Starting phenix.real_space_refine
on Tue Feb 11 17:34:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr4_34045/02_2025/7yr4_34045.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr4_34045/02_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_34045/02_2025/7yr4_34045.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr4_34045/02_2025/7yr4_34045.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr4_34045/02_2025/7yr4_34045.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr4_34045/02_2025/7yr4_34045.cif"
  }
  resolution = 4.12
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    4103      2.51       5
     N    1064      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.83, per 1000 atoms: 0.76
  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: 1.44
  Conformation dependent library (CDL) restraints added in 874.3 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: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.726A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   GLN A  42 " --> pdb=" O   ASP A  38 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 82
    Processing helix  chain 'A' and resid 92 through 101
    Processing helix  chain 'A' and resid 109 through 129
      removed outlier: 3.594A  pdb=" N   SER A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 146 through 155
      removed outlier: 3.994A  pdb=" N   GLU A 150 " --> pdb=" O   PRO A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 3.665A  pdb=" N   ARG A 161 " --> pdb=" O   ASP A 157 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 4.003A  pdb=" N   VAL A 185 " --> pdb=" O   GLU A 181 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A 186 " --> pdb=" O   GLU A 182 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLU A 189 " --> pdb=" O   VAL A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 196
      No H-bonds generated for 'chain 'A' and resid 194 through 196'
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 219 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 263 through 267
      removed outlier: 3.683A  pdb=" N   LEU A 266 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 299
      removed outlier: 3.650A  pdb=" N   MET A 297 " --> pdb=" O   THR A 294 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL A 298 " --> pdb=" O   ASP A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.564A  pdb=" N   ALA A 311 " --> pdb=" O   ILE A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 331
      removed outlier: 4.251A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
    Processing helix  chain 'A' and resid 386 through 388
      No H-bonds generated for 'chain 'A' and resid 386 through 388'
    Processing helix  chain 'A' and resid 400 through 412
      removed outlier: 3.800A  pdb=" N   GLY A 405 " --> pdb=" O   HIS A 401 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLU A 406 " --> pdb=" O   GLU A 402 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU A 410 " --> pdb=" O   GLU A 406 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   SER A 411 " --> pdb=" O   ILE A 407 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ALA A 412 " --> pdb=" O   MET A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
      removed outlier: 3.663A  pdb=" N   LEU A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 4.174A  pdb=" N   LYS A 441 " --> pdb=" O   ASN A 437 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 466
      removed outlier: 3.992A  pdb=" N   PHE A 452 " --> pdb=" O   GLY A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 484
    Processing helix  chain 'A' and resid 499 through 502
    Processing helix  chain 'A' and resid 503 through 509
      removed outlier: 4.076A  pdb=" N   SER A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ASN A 508 " --> pdb=" O   PHE A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 530
      removed outlier: 3.591A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 559
    Processing helix  chain 'A' and resid 565 through 572
    Processing helix  chain 'A' and resid 581 through 600
      Proline residue:  A 590  - end of helix
      removed outlier: 4.403A  pdb=" N   TRP A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
      removed outlier: 4.195A  pdb=" N   LYS A 596 " --> pdb=" O   PHE A 592 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   ASP A 597 " --> pdb=" O   THR A 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 337 through 342
      removed outlier: 3.624A  pdb=" N   VAL D 341 " --> pdb=" O   PRO D 337 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 366 through 371
    Processing helix  chain 'D' and resid 405 through 407
      No H-bonds generated for 'chain 'D' and resid 405 through 407'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA2, first strand: chain 'D' and resid 356 through 358
    Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.551A  pdb=" N   TYR D 473 " --> pdb=" O   TYR D 489 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

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

  Time building geometry restraints manager: 1.75 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 3445
       17.77 -    35.55: 354
       35.55 -    53.32: 58
       53.32 -    71.09: 15
       71.09 -    88.86: 10
  Dihedral angle restraints: 3882
    sinusoidal: 1571
      harmonic: 2311
  Sorted by residual:
  dihedral pdb=" CB  CYS A 133 "
           pdb=" SG  CYS A 133 "
           pdb=" SG  CYS A 141 "
           pdb=" CB  CYS A 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.27   73.73     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS D 336 "
           pdb=" SG  CYS D 336 "
           pdb=" SG  CYS D 361 "
           pdb=" CB  CYS D 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   19.50   73.50     1      1.00e+01 1.00e-02 6.87e+01
  dihedral pdb=" CB  CYS D 391 "
           pdb=" SG  CYS D 391 "
           pdb=" SG  CYS D 525 "
           pdb=" CB  CYS D 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -146.07   60.07     1      1.00e+01 1.00e-02 4.81e+01
  ... (remaining 3879 not shown)

