Starting phenix.real_space_refine
on Fri May  9 19:02:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jys_36730/05_2025/8jys_36730.cif"
  }
  resolution = 4.5
  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=   0.005 sd=   0.042
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      16      5.16       5
     C    2271      2.51       5
     N     587      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 3522
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 241
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 253
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.68, per 1000 atoms: 0.76
  Number of scatterers: 3522
  At special positions: 0
  Unit cell: (90.094, 67.36, 119.564, 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      16     16.00
     O     648      8.00
     N     587      7.00
     C    2271      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " 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=2.03
    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: 0.85
  Conformation dependent library (CDL) restraints added in 424.6 milliseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  822

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 5 sheets defined
      11.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.391A  pdb=" N   LEU B 390 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
      removed outlier: 4.104A  pdb=" N   ILE B 410 " --> pdb=" O   GLU B 406 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA B 411 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 406 through 411'
    Processing helix  chain 'D' and resid 338 through 343
    Processing helix  chain 'D' and resid 365 through 370
    Processing helix  chain 'D' and resid 383 through 388
    Processing helix  chain 'D' and resid 404 through 410
      removed outlier: 3.808A  pdb=" N   VAL D 407 " --> pdb=" O   GLY D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'D' and resid 356 through 358
      removed outlier: 4.195A  pdb=" N   VAL D 395 " --> pdb=" O   ILE D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.969A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    129 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: 0.76

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1112
        1.34 -     1.47: 1024
        1.47 -     1.59: 1473
        1.59 -     1.72: 0
        1.72 -     1.84: 16
  Bond restraints: 3625
  Sorted by residual:
  bond pdb=" N   LEU C 109 "
       pdb=" CA  LEU C 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.49e-02 4.50e+03 5.38e+00
  bond pdb=" C   GLU A  57 "
       pdb=" N   PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.328  1.353 -0.025 1.26e-02 6.30e+03 3.84e+00
  bond pdb=" C   ALA D 520 "
       pdb=" N   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.33e-02 5.65e+03 3.07e+00
  bond pdb=" C   PRO B 373 "
       pdb=" O   PRO B 373 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 1.30e-02 5.92e+03 1.81e+00
  bond pdb=" C   PRO D 521 "
       pdb=" O   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.233  1.218  0.015 1.23e-02 6.61e+03 1.46e+00
  ... (remaining 3620 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 4704
        2.01 -     4.03: 179
        4.03 -     6.04: 33
        6.04 -     8.06: 11
        8.06 -    10.07: 3
  Bond angle restraints: 4930
  Sorted by residual:
  angle pdb=" C   ASN D 422 "
        pdb=" N   TYR D 423 "
        pdb=" CA  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     121.54  131.56  -10.02 1.91e+00 2.74e-01 2.75e+01
  angle pdb=" CA  TYR D 423 "
        pdb=" CB  TYR D 423 "
        pdb=" CG  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     113.90  120.74   -6.84 1.80e+00 3.09e-01 1.44e+01
  angle pdb=" N   SER B 366 "
        pdb=" CA  SER B 366 "
        pdb=" C   SER B 366 "
      ideal   model   delta    sigma   weight residual
     113.43  108.71    4.72 1.26e+00 6.30e-01 1.40e+01
  angle pdb=" CB  LYS B 356 "
        pdb=" CG  LYS B 356 "
        pdb=" CD  LYS B 356 "
      ideal   model   delta    sigma   weight residual
     111.30  119.15   -7.85 2.30e+00 1.89e-01 1.16e+01
  angle pdb=" C   GLU B 465 "
        pdb=" CA  GLU B 465 "
        pdb=" CB  GLU B 465 "
      ideal   model   delta    sigma   weight residual
     113.37  108.12    5.25 1.61e+00 3.86e-01 1.06e+01
  ... (remaining 4925 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 1704
       16.01 -    32.01: 307
       32.01 -    48.02: 81
       48.02 -    64.02: 20
       64.02 -    80.02: 6
  Dihedral angle restraints: 2118
    sinusoidal: 826
      harmonic: 1292
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.65  -64.35     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.59   46.41     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CB  CYS D 379 "
           pdb=" SG  CYS D 379 "
           pdb=" SG  CYS D 432 "
           pdb=" CB  CYS D 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.27   40.73     1      1.00e+01 1.00e-02 2.33e+01
  ... (remaining 2115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 272
       0.031 -    0.061: 132
       0.061 -    0.092: 71
       0.092 -    0.123: 30
       0.123 -    0.153: 4
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  VAL D 511 "
            pdb=" N   VAL D 511 "
            pdb=" C   VAL D 511 "
            pdb=" CB  VAL D 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE B 402 "
            pdb=" N   ILE B 402 "
            pdb=" C   ILE B 402 "
            pdb=" CB  ILE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 506 not shown)

