cc_final: 0.8971 (tp)
REVERT: A  560 LEU cc_start: 0.9164 (mm) cc_final: 0.8433 (tp)
REVERT: A  564 GLU cc_start: 0.8906 (mp0) cc_final: 0.8171 (mp0)
REVERT: A  577 LYS cc_start: 0.8760 (mtmm) cc_final: 0.8409 (tptp)
REVERT: A  588 PHE cc_start: 0.8932 (m-80) cc_final: 0.8691 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 163
  average time/residue: 0.2083
  time to fit residues: 44.0493
Evaluate side-chains
  136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0980
   chunk 58 optimal weight:    0.0170
   chunk 61 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0010
   chunk 47 optimal weight:    0.1980
   chunk 21 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 65 optimal weight:    6.9990
   overall best weight:    0.2224

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

Flipped N/Q/H residues before XYZ refinement:
** A 388 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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.092269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.073534 restraints weight = 28767.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.075967 restraints weight = 20335.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.077837 restraints weight = 15553.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.7389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6578  Z= 0.173
  Angle     :  0.694   8.886   8938  Z= 0.352
  Chirality :  0.046   0.181    931
  Planarity :  0.004   0.040   1159
  Dihedral  :  4.702  20.363    854
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 14.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  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: -0.48 (0.30), residues: 783
  helix:  0.39 (0.27), residues: 370
  sheet: -0.03 (0.81), residues: 34
  loop : -1.01 (0.32), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 461 
 HIS   0.015   0.002   HIS A 265 
 PHE   0.030   0.002   PHE A 464 
 TYR   0.016   0.001   TYR D 495 
 ARG   0.004   0.001   ARG A 306 
Origin is already at (0, 0, 0), no shifts will be applied

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Job complete
usr+sys time: 2546.69 seconds
wall clock time: 44 minutes 51.63 seconds (2691.63 seconds total)