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.650
  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:          1.060
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     18.080
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.700
-------------------------------------------------------------------------------
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  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 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: 0.2218
  time to fit residues: 75.0959
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  : 0.753 
-------------------------------------------------------------------------------
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 = 36)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.076405 restraints weight = 26855.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.078893 restraints weight = 19059.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.080799 restraints weight = 14596.901|
|-----------------------------------------------------------------------------|
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  : 0.667 
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: 0.9150 (pttp) cc_final: 0.8924 (pptt)
REVERT: A  315 PHE cc_start: 0.9490 (m-10) cc_final: 0.8714 (m-10)
REVERT: A  355 ASP cc_start: 0.8626 (t0) cc_final: 0.8088 (t0)
REVERT: A  376 MET cc_start: 0.9446 (tpt) cc_final: 0.8722 (tpt)
REVERT: A  379 ILE cc_start: 0.9550 (mm) cc_final: 0.9305 (mm)
REVERT: A  380 GLN cc_start: 0.9569 (tp40) cc_final: 0.9314 (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: 0.9146 (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: 0.9296 (tp) cc_final: 0.9035 (tp)
REVERT: A  564 GLU cc_start: 0.9148 (mp0) cc_final: 0.8725 (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: 0.2217
  time to fit residues: 53.3099
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  : 0.747 
-------------------------------------------------------------------------------
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:    6.9990
   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:    0.0980
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.089510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.070117 restraints weight = 27451.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.072559 restraints weight = 19327.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.074452 restraints weight = 14780.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7591
moved from start:          0.4602

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= 0.164
  Angle     :  0.649   9.864   8938  Z= 0.328
  Chirality :  0.043   0.149    931
  Planarity :  0.005   0.049   1159
  Dihedral  :  5.270  27.050    854
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  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: -0.86 (0.29), residues: 783
  helix:  0.26 (0.27), residues: 358
  sheet: -0.77 (0.82), residues: 33
  loop : -1.33 (0.30), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 459 
 HIS   0.005   0.001   HIS A 265 
 PHE   0.017   0.001   PHE A 525 
 TYR   0.020   0.002   TYR A 515 
 ARG   0.006   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  : 0.829 
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: 0.9680 (mt) cc_final: 0.9393 (mt)
REVERT: A  105 SER cc_start: 0.7616 (m) cc_final: 0.7334 (p)
REVERT: A  207 TYR cc_start: 0.9309 (m-80) cc_final: 0.8859 (m-80)
REVERT: A  277 ASN cc_start: 0.9246 (m110) cc_final: 0.8681 (t0)
REVERT: A  313 LYS cc_start: 0.9207 (pttp) cc_final: 0.8946 (pptt)
REVERT: A  315 PHE cc_start: 0.9464 (m-10) cc_final: 0.8452 (m-10)
REVERT: A  355 ASP cc_start: 0.8175 (t0) cc_final: 0.7798 (t0)
REVERT: A  376 MET cc_start: 0.9382 (tpt) cc_final: 0.8616 (tpt)
REVERT: A  379 ILE cc_start: 0.9603 (mm) cc_final: 0.9282 (mm)
REVERT: A  380 GLN cc_start: 0.9552 (tp40) cc_final: 0.9228 (tp40)
REVERT: A  455 MET cc_start: 0.8491 (ppp) cc_final: 0.7736 (ppp)
REVERT: A  480 MET cc_start: 0.9194 (tpt) cc_final: 0.8728 (tpt)
REVERT: A  505 HIS cc_start: 0.8649 (m90) cc_final: 0.8355 (m90)
REVERT: A  525 PHE cc_start: 0.9489 (m-80) cc_final: 0.9045 (m-80)
REVERT: A  554 LEU cc_start: 0.9264 (tp) cc_final: 0.9005 (tp)
REVERT: A  564 GLU cc_start: 0.9125 (mp0) cc_final: 0.8703 (mp0)
REVERT: A  587 TYR cc_start: 0.8975 (t80) cc_final: 0.7452 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.2192
  time to fit residues: 50.3551
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  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 55 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 13 optimal weight:    4.9990
   chunk 66 optimal weight:    0.0670
   overall best weight:    0.6718