  Planarity restraints: 644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 372 "    0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO D 373 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO D 373 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO D 373 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  57 "    0.043 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO C  58 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 509 "   -0.184 9.50e-02 1.11e+02   8.27e-02 4.24e+00
        pdb=" NE  ARG D 509 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 509 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 509 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 641 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 349
        2.74 -     3.28: 3830
        3.28 -     3.82: 5469
        3.82 -     4.36: 6023
        4.36 -     4.90: 9633
  Nonbonded interactions: 25304
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 347 "
            pdb=" OH  TYR D 451 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER D 383 "
            pdb=" NZ  LYS D 386 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OG  SER D 438 "
            pdb=" OD1 ASP D 442 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NZ  LYS D 478 "
            pdb=" O   PRO D 479 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.245 3.040
  ... (remaining 25299 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
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 49 through 116)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

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:             0.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.820
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3633  Z= 0.199
  Angle     :  0.969  10.071   4946  Z= 0.518
  Chirality :  0.048   0.153    509
  Planarity :  0.008   0.083    644
  Dihedral  : 17.514  80.024   1272
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 20.35
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.71 %
    Favored  : 86.12 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 38.34 %
    Favored  : 59.79 %
  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: -3.49 (0.38), residues: 425
  helix: -2.42 (0.72), residues: 44
  sheet: -0.81 (0.64), residues: 68
  loop : -2.90 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B 436 
 HIS   0.001   0.000   HIS B 505 
 PHE   0.029   0.002   PHE B 456 
 TYR   0.022   0.002   TYR B 508 
 ARG   0.012   0.001   ARG B 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.20907 (   53)
  hydrogen bonds       : angle       7.89847 (  129)
  SS BOND              : bond        0.00352 (    8)
  SS BOND              : angle       2.06712 (   16)
  covalent geometry    : bond        0.00412 ( 3625)
  covalent geometry    : angle       0.96358 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.393 
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: B  374 PHE cc_start: 0.7908 (t80) cc_final: 0.7666 (m-80)
REVERT: B  451 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80)
REVERT: D  516 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.2072
  time to fit residues: 25.1763
Evaluate side-chains
  102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 21 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 12 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
D 422 ASN
D 474 GLN
D 481 ASN
D 487 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.118320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.098965 restraints weight = 12806.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.102019 restraints weight = 7888.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.104278 restraints weight = 5474.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.156
  Angle     :  0.769  12.048   4946  Z= 0.387
  Chirality :  0.046   0.159    509
  Planarity :  0.006   0.052    644
  Dihedral  :  5.630  20.140    492
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 11.71
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 11.29 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  5.36 %
    Favored  : 94.10 %
  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: -3.22 (0.38), residues: 425
  helix: -3.54 (0.49), residues: 46
  sheet: -0.45 (0.63), residues: 64
  loop : -2.49 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 436 
 HIS   0.007   0.002   HIS B 505 
 PHE   0.023   0.002   PHE D 375 
 TYR   0.023   0.002   TYR B 423 
 ARG   0.009   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03898 (   53)
  hydrogen bonds       : angle       6.81718 (  129)
  SS BOND              : bond        0.00516 (    8)
  SS BOND              : angle       1.96758 (   16)
  covalent geometry    : bond        0.00344 ( 3625)
  covalent geometry    : angle       0.76172 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.364 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 ARG cc_start: 0.7553 (mtt180) cc_final: 0.7288 (mtt90)
REVERT: B  495 TYR cc_start: 0.6467 (m-10) cc_final: 0.6244 (m-80)
REVERT: D  335 LEU cc_start: 0.8971 (mm) cc_final: 0.8678 (tp)
REVERT: D  396 TYR cc_start: 0.8494 (m-80) cc_final: 0.8272 (m-80)
REVERT: D  402 ILE cc_start: 0.9027 (tp) cc_final: 0.8746 (tp)
REVERT: D  472 ILE cc_start: 0.8593 (tp) cc_final: 0.8297 (tp)
REVERT: D  473 TYR cc_start: 0.8906 (t80) cc_final: 0.8416 (t80)
REVERT: D  516 GLU cc_start: 0.8509 (tp30) cc_final: 0.7567 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1884
  time to fit residues: 27.6782
Evaluate side-chains
  103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 32 optimal weight:    9.9990
   chunk 36 optimal weight:   10.0000
   chunk 31 optimal weight:    0.3980
   chunk 24 optimal weight:    0.4980
   chunk 8 optimal weight:    8.9990
   chunk 27 optimal weight:    7.9990
   chunk 29 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0050
   overall best weight:    2.7798

