Starting phenix.real_space_refine
on Tue Feb 11 21:00:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dv1_27730/02_2025/8dv1_27730.cif"
  }
  resolution = 3.4
  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=   0.001 sd=   0.038
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    4183      2.51       5
     N    1074      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 6543
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "D"
      Number of atoms: 4855
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4855
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 5.18, per 1000 atoms: 0.79
  Number of scatterers: 6543
  At special positions: 0
  Unit cell: (76.311, 87.57, 126.351, 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    1249      8.00
     N    1074      7.00
     C    4183      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A1301 " - " ASN A 343 "
      " NAG D1001 " - " ASN D 322 "
      " NAG D1002 " - " ASN D 103 "
      " NAG D1003 " - " ASN D 432 "
      " NAG D1004 " - " ASN D 546 "
      " NAG D1005 " - " ASN D  90 "
      " NAG D1006 " - " ASN D  53 "
  Time building additional restraints: 1.68
  Conformation dependent library (CDL) restraints added in 962.1 milliseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      58.3% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 3.677A  pdb=" N   VAL A 341 " --> pdb=" O   PRO A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.589A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.108A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 520 through 522
      No H-bonds generated for 'chain 'A' and resid 520 through 522'
    Processing helix  chain 'D' and resid 22 through 53
      removed outlier: 3.969A  pdb=" N   THR D  27 " --> pdb=" O   GLU D  23 " (cutoff:3.500A)
      removed outlier: 5.400A  pdb=" N   ASP D  38 " --> pdb=" O   SER D  34 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   TYR D  41 " --> pdb=" O   GLU D  37 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 81
    Processing helix  chain 'D' and resid 82 through 83
      No H-bonds generated for 'chain 'D' and resid 82 through 83'
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 137 through 141
    Processing helix  chain 'D' and resid 147 through 155
      removed outlier: 3.736A  pdb=" N   ILE D 151 " --> pdb=" O   GLY D 147 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   MET D 152 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 157 through 172
    Processing helix  chain 'D' and resid 172 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 4.486A  pdb=" N   VAL D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 220 through 252
      Proline residue:  D 235  - end of helix
      removed outlier: 3.996A  pdb=" N   ASN D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 277
      No H-bonds generated for 'chain 'D' and resid 275 through 277'
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 317
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 413
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 469 through 471
      No H-bonds generated for 'chain 'D' and resid 469 through 471'
    Processing helix  chain 'D' and resid 472 through 485
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.078A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
      removed outlier: 3.881A  pdb=" N   VAL D 573 " --> pdb=" O   ALA D 569 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 581 through 598
      Proline residue:  D 590  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.915A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.072A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350

    323 hydrogen bonds defined for protein.
    906 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: 1.85

  Time building geometry restraints manager: 1.93 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1266
        1.32 -     1.45: 2072
        1.45 -     1.58: 3320
        1.58 -     1.71: 9
        1.71 -     1.84: 58
  Bond restraints: 6725
  Sorted by residual:
  bond pdb=" CD2 TRP D 477 "
       pdb=" CE3 TRP D 477 "
    ideal  model  delta    sigma   weight residual
    1.398  1.306  0.092 1.60e-02 3.91e+03 3.28e+01
  bond pdb=" CB  SER D  44 "
       pdb=" OG  SER D  44 "
    ideal  model  delta    sigma   weight residual
    1.417  1.313  0.104 2.00e-02 2.50e+03 2.69e+01
  bond pdb=" CB  TYR A 421 "
       pdb=" CG  TYR A 421 "
    ideal  model  delta    sigma   weight residual
    1.512  1.402  0.110 2.20e-02 2.07e+03 2.48e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.392  0.124 2.50e-02 1.60e+03 2.45e+01
  bond pdb=" CB  HIS D 540 "