-------------------------------------------------------------------------------
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 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 429 GLN
A 437 ASN
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.095851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.075152 restraints weight = 27057.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.077532 restraints weight = 19506.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.079428 restraints weight = 15205.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.050   6578  Z= 0.156
  Angle     :  0.619   8.625   8938  Z= 0.312
  Chirality :  0.043   0.145    931
  Planarity :  0.004   0.048   1159
  Dihedral  :  4.949  24.803    854
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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: -0.66 (0.29), residues: 783
  helix:  0.38 (0.27), residues: 358
  sheet: -0.62 (0.82), residues: 33
  loop : -1.18 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 459 
 HIS   0.006   0.001   HIS A 265 
 PHE   0.017   0.001   PHE A 356 
 TYR   0.024   0.001   TYR A 515 
 ARG   0.004   0.001   ARG A 219 

*********************** 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
  171 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 0.663 
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: A   82 MET cc_start: 0.8358 (ppp) cc_final: 0.7972 (ppp)
REVERT: A   97 LEU cc_start: 0.9694 (mt) cc_final: 0.9459 (mt)
REVERT: A  203 TRP cc_start: 0.7961 (m-10) cc_final: 0.6972 (m-10)
REVERT: A  207 TYR cc_start: 0.9267 (m-80) cc_final: 0.8543 (m-80)
REVERT: A  209 VAL cc_start: 0.9070 (t) cc_final: 0.8552 (t)
REVERT: A  215 TYR cc_start: 0.8541 (m-80) cc_final: 0.8329 (m-80)
REVERT: A  227 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8734 (mm-30)
REVERT: A  273 ARG cc_start: 0.7015 (ttt-90) cc_final: 0.6431 (ptp-170)
REVERT: A  277 ASN cc_start: 0.9248 (m110) cc_final: 0.8548 (t0)
REVERT: A  313 LYS cc_start: 0.9166 (pttp) cc_final: 0.8929 (pptt)
REVERT: A  315 PHE cc_start: 0.9420 (m-10) cc_final: 0.8425 (m-10)
REVERT: A  355 ASP cc_start: 0.8156 (t0) cc_final: 0.7781 (t0)
REVERT: A  376 MET cc_start: 0.9342 (tpt) cc_final: 0.8569 (tpt)
REVERT: A  379 ILE cc_start: 0.9547 (mm) cc_final: 0.9264 (mm)
REVERT: A  380 GLN cc_start: 0.9501 (tp40) cc_final: 0.9194 (tp40)
REVERT: A  455 MET cc_start: 0.8436 (ppp) cc_final: 0.7679 (ppp)
REVERT: A  480 MET cc_start: 0.9098 (tpt) cc_final: 0.8724 (tpt)
REVERT: A  505 HIS cc_start: 0.8571 (m90) cc_final: 0.8361 (m90)
REVERT: A  512 PHE cc_start: 0.8501 (m-10) cc_final: 0.7909 (m-10)
REVERT: A  516 TYR cc_start: 0.8693 (t80) cc_final: 0.8344 (t80)
REVERT: A  525 PHE cc_start: 0.9467 (m-80) cc_final: 0.9011 (m-80)
REVERT: A  554 LEU cc_start: 0.9270 (tp) cc_final: 0.9027 (tp)
REVERT: A  564 GLU cc_start: 0.9067 (mp0) cc_final: 0.8672 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 171
  average time/residue: 0.2086
  time to fit residues: 45.8230
Evaluate side-chains
  142 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 40 optimal weight:    0.0170
   chunk 65 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 49 optimal weight:    7.9990
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    1.8026

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3830 r_free = 0.3830 target = 0.092983 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.073515 restraints weight = 27862.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.075943 restraints weight = 19483.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.077837 restraints weight = 14826.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.5696

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= 0.186
  Angle     :  0.636   7.737   8938  Z= 0.326
  Chirality :  0.043   0.147    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.949  23.852    854
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.29), residues: 783
  helix:  0.45 (0.27), residues: 358
  sheet: -0.49 (0.83), residues: 33
  loop : -1.13 (0.31), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 459 
 HIS   0.004   0.001   HIS A 241 
 PHE   0.019   0.001   PHE A 356 
 TYR   0.020   0.002   TYR A 516 
 ARG   0.004   0.001   ARG A 582 

