Starting phenix.real_space_refine
on Tue Feb 11 07:33:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7the_25893/02_2025/7the_25893.cif"
  }
  resolution = 3.87
  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=  -0.002 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1543 atoms to isotropic.
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      17      5.16       5
     C    2098      2.51       5
     N     549      2.21       5
     O     641      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3305
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1543
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 195, 1543
          Classifications: {'peptide': 195}
          Link IDs: {'PTRANS': 11, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 945
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "C"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 803
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 97}
    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
  Time building chain proxies: 3.06, per 1000 atoms: 0.93
  Number of scatterers: 3305
  At special positions: 0
  Unit cell: (65.596, 81.466, 87.814, 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      17     16.00
     O     641      8.00
     N     549      7.00
     C    2098      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  92 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " 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
  Links applied
    NAG-ASN
      " NAG A 601 " - " ASN A 343 "
  Time building additional restraints: 0.75
  Conformation dependent library (CDL) restraints added in 420.8 milliseconds
  

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  778

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 9 sheets defined
      12.5% alpha, 31.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 364 through 370
      removed outlier: 3.981A  pdb=" N   LEU A 368 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 389
      removed outlier: 4.706A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 411
      removed outlier: 4.854A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   ALA A 411 " --> pdb=" O   ARG A 408 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'C' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 334 through 335
      removed outlier: 7.513A  pdb=" N   ASN A 334 " --> pdb=" O   VAL A 362 " (cutoff:3.500A)
      removed outlier: 6.234A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.975A  pdb=" N   VAL A 395 " --> pdb=" O   ILE A 358 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASN A 394 " --> pdb=" O   GLU A 516 " (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 'B' and resid 3 through 6
    Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   ILE B  34 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   ARG B  50 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11
      removed outlier: 6.378A  pdb=" N   GLU B  10 " --> pdb=" O   THR B 110 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   VAL B 102 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 4 through 7
    Processing sheet with id=AA9, first strand: chain 'C' and resid 10 through 12
      removed outlier: 6.730A  pdb=" N   LEU C  11 " --> pdb=" O   GLU C 105 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   TRP C  35 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    252 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: 0.89

  Time building geometry restraints manager: 0.90 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 928
        1.33 -     1.45: 657
        1.45 -     1.57: 1781
        1.57 -     1.69: 0
        1.69 -     1.81: 22
  Bond restraints: 3388
  Sorted by residual:
  bond pdb=" C5  NAG A 601 "
       pdb=" O5  NAG A 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.482 -0.069 2.00e-02 2.50e+03 1.19e+01
  bond pdb=" CZ  ARG B  94 "
       pdb=" NH2 ARG B  94 "
    ideal  model  delta    sigma   weight residual
    1.330  1.287  0.043 1.30e-02 5.92e+03 1.10e+01
  bond pdb=" CZ  ARG A 509 "
       pdb=" NH2 ARG A 509 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.04e+01
  bond pdb=" CZ  ARG A 457 "
       pdb=" NH2 ARG A 457 "
    ideal  model  delta    sigma   weight residual
    1.330  1.288  0.042 1.30e-02 5.92e+03 1.02e+01
  bond pdb=" CZ  ARG A 357 "
       pdb=" NH2 ARG A 357 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.02e+01
  ... (remaining 3383 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 3171
        1.82 -     3.63: 1161
        3.63 -     5.45: 247
        5.45 -     7.26: 22
        7.26 -     9.08: 4
  Bond angle restraints: 4605
  Sorted by residual:
  angle pdb=" CA  PHE A 347 "
        pdb=" CB  PHE A 347 "
        pdb=" CG  PHE A 347 "
      ideal   model   delta    sigma   weight residual
     113.80  119.35   -5.55 1.00e+00 1.00e+00 3.08e+01
  angle pdb=" N   CYS A 361 "
        pdb=" CA  CYS A 361 "
        pdb=" C   CYS A 361 "
      ideal   model   delta    sigma   weight residual
     108.79  117.19   -8.40 1.53e+00 4.27e-01 3.01e+01
  angle pdb=" C   THR A 393 "
        pdb=" N   ASN A 394 "
        pdb=" CA  ASN A 394 "
      ideal   model   delta    sigma   weight residual
     121.75  130.83   -9.08 1.73e+00 3.34e-01 2.75e+01
  angle pdb=" CA  ASP A 405 "
        pdb=" CB  ASP A 405 "
        pdb=" CG  ASP A 405 "
      ideal   model   delta    sigma   weight residual
     112.60  117.25   -4.65 1.00e+00 1.00e+00 2.16e+01
  angle pdb=" CA  ASP C  70 "
        pdb=" CB  ASP C  70 "
        pdb=" CG  ASP C  70 "
      ideal   model   delta    sigma   weight residual
     112.60  117.16   -4.56 1.00e+00 1.00e+00 2.08e+01
  ... (remaining 4600 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.95: 1841
       16.95 -    33.89: 139
       33.89 -    50.84: 30
       50.84 -    67.79: 8
       67.79 -    84.73: 4
  Dihedral angle restraints: 2022
    sinusoidal: 794
      harmonic: 1228
  Sorted by residual:
  dihedral pdb=" CA  ARG B  83 "
           pdb=" C   ARG B  83 "
           pdb=" N   SER B  84 "
           pdb=" CA  SER B  84 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.24   28.76     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  TYR B  32 "
           pdb=" C   TYR B  32 "
           pdb=" N   ALA B  33 "
           pdb=" CA  ALA B  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.82   28.18     0      5.00e+00 4.00e-02 3.18e+01
  dihedral pdb=" CA  TYR B  91 "
           pdb=" C   TYR B  91 "
           pdb=" N   CYS B  92 "
           pdb=" CA  CYS B  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.36   27.64     0      5.00e+00 4.00e-02 3.06e+01
  ... (remaining 2019 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 270
       0.076 -    0.152: 164
       0.152 -    0.228: 49
       0.228 -    0.303: 10
       0.303 -    0.379: 6
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" CA  ALA A 520 "
            pdb=" N   ALA A 520 "
            pdb=" C   ALA A 520 "
            pdb=" CB  ALA A 520 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.11    0.38 2.00e-01 2.50e+01 3.60e+00
  chirality pdb=" CA  ARG B  83 "
            pdb=" N   ARG B  83 "
            pdb=" C   ARG B  83 "
            pdb=" CB  ARG B  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CA  LEU A 455 "
            pdb=" N   LEU A 455 "
            pdb=" C   LEU A 455 "
            pdb=" CB  LEU A 455 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.86e+00
  ... (remaining 496 not shown)