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.111678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.092728 restraints weight = 13119.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.095607 restraints weight = 8079.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.097600 restraints weight = 5613.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.4133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3633  Z= 0.183
  Angle     :  0.750  11.362   4946  Z= 0.382
  Chirality :  0.048   0.171    509
  Planarity :  0.006   0.049    644
  Dihedral  :  5.816  19.513    492
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.05
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.71 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  4.02 %
    Favored  : 95.44 %
  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: -3.18 (0.38), residues: 425
  helix: -2.88 (0.58), residues: 52
  sheet: -0.52 (0.60), residues: 68
  loop : -2.55 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 436 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.017   0.002   PHE D 375 
 TYR   0.020   0.002   TYR B 423 
 ARG   0.012   0.001   ARG D 498 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03743 (   53)
  hydrogen bonds       : angle       6.78295 (  129)
  SS BOND              : bond        0.00304 (    8)
  SS BOND              : angle       1.48433 (   16)
  covalent geometry    : bond        0.00390 ( 3625)
  covalent geometry    : angle       0.74616 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 127
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.9406 (tppt) cc_final: 0.9145 (tppt)
REVERT: B  453 TYR cc_start: 0.8512 (t80) cc_final: 0.8102 (t80)
REVERT: D  355 ARG cc_start: 0.8943 (tpp80) cc_final: 0.8236 (tpp80)
REVERT: D  396 TYR cc_start: 0.8604 (m-80) cc_final: 0.8403 (m-80)
REVERT: D  401 VAL cc_start: 0.8614 (m) cc_final: 0.8361 (m)
REVERT: D  402 ILE cc_start: 0.9119 (tp) cc_final: 0.8819 (tp)
REVERT: D  516 GLU cc_start: 0.8458 (tp30) cc_final: 0.7978 (tm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 129
  average time/residue: 0.1994
  time to fit residues: 29.8266
Evaluate side-chains
  93 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 3 optimal weight:    9.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 27 optimal weight:   10.0000
   chunk 30 optimal weight:   10.0000
   chunk 12 optimal weight:    0.9980
   chunk 34 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
D 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.093035 restraints weight = 13252.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.095950 restraints weight = 8180.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.098054 restraints weight = 5708.668|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.4426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3633  Z= 0.145
  Angle     :  0.703  10.834   4946  Z= 0.358
  Chirality :  0.046   0.182    509
  Planarity :  0.005   0.037    644
  Dihedral  :  5.635  18.651    492
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.24 %
    Favored  : 86.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.68 %
    Favored  : 97.32 %
  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: -3.21 (0.38), residues: 425
  helix: -3.20 (0.58), residues: 46
  sheet: -0.59 (0.59), residues: 68
  loop : -2.53 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.015   0.002   PHE D 400 
 TYR   0.025   0.001   TYR D 421 
 ARG   0.006   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03353 (   53)
  hydrogen bonds       : angle       6.82921 (  129)
  SS BOND              : bond        0.00460 (    8)
  SS BOND              : angle       1.52435 (   16)
  covalent geometry    : bond        0.00327 ( 3625)
  covalent geometry    : angle       0.69874 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  356 LYS cc_start: 0.9407 (tppt) cc_final: 0.9193 (tppt)
REVERT: B  388 ASN cc_start: 0.6801 (t0) cc_final: 0.6389 (m110)
REVERT: B  423 TYR cc_start: 0.8744 (t80) cc_final: 0.8324 (t80)
REVERT: B  453 TYR cc_start: 0.8296 (t80) cc_final: 0.8054 (t80)
REVERT: D  355 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8164 (tpp80)
REVERT: D  394 ASN cc_start: 0.9292 (t0) cc_final: 0.8203 (p0)
REVERT: D  396 TYR cc_start: 0.8554 (m-80) cc_final: 0.8174 (m-80)
REVERT: D  403 ARG cc_start: 0.6898 (ppt170) cc_final: 0.6088 (ppt170)
REVERT: D  409 GLN cc_start: 0.8911 (mt0) cc_final: 0.8610 (tt0)
REVERT: D  424 LYS cc_start: 0.9143 (pptt) cc_final: 0.8789 (pptt)
REVERT: D  425 LEU cc_start: 0.9119 (pp) cc_final: 0.8707 (pp)
REVERT: D  472 ILE cc_start: 0.7693 (tp) cc_final: 0.6377 (tp)
REVERT: D  473 TYR cc_start: 0.9017 (t80) cc_final: 0.8631 (t80)
REVERT: D  478 LYS cc_start: 0.9050 (tptp) cc_final: 0.8846 (tptt)
REVERT: D  486 PHE cc_start: 0.7552 (t80) cc_final: 0.7162 (t80)
REVERT: D  516 GLU cc_start: 0.8432 (tp30) cc_final: 0.7417 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1980
  time to fit residues: 29.9222
Evaluate side-chains
  96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 2 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 11 optimal weight:    0.9980
   chunk 41 optimal weight:    7.9990
   chunk 37 optimal weight:    4.9990
   chunk 18 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 22 optimal weight:   20.0000
   chunk 26 optimal weight:    6.9990
   chunk 4 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    3.0986