*********************** 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
  167 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.706 
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: A   82 MET cc_start: 0.8378 (ppp) cc_final: 0.7989 (ppp)
REVERT: A  154 ASN cc_start: 0.8536 (m-40) cc_final: 0.8335 (m-40)
REVERT: A  159 ASN cc_start: 0.9182 (m110) cc_final: 0.8748 (m110)
REVERT: A  203 TRP cc_start: 0.8140 (m-10) cc_final: 0.7213 (m-10)
REVERT: A  207 TYR cc_start: 0.9343 (m-80) cc_final: 0.8833 (m-80)
REVERT: A  227 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8762 (mm-30)
REVERT: A  273 ARG cc_start: 0.7652 (ttt-90) cc_final: 0.6875 (ptp-170)
REVERT: A  277 ASN cc_start: 0.9333 (m110) cc_final: 0.9130 (m-40)
REVERT: A  313 LYS cc_start: 0.9180 (pttp) cc_final: 0.8946 (pptt)
REVERT: A  315 PHE cc_start: 0.9450 (m-10) cc_final: 0.8121 (m-10)
REVERT: A  355 ASP cc_start: 0.8423 (t0) cc_final: 0.7838 (t0)
REVERT: A  376 MET cc_start: 0.9399 (tpt) cc_final: 0.8557 (tpt)
REVERT: A  379 ILE cc_start: 0.9591 (mm) cc_final: 0.9309 (mm)
REVERT: A  455 MET cc_start: 0.8432 (ppp) cc_final: 0.7738 (ppp)
REVERT: A  461 TRP cc_start: 0.8303 (m-10) cc_final: 0.7736 (m-90)
REVERT: A  480 MET cc_start: 0.9003 (tpt) cc_final: 0.8685 (tpt)
REVERT: A  505 HIS cc_start: 0.8658 (m90) cc_final: 0.8329 (m90)
REVERT: A  512 PHE cc_start: 0.8393 (m-10) cc_final: 0.7778 (m-10)
REVERT: A  525 PHE cc_start: 0.9508 (m-80) cc_final: 0.9021 (m-80)
REVERT: A  554 LEU cc_start: 0.9263 (tp) cc_final: 0.8990 (tp)
REVERT: A  564 GLU cc_start: 0.9043 (mp0) cc_final: 0.8629 (mp0)
REVERT: A  588 PHE cc_start: 0.8944 (m-80) cc_final: 0.8703 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1843
  time to fit residues: 40.4768
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  : 0.778 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 47 optimal weight:    5.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:   10.0000
   chunk 70 optimal weight:    0.3980
   chunk 24 optimal weight:   30.0000
   chunk 22 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    4.0788

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
** A  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 239 HIS
** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 ASN
** A 493 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.085608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.068273 restraints weight = 29461.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.070545 restraints weight = 20634.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.072245 restraints weight = 15606.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.6814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   6578  Z= 0.317
  Angle     :  0.753   8.054   8938  Z= 0.398
  Chirality :  0.045   0.147    931
  Planarity :  0.005   0.077   1159
  Dihedral  :  5.423  28.347    854
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 23.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  3.04 %
    Favored  : 96.82 %
  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: -0.96 (0.29), residues: 783
  helix:  0.00 (0.26), residues: 365
  sheet: -1.38 (0.71), residues: 44
  loop : -1.13 (0.31), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.063   0.003   TRP A 163 
 HIS   0.010   0.002   HIS A 241 
 PHE   0.028   0.002   PHE A 356 
 TYR   0.029   0.003   TYR D 495 
 ARG   0.010   0.001   ARG D 457 