       pdb=" CG  HIS D 540 "
    ideal  model  delta    sigma   weight residual
    1.497  1.430  0.067 1.40e-02 5.10e+03 2.29e+01
  ... (remaining 6720 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 7553
        2.16 -     4.32: 1363
        4.32 -     6.47: 181
        6.47 -     8.63: 35
        8.63 -    10.79: 8
  Bond angle restraints: 9140
  Sorted by residual:
  angle pdb=" C   GLY D 537 "
        pdb=" N   PRO D 538 "
        pdb=" CA  PRO D 538 "
      ideal   model   delta    sigma   weight residual
     119.78  128.55   -8.77 1.03e+00 9.43e-01 7.24e+01
  angle pdb=" C   ALA A 520 "
        pdb=" N   PRO A 521 "
        pdb=" CA  PRO A 521 "
      ideal   model   delta    sigma   weight residual
     119.47  129.12   -9.65 1.16e+00 7.43e-01 6.93e+01
  angle pdb=" C   ASN D 137 "
        pdb=" N   PRO D 138 "
        pdb=" CA  PRO D 138 "
      ideal   model   delta    sigma   weight residual
     119.56  127.64   -8.08 1.02e+00 9.61e-01 6.28e+01
  angle pdb=" C   VAL D 283 "
        pdb=" N   PRO D 284 "
        pdb=" CA  PRO D 284 "
      ideal   model   delta    sigma   weight residual
     119.24  127.24   -8.00 1.04e+00 9.25e-01 5.91e+01
  angle pdb=" C   SER D 611 "
        pdb=" N   PRO D 612 "
        pdb=" CA  PRO D 612 "
      ideal   model   delta    sigma   weight residual
     119.82  127.13   -7.31 9.80e-01 1.04e+00 5.57e+01
  ... (remaining 9135 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.80: 3870
       17.80 -    35.59: 146
       35.59 -    53.39: 29
       53.39 -    71.19: 12
       71.19 -    88.98: 5
  Dihedral angle restraints: 4062
    sinusoidal: 1727
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -140.80   54.80     1      1.00e+01 1.00e-02 4.07e+01
  dihedral pdb=" C   TYR A 421 "
           pdb=" N   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -135.05   12.45     0      2.50e+00 1.60e-01 2.48e+01
  dihedral pdb=" CA  ALA D 153 "
           pdb=" C   ALA D 153 "
           pdb=" N   ASN D 154 "
           pdb=" CA  ASN D 154 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.26  -22.74     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 4059 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.137: 838
       0.137 -    0.274: 124
       0.274 -    0.412: 10
       0.412 -    0.549: 3
       0.549 -    0.686: 1
  Chirality restraints: 976
  Sorted by residual:
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.82    0.69 2.00e-01 2.50e+01 1.18e+01
  chirality pdb=" C1  NAG D1002 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG D1002 "
            pdb=" O5  NAG D1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.93    0.53 2.00e-01 2.50e+01 6.96e+00
  chirality pdb=" C2  NAG D1002 "
            pdb=" C1  NAG D1002 "
            pdb=" C3  NAG D1002 "
            pdb=" N2  NAG D1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -3.00    0.50 2.00e-01 2.50e+01 6.35e+00
  ... (remaining 973 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  90 "    0.217 2.00e-02 2.50e+03   2.54e-01 8.05e+02
        pdb=" CG  ASN D  90 "   -0.123 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  90 "   -0.004 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  90 "   -0.403 2.00e-02 2.50e+03
        pdb=" C1  NAG D1005 "    0.312 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 163 "    0.287 2.00e-02 2.50e+03   1.39e-01 4.80e+02
        pdb=" CG  TRP D 163 "   -0.082 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 163 "   -0.075 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 163 "   -0.148 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 163 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 163 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 163 "   -0.174 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 163 "    0.148 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 163 "   -0.037 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 163 "    0.139 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 343 "   -0.135 2.00e-02 2.50e+03   1.44e-01 2.59e+02
        pdb=" CG  ASN A 343 "    0.075 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 343 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 343 "    0.225 2.00e-02 2.50e+03
        pdb=" C1  NAG A1301 "   -0.171 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1716
        2.80 -     3.33: 6477
        3.33 -     3.85: 11592
        3.85 -     4.38: 14234
        4.38 -     4.90: 22417
  Nonbonded interactions: 56436
  Sorted by model distance:
  nonbonded pdb=" O4  NAG D1004 "
            pdb=" O6  NAG D1004 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" N   ASN D 103 "
            pdb=" OD1 ASN D 103 "