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.110270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.090618 restraints weight = 13334.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.093499 restraints weight = 8312.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.095580 restraints weight = 5825.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7395
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3633  Z= 0.186
  Angle     :  0.767  11.521   4946  Z= 0.392
  Chirality :  0.048   0.172    509
  Planarity :  0.005   0.038    644
  Dihedral  :  6.031  22.410    492
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 16.25
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.47 %
    Favored  : 86.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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: -3.36 (0.38), residues: 425
  helix: -2.65 (0.64), residues: 52
  sheet: -1.03 (0.57), residues: 68
  loop : -2.64 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D 436 
 HIS   0.003   0.001   HIS B 519 
 PHE   0.030   0.002   PHE B 375 
 TYR   0.017   0.002   TYR D 501 
 ARG   0.007   0.001   ARG B 493 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03694 (   53)
  hydrogen bonds       : angle       6.97747 (  129)
  SS BOND              : bond        0.00409 (    8)
  SS BOND              : angle       1.64349 (   16)
  covalent geometry    : bond        0.00421 ( 3625)
  covalent geometry    : angle       0.76234 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8329 (pm20) cc_final: 0.7143 (tp30)
REVERT: B  356 LYS cc_start: 0.9425 (tppt) cc_final: 0.9165 (tppt)
REVERT: B  409 GLN cc_start: 0.9107 (mp10) cc_final: 0.8783 (mt0)
REVERT: B  453 TYR cc_start: 0.8683 (t80) cc_final: 0.8264 (t80)
REVERT: B  489 TYR cc_start: 0.7580 (m-80) cc_final: 0.7358 (m-80)
REVERT: D  355 ARG cc_start: 0.9080 (tpp80) cc_final: 0.7835 (tpp80)
REVERT: D  394 ASN cc_start: 0.9278 (t0) cc_final: 0.8067 (p0)
REVERT: D  396 TYR cc_start: 0.8574 (m-80) cc_final: 0.7961 (m-80)
REVERT: D  402 ILE cc_start: 0.9102 (tp) cc_final: 0.8791 (tp)
REVERT: D  406 GLU cc_start: 0.8940 (pm20) cc_final: 0.8594 (pm20)
REVERT: D  473 TYR cc_start: 0.9214 (t80) cc_final: 0.8943 (t80)
REVERT: D  478 LYS cc_start: 0.8974 (tptp) cc_final: 0.8739 (tptt)
REVERT: D  486 PHE cc_start: 0.7840 (t80) cc_final: 0.7271 (t80)
REVERT: D  506 GLN cc_start: 0.8507 (mt0) cc_final: 0.8242 (mt0)
REVERT: D  516 GLU cc_start: 0.8395 (tp30) cc_final: 0.7417 (tm-30)
REVERT: D  518 LEU cc_start: 0.9009 (tp) cc_final: 0.8808 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1957
  time to fit residues: 27.4044
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 10 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 1 optimal weight:    0.0060
   chunk 7 optimal weight:    6.9990
   chunk 25 optimal weight:    7.9990
   chunk 6 optimal weight:    0.3980
   chunk 37 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.8600