*********************** 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
  160 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 159
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.8171 (ppp) cc_final: 0.7915 (ppp)
REVERT: A  203 TRP cc_start: 0.8353 (m-10) cc_final: 0.7530 (m-10)
REVERT: A  207 TYR cc_start: 0.9318 (m-80) cc_final: 0.8955 (m-80)
REVERT: A  239 HIS cc_start: 0.8490 (m90) cc_final: 0.8129 (m-70)
REVERT: A  313 LYS cc_start: 0.9327 (pttp) cc_final: 0.9061 (pptt)
REVERT: A  315 PHE cc_start: 0.9554 (m-10) cc_final: 0.8661 (m-10)
REVERT: A  351 LEU cc_start: 0.9249 (mt) cc_final: 0.8595 (mt)
REVERT: A  355 ASP cc_start: 0.8532 (t0) cc_final: 0.7799 (t0)
REVERT: A  376 MET cc_start: 0.9367 (tpt) cc_final: 0.8718 (tpt)
REVERT: A  379 ILE cc_start: 0.9543 (mm) cc_final: 0.9283 (mm)
REVERT: A  480 MET cc_start: 0.9004 (tpt) cc_final: 0.8651 (tpt)
REVERT: A  505 HIS cc_start: 0.8770 (m90) cc_final: 0.8302 (m90)
REVERT: A  512 PHE cc_start: 0.8581 (m-10) cc_final: 0.8064 (m-10)
REVERT: A  515 TYR cc_start: 0.8566 (m-80) cc_final: 0.8045 (m-80)
REVERT: A  523 PHE cc_start: 0.9543 (m-80) cc_final: 0.8960 (m-80)
REVERT: A  525 PHE cc_start: 0.9473 (m-80) cc_final: 0.9010 (m-80)
REVERT: A  544 ILE cc_start: 0.9396 (pt) cc_final: 0.9141 (tp)
REVERT: A  554 LEU cc_start: 0.9292 (tp) cc_final: 0.8986 (tp)
REVERT: A  564 GLU cc_start: 0.9086 (mp0) cc_final: 0.8656 (mp0)
REVERT: A  587 TYR cc_start: 0.9282 (t80) cc_final: 0.8196 (t80)
REVERT: A  588 PHE cc_start: 0.9112 (m-80) cc_final: 0.8227 (m-80)
REVERT: D  365 TYR cc_start: 0.8027 (m-80) cc_final: 0.7682 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 160
  average time/residue: 0.1782
  time to fit residues: 37.5492
Evaluate side-chains
  136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 135
  time to evaluate  : 0.688 
-------------------------------------------------------------------------------
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:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 17 optimal weight:    2.9990
   chunk 33 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 535 HIS
A 540 HIS
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.091085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.072544 restraints weight = 28003.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.074858 restraints weight = 19919.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.076662 restraints weight = 15350.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.6886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6578  Z= 0.181
  Angle     :  0.663   6.591   8938  Z= 0.340
  Chirality :  0.045   0.175    931
  Planarity :  0.004   0.041   1159
  Dihedral  :  5.006  27.076    854
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 13.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    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: -0.51 (0.29), residues: 783
  helix:  0.35 (0.27), residues: 361
  sheet: -0.35 (0.82), residues: 34
  loop : -0.97 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 606 
 HIS   0.007   0.001   HIS A 241 
 PHE   0.019   0.001   PHE A 356 
 TYR   0.017   0.001   TYR A 516 
 ARG   0.006   0.001   ARG D 457 