     model   vdw
     2.318 3.120
  nonbonded pdb=" N   ASN D 432 "
            pdb=" OD1 ASN D 432 "
     model   vdw
     2.327 3.120
  nonbonded pdb=" N   ASN D 546 "
            pdb=" OD1 ASN D 546 "
     model   vdw
     2.356 3.120
  nonbonded pdb=" N   ASN D 322 "
            pdb=" OD1 ASN D 322 "
     model   vdw
     2.411 3.120
  ... (remaining 56431 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 individual isotropic
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:             2.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.370
  Find NCS groups from input model:        0.060
  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:2.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
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      :  0.018   0.125   6725  Z= 1.160
  Angle     :  1.709  10.789   9140  Z= 1.169
  Chirality :  0.101   0.686    976
  Planarity :  0.011   0.139   1177
  Dihedral  : 10.891  88.982   2543
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 1.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  1.57 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.27 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.28), residues: 792
  helix: -0.33 (0.23), residues: 378
  sheet:  0.33 (0.67), residues: 58
  loop :  0.18 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.287   0.015   TRP D 163 
 HIS   0.010   0.002   HIS D 241 
 PHE   0.069   0.008   PHE D  32 
 TYR   0.070   0.011   TYR D 180 
 ARG   0.016   0.001   ARG D 177 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 198
  time to evaluate  : 0.707 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 ASN cc_start: 0.7661 (m-40) cc_final: 0.7098 (p0)
REVERT: A  472 ILE cc_start: 0.7249 (mm) cc_final: 0.7040 (mm)
REVERT: A  500 THR cc_start: 0.8413 (p) cc_final: 0.8103 (p)
REVERT: D  476 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (mptt)
  outliers start: 3
  outliers final: 1
  residues processed: 200
  average time/residue: 0.2294
  time to fit residues: 57.9394
Evaluate side-chains
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  322 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 20 optimal weight:    0.5980
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0570
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.5298

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

Flipped N/Q/H residues before XYZ refinement:
D  61 ASN
D  96 GLN
D 401 HIS
D 437 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.111989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.098767 restraints weight = 14997.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.99
r_work: 0.3343 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6725  Z= 0.237
  Angle     :  0.685  11.810   9140  Z= 0.354
  Chirality :  0.054   0.662    976
  Planarity :  0.005   0.040   1177
  Dihedral  :  7.471  89.057   1013
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  :  9.44 %
    Favored  : 88.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.13 (0.30), residues: 792
  helix:  1.32 (0.27), residues: 375
  sheet:  0.07 (0.66), residues: 60
  loop :  0.41 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 165 
 HIS   0.006   0.001   HIS D 374 
 PHE   0.018   0.002   PHE D 369 
 TYR   0.022   0.002   TYR D 183 
 ARG   0.004   0.001   ARG A 466 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 152
  time to evaluate  : 0.767 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 ILE cc_start: 0.7892 (pt) cc_final: 0.7421 (pt)
REVERT: A  355 ARG cc_start: 0.8621 (tpt170) cc_final: 0.8136 (tpt170)
REVERT: A  409 GLN cc_start: 0.8997 (mt0) cc_final: 0.8794 (mt0)
REVERT: A  469 SER cc_start: 0.8828 (t) cc_final: 0.8513 (p)
REVERT: A  523 THR cc_start: 0.7886 (m) cc_final: 0.7664 (p)
REVERT: D   26 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8310 (ttmt)
REVERT: D   56 GLU cc_start: 0.8118 (pm20) cc_final: 0.7669 (pm20)
REVERT: D   60 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8202 (mm-40)
REVERT: D  115 ARG cc_start: 0.8360 (mmm-85) cc_final: 0.7884 (mmm-85)
REVERT: D  168 TRP cc_start: 0.6873 (t-100) cc_final: 0.6353 (t-100)
REVERT: D  174 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8028 (ttmm)
REVERT: D  206 ASP cc_start: 0.9109 (t70) cc_final: 0.8713 (t0)
REVERT: D  210 ASN cc_start: 0.7676 (m-40) cc_final: 0.7407 (m110)
REVERT: D  270 MET cc_start: 0.7661 (mmt) cc_final: 0.7345 (tpp)
REVERT: D  472 GLN cc_start: 0.7176 (mt0) cc_final: 0.6642 (mp10)
REVERT: D  476 LYS cc_start: 0.8352 (mmmt) cc_final: 0.8061 (tptt)
REVERT: D  577 LYS cc_start: 0.7404 (mttt) cc_final: 0.7135 (mtpt)
  outliers start: 12
  outliers final: 6
  residues processed: 157