-------------------------------------------------------------------------------
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 = 0.3695 r_free = 0.3695 target = 0.111512 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.092043 restraints weight = 13611.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.095015 restraints weight = 8490.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.097127 restraints weight = 5920.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7363
moved from start:          0.5039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3633  Z= 0.139
  Angle     :  0.710  11.304   4946  Z= 0.358
  Chirality :  0.046   0.194    509
  Planarity :  0.005   0.039    644
  Dihedral  :  5.676  19.191    492
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.00 %
    Favored  : 86.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  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: -3.27 (0.39), residues: 425
  helix: -2.77 (0.62), residues: 53
  sheet: -0.80 (0.58), residues: 72
  loop : -2.60 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.022   0.002   PHE D 400 
 TYR   0.017   0.002   TYR D 421 
 ARG   0.006   0.001   ARG A 110 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03474 (   53)
  hydrogen bonds       : angle       6.90569 (  129)
  SS BOND              : bond        0.00272 (    8)
  SS BOND              : angle       1.32758 (   16)
  covalent geometry    : bond        0.00313 ( 3625)
  covalent geometry    : angle       0.70706 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8367 (pm20) cc_final: 0.7159 (tp30)
REVERT: B  356 LYS cc_start: 0.9405 (tppt) cc_final: 0.9130 (tppt)
REVERT: B  403 ARG cc_start: 0.7861 (mtt180) cc_final: 0.7466 (mpp80)
REVERT: D  394 ASN cc_start: 0.9235 (t0) cc_final: 0.8378 (p0)
REVERT: D  396 TYR cc_start: 0.8464 (m-80) cc_final: 0.8041 (m-80)
REVERT: D  402 ILE cc_start: 0.9130 (tp) cc_final: 0.8744 (tp)
REVERT: D  406 GLU cc_start: 0.9010 (pm20) cc_final: 0.8502 (pm20)
REVERT: D  409 GLN cc_start: 0.8751 (mt0) cc_final: 0.8479 (tt0)
REVERT: D  424 LYS cc_start: 0.9056 (pptt) cc_final: 0.8639 (pptt)
REVERT: D  506 GLN cc_start: 0.8483 (mt0) cc_final: 0.8219 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 113
  average time/residue: 0.2000
  time to fit residues: 26.7205
Evaluate side-chains
  95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 29 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 15 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 481 ASN
B 505 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.111301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.091706 restraints weight = 13157.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094578 restraints weight = 8162.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.096728 restraints weight = 5710.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.5416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3633  Z= 0.150
  Angle     :  0.741  11.363   4946  Z= 0.372
  Chirality :  0.048   0.245    509
  Planarity :  0.006   0.073    644
  Dihedral  :  5.693  18.975    492
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.88 %
    Favored  : 84.94 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.41 %
    Favored  : 97.32 %
  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: -3.29 (0.38), residues: 425
  helix: -2.79 (0.63), residues: 47
  sheet: -1.05 (0.56), residues: 74
  loop : -2.57 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 436 
 HIS   0.005   0.002   HIS B 505 
 PHE   0.041   0.002   PHE B 375 
 TYR   0.017   0.002   TYR B 453 
 ARG   0.007   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03368 (   53)
  hydrogen bonds       : angle       6.91756 (  129)
  SS BOND              : bond        0.00269 (    8)
  SS BOND              : angle       1.62578 (   16)
  covalent geometry    : bond        0.00335 ( 3625)
  covalent geometry    : angle       0.73646 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8444 (pm20) cc_final: 0.7317 (tp30)
REVERT: B  354 ASN cc_start: 0.9346 (t0) cc_final: 0.9054 (t0)
REVERT: B  356 LYS cc_start: 0.9400 (tppt) cc_final: 0.9021 (tppt)
REVERT: D  394 ASN cc_start: 0.9226 (t0) cc_final: 0.8366 (p0)
REVERT: D  396 TYR cc_start: 0.8599 (m-80) cc_final: 0.8082 (m-80)
REVERT: D  402 ILE cc_start: 0.9074 (tp) cc_final: 0.8691 (tp)
REVERT: D  406 GLU cc_start: 0.9020 (pm20) cc_final: 0.8518 (pm20)
REVERT: D  473 TYR cc_start: 0.9161 (t80) cc_final: 0.8835 (t80)
REVERT: D  506 GLN cc_start: 0.8474 (mt0) cc_final: 0.8195 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1900
  time to fit residues: 25.7485
Evaluate side-chains
  88 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 17 optimal weight:    9.9990
   chunk 28 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 7 optimal weight:    8.9990
   chunk 16 optimal weight:    7.9990
   chunk 34 optimal weight:    7.9990
   chunk 12 optimal weight:    0.0770
   chunk 33 optimal weight:    5.9990
   chunk 24 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0870
   overall best weight:    2.4322