*********************** 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
  165 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9550 (ppp) cc_final: 0.9320 (ppp)
REVERT: A  203 TRP cc_start: 0.8179 (m-10) cc_final: 0.7498 (m-10)
REVERT: A  207 TYR cc_start: 0.9328 (m-80) cc_final: 0.9124 (m-80)
REVERT: A  215 TYR cc_start: 0.8429 (m-80) cc_final: 0.8100 (m-80)
REVERT: A  227 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8539 (mm-30)
REVERT: A  239 HIS cc_start: 0.8465 (m90) cc_final: 0.8139 (m-70)
REVERT: A  277 ASN cc_start: 0.9310 (m110) cc_final: 0.8583 (t0)
REVERT: A  313 LYS cc_start: 0.9193 (pttp) cc_final: 0.8947 (pptt)
REVERT: A  315 PHE cc_start: 0.9482 (m-10) cc_final: 0.8200 (m-10)
REVERT: A  355 ASP cc_start: 0.8668 (t0) cc_final: 0.8294 (t0)
REVERT: A  376 MET cc_start: 0.9429 (tpt) cc_final: 0.8760 (tpt)
REVERT: A  379 ILE cc_start: 0.9488 (mm) cc_final: 0.9270 (mm)
REVERT: A  455 MET cc_start: 0.8414 (ppp) cc_final: 0.7509 (ppp)
REVERT: A  461 TRP cc_start: 0.8494 (m-10) cc_final: 0.7988 (m-10)
REVERT: A  480 MET cc_start: 0.8884 (tpt) cc_final: 0.8442 (tpt)
REVERT: A  505 HIS cc_start: 0.8690 (m90) cc_final: 0.8385 (m170)
REVERT: A  512 PHE cc_start: 0.8358 (m-10) cc_final: 0.8005 (m-80)
REVERT: A  523 PHE cc_start: 0.9470 (m-80) cc_final: 0.8842 (m-80)
REVERT: A  525 PHE cc_start: 0.9438 (m-80) cc_final: 0.9012 (m-80)
REVERT: A  544 ILE cc_start: 0.9356 (pt) cc_final: 0.9081 (tp)
REVERT: A  554 LEU cc_start: 0.9219 (tp) cc_final: 0.8925 (tp)
REVERT: A  564 GLU cc_start: 0.9020 (mp0) cc_final: 0.8781 (mp0)
REVERT: A  577 LYS cc_start: 0.8338 (tmtt) cc_final: 0.7973 (tptp)
REVERT: A  587 TYR cc_start: 0.9186 (t80) cc_final: 0.8080 (t80)
REVERT: A  588 PHE cc_start: 0.8996 (m-80) cc_final: 0.8004 (m-80)
REVERT: D  365 TYR cc_start: 0.7890 (m-80) cc_final: 0.7664 (m-10)
REVERT: D  386 LYS cc_start: 0.9002 (pttp) cc_final: 0.8595 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 165
  average time/residue: 0.1962
  time to fit residues: 42.3015
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  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 29 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 34 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 23 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 330 ASN
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.089956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.071852 restraints weight = 28113.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.074256 restraints weight = 19627.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.076107 restraints weight = 14845.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.7040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6578  Z= 0.184
  Angle     :  0.678   7.175   8938  Z= 0.347
  Chirality :  0.045   0.170    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.812  23.229    854
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 14.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  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: -0.35 (0.30), residues: 783
  helix:  0.48 (0.27), residues: 358
  sheet: -0.23 (0.81), residues: 34
  loop : -0.86 (0.32), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 302 
 HIS   0.009   0.001   HIS A 241 
 PHE   0.021   0.001   PHE A  32 
 TYR   0.015   0.001   TYR A 516 
 ARG   0.005   0.001   ARG D 457 

*********************** 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
  156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.744 
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: A   82 MET cc_start: 0.8275 (ppp) cc_final: 0.8031 (ppp)
REVERT: A   85 LEU cc_start: 0.9343 (pt) cc_final: 0.9083 (tp)
REVERT: A  203 TRP cc_start: 0.8131 (m-10) cc_final: 0.7454 (m-10)
REVERT: A  207 TYR cc_start: 0.9380 (m-80) cc_final: 0.9174 (m-80)
REVERT: A  227 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8686 (mm-30)
REVERT: A  270 MET cc_start: 0.9123 (tpp) cc_final: 0.8154 (tpp)
REVERT: A  313 LYS cc_start: 0.9313 (pttp) cc_final: 0.9066 (pptt)
REVERT: A  315 PHE cc_start: 0.9440 (m-10) cc_final: 0.8093 (m-10)
REVERT: A  355 ASP cc_start: 0.8577 (t0) cc_final: 0.8229 (m-30)
REVERT: A  376 MET cc_start: 0.9355 (tpt) cc_final: 0.8691 (tpt)
REVERT: A  440 LEU cc_start: 0.9768 (tp) cc_final: 0.9547 (mt)
REVERT: A  455 MET cc_start: 0.8408 (ppp) cc_final: 0.7580 (ppp)
REVERT: A  461 TRP cc_start: 0.8495 (m-10) cc_final: 0.7961 (m-10)
REVERT: A  480 MET cc_start: 0.8901 (tpt) cc_final: 0.8472 (tpt)
REVERT: A  505 HIS cc_start: 0.8678 (m90) cc_final: 0.8371 (m170)
REVERT: A  512 PHE cc_start: 0.8313 (m-10) cc_final: 0.7982 (m-80)
REVERT: A  523 PHE cc_start: 0.9501 (m-80) cc_final: 0.8823 (m-80)
REVERT: A  525 PHE cc_start: 0.9423 (m-80) cc_final: 0.9016 (m-80)
REVERT: A  544 ILE cc_start: 0.9326 (pt) cc_final: 0.9067 (tp)
REVERT: A  554 LEU cc_start: 0.9217 (tp) cc_final: 0.8928 (tp)
REVERT: A  564 GLU cc_start: 0.8999 (mp0) cc_final: 0.8711 (mp0)
REVERT: A  577 LYS cc_start: 0.8449 (tmtt) cc_final: 0.8087 (tptp)
REVERT: A  587 TYR cc_start: 0.9231 (t80) cc_final: 0.8171 (t80)
REVERT: A  588 PHE cc_start: 0.9050 (m-80) cc_final: 0.8067 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1868
  time to fit residues: 38.4033
Evaluate side-chains
  133 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:   10.0000
   chunk 38 optimal weight:    0.2980
   chunk 12 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 65 optimal weight:    7.9990
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   chunk 72 optimal weight:    0.5980
   chunk 39 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.5180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.091142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.072916 restraints weight = 28491.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.075325 restraints weight = 20118.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.077205 restraints weight = 15266.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.7136