  average time/residue: 0.2116
  time to fit residues: 43.1010
Evaluate side-chains
  132 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.816 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   26 LYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue  233 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0000
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
D  61 ASN
D 373 HIS
D 437 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.110480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.097206 restraints weight = 15421.268|
|-----------------------------------------------------------------------------|
r_work (start): 0.3428 rms_B_bonded: 3.01
r_work: 0.3326 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6725  Z= 0.218
  Angle     :  0.647  13.842   9140  Z= 0.323
  Chirality :  0.051   0.583    976
  Planarity :  0.004   0.029   1177
  Dihedral  :  6.951  79.608   1011
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 10.16 %
    Favored  : 87.12 %
  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:  1.13 (0.30), residues: 792
  helix:  1.44 (0.27), residues: 380
  sheet: -0.35 (0.66), residues: 61
  loop :  0.33 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 165 
 HIS   0.005   0.001   HIS D 378 
 PHE   0.014   0.002   PHE D 369 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.004   0.001   ARG A 466 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
REVERT: A  423 TYR cc_start: 0.8721 (t80) cc_final: 0.8415 (t80)
REVERT: A  469 SER cc_start: 0.8761 (t) cc_final: 0.8479 (p)
REVERT: A  498 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8109 (mt0)
REVERT: A  523 THR cc_start: 0.7985 (m) cc_final: 0.7582 (p)
REVERT: D   26 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8501 (ttmt)
REVERT: D   30 ASP cc_start: 0.8723 (m-30) cc_final: 0.8504 (m-30)
REVERT: D   56 GLU cc_start: 0.8182 (pm20) cc_final: 0.7660 (pm20)
REVERT: D   60 GLN cc_start: 0.8432 (mm-40) cc_final: 0.8160 (mm-40)
REVERT: D  115 ARG cc_start: 0.8426 (mmm-85) cc_final: 0.8031 (mmm-85)
REVERT: D  168 TRP cc_start: 0.6849 (t-100) cc_final: 0.6261 (t-100)
REVERT: D  206 ASP cc_start: 0.9061 (t70) cc_final: 0.8729 (t0)
REVERT: D  210 ASN cc_start: 0.7765 (m-40) cc_final: 0.7545 (m110)
REVERT: D  249 MET cc_start: 0.7733 (tpt) cc_final: 0.7447 (tpt)
REVERT: D  270 MET cc_start: 0.7813 (mmt) cc_final: 0.7499 (tpp)
REVERT: D  472 GLN cc_start: 0.7275 (mt0) cc_final: 0.6732 (mp10)
  outliers start: 19
  outliers final: 9
  residues processed: 137
  average time/residue: 0.1953
  time to fit residues: 35.3683
Evaluate side-chains
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   26 LYS
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  233 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9980
   chunk 8 optimal weight:    0.3980
   chunk 31 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
D 437 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.108049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094911 restraints weight = 15679.156|
|-----------------------------------------------------------------------------|
r_work (start): 0.3396 rms_B_bonded: 3.00
r_work: 0.3293 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6725  Z= 0.258
  Angle     :  0.640  10.999   9140  Z= 0.321
  Chirality :  0.051   0.605    976
  Planarity :  0.004   0.027   1177
  Dihedral  :  6.308  52.572   1011
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.59 %
    Favored  : 86.12 %
  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:  1.04 (0.30), residues: 792
  helix:  1.45 (0.27), residues: 380
  sheet: -0.38 (0.65), residues: 61
  loop :  0.18 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 165 
 HIS   0.007   0.001   HIS D 378 
 PHE   0.013   0.002   PHE D 230 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.004   0.001   ARG A 466 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  469 SER cc_start: 0.8681 (t) cc_final: 0.8400 (p)
REVERT: A  498 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8100 (mt0)
REVERT: D   26 LYS cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (ttmt)
REVERT: D   56 GLU cc_start: 0.8135 (pm20) cc_final: 0.7609 (pm20)
REVERT: D   60 GLN cc_start: 0.8471 (mm-40) cc_final: 0.8261 (mm-40)
REVERT: D   63 ASN cc_start: 0.8591 (m-40) cc_final: 0.8164 (m-40)
REVERT: D  115 ARG cc_start: 0.8359 (mmm-85) cc_final: 0.8007 (mmm-85)
REVERT: D  206 ASP cc_start: 0.9063 (t70) cc_final: 0.8763 (t0)
REVERT: D  210 ASN cc_start: 0.7877 (m-40) cc_final: 0.7625 (m110)
REVERT: D  238 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: D  249 MET cc_start: 0.7753 (tpt) cc_final: 0.7447 (tpt)