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.110170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.091953 restraints weight = 13678.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.094733 restraints weight = 8387.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.096768 restraints weight = 5814.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.5613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   3633  Z= 0.164
  Angle     :  0.764  13.801   4946  Z= 0.383
  Chirality :  0.049   0.314    509
  Planarity :  0.006   0.071    644
  Dihedral  :  5.776  19.461    492
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.76
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.88 %
    Favored  : 84.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  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: -3.41 (0.38), residues: 425
  helix: -2.91 (0.62), residues: 47
  sheet: -1.15 (0.56), residues: 74
  loop : -2.65 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.026   0.002   PHE D 400 
 TYR   0.018   0.002   TYR D 501 
 ARG   0.020   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03507 (   53)
  hydrogen bonds       : angle       7.16248 (  129)
  SS BOND              : bond        0.00314 (    8)
  SS BOND              : angle       1.70574 (   16)
  covalent geometry    : bond        0.00373 ( 3625)
  covalent geometry    : angle       0.75934 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8507 (pm20) cc_final: 0.7436 (tp30)
REVERT: B  354 ASN cc_start: 0.9326 (t0) cc_final: 0.8984 (t0)
REVERT: B  356 LYS cc_start: 0.9407 (tppt) cc_final: 0.9021 (tppt)
REVERT: B  388 ASN cc_start: 0.6977 (t0) cc_final: 0.6506 (m110)
REVERT: B  489 TYR cc_start: 0.7741 (m-80) cc_final: 0.7518 (m-80)
REVERT: D  394 ASN cc_start: 0.9254 (t0) cc_final: 0.8342 (p0)
REVERT: D  396 TYR cc_start: 0.8622 (m-80) cc_final: 0.7813 (m-80)
REVERT: D  402 ILE cc_start: 0.9063 (tp) cc_final: 0.8694 (tp)
REVERT: D  406 GLU cc_start: 0.9012 (pm20) cc_final: 0.8501 (pm20)
REVERT: D  409 GLN cc_start: 0.8868 (mt0) cc_final: 0.8620 (tt0)
REVERT: D  473 TYR cc_start: 0.9124 (t80) cc_final: 0.8841 (t80)
REVERT: D  506 GLN cc_start: 0.8559 (mt0) cc_final: 0.8344 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1981
  time to fit residues: 25.7257
Evaluate side-chains
  85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 28 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0050
   chunk 10 optimal weight:    0.3980
   chunk 0 optimal weight:   20.0000
   chunk 19 optimal weight:    0.0470
   chunk 39 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    0.8896