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= 0.176
  Angle     :  0.688   8.386   8938  Z= 0.353
  Chirality :  0.045   0.148    931
  Planarity :  0.004   0.042   1159
  Dihedral  :  4.819  22.033    854
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 12.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.11 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.36 (0.30), residues: 783
  helix:  0.54 (0.27), residues: 361
  sheet: -0.16 (0.80), residues: 34
  loop : -0.97 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 302 
 HIS   0.005   0.001   HIS A 265 
 PHE   0.020   0.001   PHE A 400 
 TYR   0.015   0.001   TYR A 516 
 ARG   0.004   0.001   ARG D 457 

*********************** 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
  157 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 MET cc_start: 0.9502 (ppp) cc_final: 0.9288 (ppp)
REVERT: A   82 MET cc_start: 0.8280 (ppp) cc_final: 0.8009 (ppp)
REVERT: A   85 LEU cc_start: 0.9401 (pt) cc_final: 0.9108 (tp)
REVERT: A  203 TRP cc_start: 0.8122 (m-10) cc_final: 0.7465 (m-10)
REVERT: A  207 TYR cc_start: 0.9334 (m-80) cc_final: 0.9054 (m-80)
REVERT: A  227 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8691 (mm-30)
REVERT: A  270 MET cc_start: 0.9096 (tpp) cc_final: 0.8164 (tpp)
REVERT: A  313 LYS cc_start: 0.9303 (pttp) cc_final: 0.9057 (pptt)
REVERT: A  315 PHE cc_start: 0.9344 (m-10) cc_final: 0.8077 (m-10)
REVERT: A  355 ASP cc_start: 0.8211 (t0) cc_final: 0.7975 (t0)
REVERT: A  376 MET cc_start: 0.9382 (tpt) cc_final: 0.8630 (tpt)
REVERT: A  379 ILE cc_start: 0.9458 (mm) cc_final: 0.9234 (mm)
REVERT: A  440 LEU cc_start: 0.9751 (tp) cc_final: 0.9545 (mt)
REVERT: A  455 MET cc_start: 0.8394 (ppp) cc_final: 0.7673 (ppp)
REVERT: A  461 TRP cc_start: 0.8446 (m-10) cc_final: 0.7984 (m-10)
REVERT: A  480 MET cc_start: 0.8895 (tpt) cc_final: 0.8466 (tpt)
REVERT: A  523 PHE cc_start: 0.9370 (m-80) cc_final: 0.9007 (m-80)
REVERT: A  525 PHE cc_start: 0.9454 (m-80) cc_final: 0.9037 (m-80)
REVERT: A  544 ILE cc_start: 0.9305 (pt) cc_final: 0.9062 (tp)
REVERT: A  554 LEU cc_start: 0.9195 (tp) cc_final: 0.8917 (tp)
REVERT: A  564 GLU cc_start: 0.8950 (mp0) cc_final: 0.8671 (mp0)
REVERT: A  588 PHE cc_start: 0.9071 (m-80) cc_final: 0.8763 (m-80)
  outliers start: 1
  outliers final: 1
  residues processed: 157
  average time/residue: 0.1770
  time to fit residues: 37.3087
Evaluate side-chains
  131 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 52 optimal weight:    0.3980
   chunk 27 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 10 optimal weight:    0.9990
   chunk 75 optimal weight:    8.9990
   chunk 16 optimal weight:    2.9990
   chunk 68 optimal weight:    9.9990
   chunk 26 optimal weight:    0.0270
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.9042