REVERT: D  376 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8756 (ttp)
REVERT: D  401 HIS cc_start: 0.8739 (OUTLIER) cc_final: 0.7610 (t-90)
  outliers start: 16
  outliers final: 8
  residues processed: 128
  average time/residue: 0.1935
  time to fit residues: 32.8848
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   26 LYS
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  401 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 76 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 2 optimal weight:    0.5980
   chunk 46 optimal weight:    0.0070
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
D 493 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.110388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.097651 restraints weight = 15437.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 2.74
r_work: 0.3375 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.5020

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6725  Z= 0.207
  Angle     :  0.610   9.317   9140  Z= 0.303
  Chirality :  0.049   0.570    976
  Planarity :  0.003   0.028   1177
  Dihedral  :  5.676  51.317   1011
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 12.02 %
    Favored  : 85.26 %
  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:  1.01 (0.30), residues: 792
  helix:  1.46 (0.27), residues: 381
  sheet: -0.58 (0.64), residues: 62
  loop :  0.15 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 378 
 PHE   0.011   0.001   PHE D 369 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 121
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: A  386 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8390 (ptpp)
REVERT: A  469 SER cc_start: 0.8650 (t) cc_final: 0.8378 (p)
REVERT: A  498 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7928 (mt0)
REVERT: D   56 GLU cc_start: 0.8122 (pm20) cc_final: 0.7560 (pm20)
REVERT: D   63 ASN cc_start: 0.8488 (m-40) cc_final: 0.8124 (m-40)
REVERT: D  115 ARG cc_start: 0.8261 (mmm-85) cc_final: 0.7981 (mmm-85)
REVERT: D  494 ASP cc_start: 0.8500 (t70) cc_final: 0.8261 (t70)
  outliers start: 19
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1943
  time to fit residues: 33.6520
Evaluate side-chains
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 113
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  440 LEU
Chi-restraints excluded: chain D residue  530 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 73 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
D  81 GLN
D 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.107714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.095238 restraints weight = 15438.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.3434 rms_B_bonded: 2.70
r_work: 0.3337 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.5215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   6725  Z= 0.291
  Angle     :  0.638   8.509   9140  Z= 0.324
  Chirality :  0.051   0.606    976
  Planarity :  0.004   0.031   1177
  Dihedral  :  5.796  49.810   1011
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 13.88 %
    Favored  : 83.55 %
  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:  0.88 (0.30), residues: 792
  helix:  1.37 (0.26), residues: 383
  sheet: -0.44 (0.65), residues: 63
  loop :  0.01 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 168 
 HIS   0.005   0.001   HIS D 378 
 PHE   0.014   0.001   PHE D 523 
 TYR   0.017   0.001   TYR D 385 
 ARG   0.004   0.000   ARG D 582 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.714 
Fit side-chains
REVERT: A  469 SER cc_start: 0.8804 (t) cc_final: 0.8494 (p)
REVERT: A  498 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8024 (mt0)
REVERT: D   56 GLU cc_start: 0.8110 (pm20) cc_final: 0.7709 (pm20)
REVERT: D   63 ASN cc_start: 0.8545 (m-40) cc_final: 0.8239 (m-40)
REVERT: D   79 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8686 (mm)
REVERT: D  115 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.8005 (mmm160)
REVERT: D  249 MET cc_start: 0.7845 (tpt) cc_final: 0.7475 (tpt)
REVERT: D  494 ASP cc_start: 0.8614 (t70) cc_final: 0.8305 (t70)
  outliers start: 18
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1901
  time to fit residues: 31.5303
Evaluate side-chains
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  440 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 77 optimal weight:    0.3980
   chunk 27 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 9 optimal weight:    0.1980
   chunk 48 optimal weight:    0.6980
   chunk 8 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
D 437 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.109344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.096865 restraints weight = 15404.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.72