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

Flipped N/Q/H residues before XYZ refinement:
B 505 HIS
D 360 ASN
D 474 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.114778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.095621 restraints weight = 12896.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.098566 restraints weight = 8046.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.100640 restraints weight = 5636.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7278
moved from start:          0.5843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3633  Z= 0.129
  Angle     :  0.747  14.558   4946  Z= 0.371
  Chirality :  0.049   0.340    509
  Planarity :  0.005   0.048    644
  Dihedral  :  5.623  22.500    492
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.41 %
    Favored  : 85.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.54 %
    Favored  : 99.20 %
  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: -3.35 (0.38), residues: 425
  helix: -3.05 (0.63), residues: 41
  sheet: -1.20 (0.58), residues: 73
  loop : -2.56 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.025   0.002   PHE B 375 
 TYR   0.018   0.001   TYR B 508 
 ARG   0.009   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03234 (   53)
  hydrogen bonds       : angle       6.91952 (  129)
  SS BOND              : bond        0.00244 (    8)
  SS BOND              : angle       1.47552 (   16)
  covalent geometry    : bond        0.00281 ( 3625)
  covalent geometry    : angle       0.74326 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.417 
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   57 GLU cc_start: 0.8461 (pm20) cc_final: 0.7368 (tp30)
REVERT: B  354 ASN cc_start: 0.9303 (t0) cc_final: 0.8984 (t0)
REVERT: B  356 LYS cc_start: 0.9390 (tppt) cc_final: 0.8985 (tppt)
REVERT: B  388 ASN cc_start: 0.6814 (t0) cc_final: 0.6436 (m110)
REVERT: D  394 ASN cc_start: 0.9150 (t0) cc_final: 0.8360 (p0)
REVERT: D  396 TYR cc_start: 0.8485 (m-80) cc_final: 0.7915 (m-80)
REVERT: D  402 ILE cc_start: 0.8995 (tp) cc_final: 0.8532 (tp)
REVERT: D  406 GLU cc_start: 0.8968 (pm20) cc_final: 0.8333 (pm20)
REVERT: D  409 GLN cc_start: 0.8843 (mt0) cc_final: 0.8601 (tt0)
REVERT: D  473 TYR cc_start: 0.9003 (t80) cc_final: 0.8752 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1816
  time to fit residues: 24.8032
Evaluate side-chains
  85 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 14 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    0.5980
   chunk 38 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
D 360 ASN
D 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.112415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.093623 restraints weight = 13179.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.096434 restraints weight = 8195.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.098425 restraints weight = 5757.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.5954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3633  Z= 0.142
  Angle     :  0.767  14.953   4946  Z= 0.379
  Chirality :  0.050   0.333    509
  Planarity :  0.005   0.053    644
  Dihedral  :  5.579  20.346    492
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 13.91
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 14.82 %
    Favored  : 84.00 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.46 %
  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: -3.43 (0.38), residues: 425
  helix: -3.15 (0.58), residues: 47
  sheet: -1.27 (0.56), residues: 74
  loop : -2.58 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 436 
 HIS   0.001   0.001   HIS D 505 
 PHE   0.020   0.002   PHE B 377 
 TYR   0.019   0.002   TYR B 421 
 ARG   0.009   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03247 (   53)
  hydrogen bonds       : angle       6.96662 (  129)
  SS BOND              : bond        0.00272 (    8)
  SS BOND              : angle       1.82651 (   16)
  covalent geometry    : bond        0.00317 ( 3625)
  covalent geometry    : angle       0.76157 ( 4930)