-------------------------------------------------------------------------------
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 535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.090852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.072568 restraints weight = 28174.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.074941 restraints weight = 19818.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.076639 restraints weight = 15086.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.7296

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= 0.178
  Angle     :  0.700   9.916   8938  Z= 0.355
  Chirality :  0.044   0.150    931
  Planarity :  0.004   0.041   1159
  Dihedral  :  4.716  22.732    854
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  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: -0.34 (0.30), residues: 783
  helix:  0.56 (0.27), residues: 364
  sheet: -0.18 (0.79), residues: 34
  loop : -0.97 (0.32), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 302 
 HIS   0.011   0.001   HIS A 505 
 PHE   0.013   0.001   PHE A 390 
 TYR   0.014   0.001   TYR A 516 
 ARG   0.009   0.001   ARG A 306 

********************** 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
  161 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.724 
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: 0.9523 (ppp) cc_final: 0.9300 (ppp)
REVERT: A   85 LEU cc_start: 0.9362 (pt) cc_final: 0.9073 (tp)
REVERT: A  203 TRP cc_start: 0.8112 (m-10) cc_final: 0.7414 (m-10)
REVERT: A  227 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8651 (mm-30)
REVERT: A  270 MET cc_start: 0.9119 (tpp) cc_final: 0.8189 (tpp)
REVERT: A  313 LYS cc_start: 0.9315 (pttp) cc_final: 0.9050 (pptt)
REVERT: A  315 PHE cc_start: 0.9404 (m-10) cc_final: 0.8187 (m-10)
REVERT: A  376 MET cc_start: 0.9339 (tpt) cc_final: 0.8646 (tpt)
REVERT: A  407 ILE cc_start: 0.8966 (mt) cc_final: 0.8747 (mt)
REVERT: A  408 MET cc_start: 0.9484 (mmm) cc_final: 0.9190 (mmp)
REVERT: A  455 MET cc_start: 0.8376 (ppp) cc_final: 0.7681 (ppp)
REVERT: A  461 TRP cc_start: 0.8429 (m-10) cc_final: 0.7958 (m-10)
REVERT: A  480 MET cc_start: 0.8865 (tpt) cc_final: 0.8474 (tpt)
REVERT: A  523 PHE cc_start: 0.9404 (m-80) cc_final: 0.8832 (m-80)
REVERT: A  525 PHE cc_start: 0.9407 (m-80) cc_final: 0.9035 (m-80)
REVERT: A  544 ILE cc_start: 0.9265 (pt) cc_final: 0.9020 (tp)
REVERT: A  554 LEU cc_start: 0.9201 (tp) cc_final: 0.8929 (tp)
REVERT: A  564 GLU cc_start: 0.8905 (mp0) cc_final: 0.8591 (mp0)
REVERT: A  587 TYR cc_start: 0.9222 (t80) cc_final: 0.8073 (t80)
REVERT: A  588 PHE cc_start: 0.9108 (m-80) cc_final: 0.8061 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1754
  time to fit residues: 37.7918
Evaluate side-chains
  140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 23 optimal weight:    4.9990
   chunk 37 optimal weight:   10.0000
   chunk 58 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0170
   chunk 47 optimal weight:    8.9990
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   overall best weight:    1.0820

-------------------------------------------------------------------------------
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 535 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.090322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.071887 restraints weight = 29256.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.074223 restraints weight = 20753.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.076075 restraints weight = 15892.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.7460

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= 0.175
  Angle     :  0.693   9.633   8938  Z= 0.352
  Chirality :  0.044   0.149    931
  Planarity :  0.004   0.041   1159
  Dihedral  :  4.725  20.623    854
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 14.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.30), residues: 783
  helix:  0.59 (0.27), residues: 365
  sheet: -0.41 (0.76), residues: 34
  loop : -0.95 (0.32), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 302 
 HIS   0.011   0.001   HIS A 505 
 PHE   0.017   0.001   PHE A 356 
 TYR   0.014   0.001   TYR A 497 
 ARG   0.006   0.001   ARG A 306 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2406.89 seconds
wall clock time: 43 minutes 54.52 seconds (2634.52 seconds total)