r_work: 0.3367 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.5392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6725  Z= 0.213
  Angle     :  0.585   8.044   9140  Z= 0.298
  Chirality :  0.048   0.560    976
  Planarity :  0.003   0.027   1177
  Dihedral  :  5.594  51.401   1011
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 13.88 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.91 (0.30), residues: 792
  helix:  1.44 (0.26), residues: 383
  sheet: -0.42 (0.66), residues: 63
  loop : -0.04 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 165 
 HIS   0.005   0.001   HIS D 378 
 PHE   0.012   0.001   PHE D 369 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 115
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
REVERT: A  383 SER cc_start: 0.8266 (p) cc_final: 0.7910 (t)
REVERT: A  469 SER cc_start: 0.8634 (t) cc_final: 0.8349 (p)
REVERT: A  498 GLN cc_start: 0.8845 (OUTLIER) cc_final: 0.7847 (mt0)
REVERT: D   63 ASN cc_start: 0.8493 (m-40) cc_final: 0.8174 (m-40)
REVERT: D   79 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8579 (mm)
REVERT: D  115 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.7982 (mmm160)
REVERT: D  249 MET cc_start: 0.7968 (tpt) cc_final: 0.7530 (tpp)
REVERT: D  310 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7919 (mm-30)
REVERT: D  494 ASP cc_start: 0.8542 (t70) cc_final: 0.8208 (t70)
  outliers start: 16
  outliers final: 13
  residues processed: 124
  average time/residue: 0.1968
  time to fit residues: 32.9719
Evaluate side-chains
  124 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  440 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.0970
   chunk 56 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 19 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
D 437 ASN
D 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.109661 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.097070 restraints weight = 15561.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.76
r_work: 0.3371 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.5521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6725  Z= 0.212
  Angle     :  0.588   7.855   9140  Z= 0.301
  Chirality :  0.049   0.553    976
  Planarity :  0.003   0.028   1177
  Dihedral  :  5.566  51.443   1011
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.88 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.30), residues: 792
  helix:  1.40 (0.26), residues: 383
  sheet: -0.37 (0.67), residues: 62
  loop : -0.06 (0.36), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 165 
 HIS   0.004   0.001   HIS D 378 
 PHE   0.016   0.001   PHE A 374 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.680 
Fit side-chains
   revert: symmetry clash
REVERT: A  469 SER cc_start: 0.8643 (t) cc_final: 0.8341 (p)
REVERT: A  498 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.7829 (mt0)
REVERT: D   63 ASN cc_start: 0.8534 (m-40) cc_final: 0.8228 (m-40)
REVERT: D   79 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8614 (mm)
REVERT: D  115 ARG cc_start: 0.8312 (mmm-85) cc_final: 0.8016 (mmm160)
REVERT: D  249 MET cc_start: 0.7939 (tpt) cc_final: 0.7509 (tpp)
REVERT: D  310 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7887 (mm-30)
REVERT: D  494 ASP cc_start: 0.8576 (t70) cc_final: 0.8234 (t70)
REVERT: D  530 CYS cc_start: 0.7362 (t) cc_final: 0.7121 (t)
  outliers start: 16
  outliers final: 13
  residues processed: 123
  average time/residue: 0.1864
  time to fit residues: 30.5013
Evaluate side-chains
  123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  440 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 19 optimal weight:    0.0670
   chunk 58 optimal weight:    0.9990
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 28 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0000
   chunk 41 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.3322

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.111452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.098853 restraints weight = 15562.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3499 rms_B_bonded: 2.76
r_work: 0.3399 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.5673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6725  Z= 0.180
  Angle     :  0.594  11.028   9140  Z= 0.300
  Chirality :  0.048   0.528    976
  Planarity :  0.003   0.027   1177
  Dihedral  :  5.410  52.340   1011
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.45 %
    Favored  : 82.12 %
  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:  0.92 (0.31), residues: 792