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

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

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.383 
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   57 GLU cc_start: 0.8469 (pm20) cc_final: 0.7395 (tp30)
REVERT: B  354 ASN cc_start: 0.9273 (t0) cc_final: 0.8937 (t0)
REVERT: B  356 LYS cc_start: 0.9402 (tppt) cc_final: 0.8959 (tppt)
REVERT: B  388 ASN cc_start: 0.6950 (t0) cc_final: 0.6541 (m110)
REVERT: B  423 TYR cc_start: 0.8614 (t80) cc_final: 0.8297 (t80)
REVERT: D  394 ASN cc_start: 0.9119 (t0) cc_final: 0.8295 (p0)
REVERT: D  396 TYR cc_start: 0.8441 (m-80) cc_final: 0.7661 (m-80)
REVERT: D  402 ILE cc_start: 0.8992 (tp) cc_final: 0.8592 (tp)
REVERT: D  406 GLU cc_start: 0.8865 (pm20) cc_final: 0.8406 (pm20)
REVERT: D  409 GLN cc_start: 0.8918 (mt0) cc_final: 0.8649 (tt0)
REVERT: D  473 TYR cc_start: 0.9113 (t80) cc_final: 0.8815 (t80)
REVERT: D  506 GLN cc_start: 0.8547 (mt0) cc_final: 0.8307 (mt0)
  outliers start: 1
  outliers final: 0
  residues processed: 115
  average time/residue: 0.1868
  time to fit residues: 25.1690
Evaluate side-chains
  92 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 5 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 3 optimal weight:    3.9990
   chunk 4 optimal weight:    0.6980
   chunk 29 optimal weight:    6.9990
   chunk 7 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0030
   chunk 34 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    3.5396

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

Flipped N/Q/H residues before XYZ refinement:
** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 360 ASN
D 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.107786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.089106 restraints weight = 13623.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.091825 restraints weight = 8540.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.093782 restraints weight = 6023.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.6217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   3633  Z= 0.206
  Angle     :  0.840  16.975   4946  Z= 0.422
  Chirality :  0.052   0.333    509
  Planarity :  0.005   0.055    644
  Dihedral  :  6.092  21.168    492
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 18.74
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 16.00 %
    Favored  : 82.82 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.46 %
  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: -3.40 (0.39), residues: 425
  helix: -3.04 (0.61), residues: 46
  sheet: -1.43 (0.57), residues: 69
  loop : -2.53 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 436 
 HIS   0.002   0.001   HIS D 519 
 PHE   0.032   0.002   PHE D 429 
 TYR   0.026   0.002   TYR D 501 
 ARG   0.017   0.001   ARG D 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03765 (   53)
  hydrogen bonds       : angle       7.41926 (  129)
  SS BOND              : bond        0.00440 (    8)
  SS BOND              : angle       2.20972 (   16)
  covalent geometry    : bond        0.00465 ( 3625)
  covalent geometry    : angle       0.83144 ( 4930)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1529.61 seconds
wall clock time: 27 minutes 14.89 seconds (1634.89 seconds total)