  helix:  1.45 (0.26), residues: 383
  sheet: -0.55 (0.66), residues: 63
  loop : -0.02 (0.36), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 163 
 HIS   0.004   0.001   HIS D 374 
 PHE   0.017   0.001   PHE A 374 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  469 SER cc_start: 0.8656 (t) cc_final: 0.8398 (p)
REVERT: A  498 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.7780 (mt0)
REVERT: D   56 GLU cc_start: 0.8041 (pm20) cc_final: 0.7772 (pm20)
REVERT: D   63 ASN cc_start: 0.8542 (m-40) cc_final: 0.8247 (m-40)
REVERT: D   79 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8615 (mm)
REVERT: D  115 ARG cc_start: 0.8303 (mmm-85) cc_final: 0.8010 (mmm160)
REVERT: D  189 GLU cc_start: 0.8246 (tp30) cc_final: 0.8013 (tp30)
REVERT: D  290 ASN cc_start: 0.7734 (t0) cc_final: 0.7431 (t0)
REVERT: D  530 CYS cc_start: 0.7383 (t) cc_final: 0.7151 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 128
  average time/residue: 0.1975
  time to fit residues: 33.4081
Evaluate side-chains
  125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  519 HIS
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  331 SER
Chi-restraints excluded: chain D residue  440 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0470
   chunk 16 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
D 493 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.110526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.097931 restraints weight = 15629.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 2.74
r_work: 0.3383 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8140
moved from start:          0.5823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6725  Z= 0.214
  Angle     :  0.616   8.642   9140  Z= 0.314
  Chirality :  0.048   0.546    976
  Planarity :  0.003   0.027   1177
  Dihedral  :  5.440  51.656   1011
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.02 %
    Favored  : 81.12 %
  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 (0.31), residues: 792
  helix:  1.39 (0.26), residues: 382
  sheet: -0.45 (0.67), residues: 62
  loop : -0.06 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 477 
 HIS   0.005   0.001   HIS D 378 
 PHE   0.021   0.001   PHE A 374 
 TYR   0.018   0.001   TYR D 385 
 ARG   0.003   0.000   ARG A 466 

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  469 SER cc_start: 0.8579 (t) cc_final: 0.8333 (p)
REVERT: A  498 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.7830 (mt0)
REVERT: D   63 ASN cc_start: 0.8560 (m-40) cc_final: 0.8278 (m-40)
REVERT: D   79 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8623 (mm)
REVERT: D  115 ARG cc_start: 0.8344 (mmm-85) cc_final: 0.8051 (mmm160)
REVERT: D  290 ASN cc_start: 0.7737 (t0) cc_final: 0.7454 (t0)
REVERT: D  530 CYS cc_start: 0.7384 (t) cc_final: 0.7162 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2049
  time to fit residues: 33.0009
Evaluate side-chains
  123 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  483 VAL
Chi-restraints excluded: chain A residue  498 GLN
Chi-restraints excluded: chain A residue  525 CYS
Chi-restraints excluded: chain D residue   62 MET
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   91 LEU
Chi-restraints excluded: chain D residue  151 ILE
Chi-restraints excluded: chain D residue  183 TYR
Chi-restraints excluded: chain D residue  233 ILE
Chi-restraints excluded: chain D residue  267 LEU
Chi-restraints excluded: chain D residue  440 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 493 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.111383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.098536 restraints weight = 15431.719|
|-----------------------------------------------------------------------------|
r_work (start): 0.3492 rms_B_bonded: 2.72
r_work: 0.3395 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.5887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6725  Z= 0.221
  Angle     :  0.623   7.789   9140  Z= 0.317
  Chirality :  0.049   0.555    976
  Planarity :  0.003   0.029   1177
  Dihedral  :  5.457  51.843   1011
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 16.60 %
    Favored  : 81.26 %
  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:  0.82 (0.31), residues: 792
  helix:  1.35 (0.26), residues: 382
  sheet: -0.46 (0.66), residues: 62
  loop : -0.07 (0.36), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 163 
 HIS   0.005   0.001   HIS D 378 
 PHE   0.020   0.001   PHE A 374 
 TYR   0.019   0.001   TYR D 385 
 ARG   0.003   0.000   ARG D 582 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3157.10 seconds
wall clock time: 57 minutes 10.20 seconds (3430.20 seconds total)