  Planarity restraints: 595
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  47 "   -0.113 2.00e-02 2.50e+03   5.99e-02 8.96e+01
        pdb=" CG  TRP B  47 "    0.011 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  47 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  47 "    0.069 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  47 "    0.035 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  47 "    0.009 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  47 "    0.087 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  47 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  47 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  47 "   -0.071 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 103 "    0.104 2.00e-02 2.50e+03   5.15e-02 6.64e+01
        pdb=" CG  TRP B 103 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 103 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 103 "   -0.039 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 103 "   -0.016 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 103 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 103 "   -0.070 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 103 "    0.056 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 103 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 103 "    0.054 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 351 "    0.102 2.00e-02 2.50e+03   5.49e-02 6.03e+01
        pdb=" CG  TYR A 351 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 351 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 351 "   -0.039 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 351 "   -0.024 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 351 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 351 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 351 "    0.085 2.00e-02 2.50e+03
  ... (remaining 592 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 1818
        3.02 -     3.49: 3232
        3.49 -     3.96: 5382
        3.96 -     4.43: 5919
        4.43 -     4.90: 9826
  Nonbonded interactions: 26177
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 442 "
            pdb=" OH  TYR A 451 "
     model   vdw
     2.548 3.040
  nonbonded pdb=" OD1 ASP A 467 "
            pdb=" OG  SER A 469 "
     model   vdw
     2.565 3.040
  nonbonded pdb=" OE2 GLU A 484 "
            pdb=" OH  TYR B  95 "
     model   vdw
     2.566 3.040
  nonbonded pdb=" OH  TYR B 100B"
            pdb=" OD1 ASN C  34 "
     model   vdw
     2.569 3.040
  nonbonded pdb=" OE2 GLU A 406 "
            pdb=" OH  TYR A 495 "
     model   vdw
     2.588 3.040
  ... (remaining 26172 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     12.970
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.010
  Total:   18.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.013   0.069   3388  Z= 0.844
  Angle     :  1.877   9.080   4605  Z= 1.234
  Chirality :  0.106   0.379    499
  Planarity :  0.015   0.104    594
  Dihedral  : 13.764  84.731   1226
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 0.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.15 %
    Favored  : 91.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -2.01 (0.39), residues: 417
  helix: -4.02 (0.48), residues: 40
  sheet:  0.21 (0.50), residues: 117
  loop : -1.70 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.113   0.029   TRP B  47 
 HIS   0.007   0.004   HIS A 519 
 PHE   0.062   0.013   PHE B  54 
 TYR   0.102   0.022   TYR A 351 
 ARG   0.015   0.002   ARG A 346 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  353 TRP cc_start: 0.7767 (p-90) cc_final: 0.7518 (p-90)
REVERT: A  484 GLU cc_start: 0.8295 (pm20) cc_final: 0.7878 (pm20)
REVERT: A  493 GLN cc_start: 0.8765 (tt0) cc_final: 0.8364 (tt0)
REVERT: A  506 GLN cc_start: 0.7602 (mt0) cc_final: 0.7191 (mt0)
REVERT: B   36 TRP cc_start: 0.9068 (m100) cc_final: 0.8253 (m-10)
REVERT: B   48 MET cc_start: 0.8169 (mtp) cc_final: 0.7521 (mtm)
REVERT: B   56 ILE cc_start: 0.8594 (mt) cc_final: 0.8365 (tt)
REVERT: B  105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8165 (pt0)
REVERT: C   34 ASN cc_start: 0.8908 (m-40) cc_final: 0.7510 (m-40)
REVERT: C   89 GLN cc_start: 0.8051 (tm-30) cc_final: 0.7010 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.2115
  time to fit residues: 31.1639
Evaluate side-chains
  90 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 501 ASN
B  58 ASN
** B  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.115026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.102663 restraints weight = 8782.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.105540 restraints weight = 4533.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.107438 restraints weight = 2801.696|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3388  Z= 0.246
  Angle     :  0.723   6.328   4605  Z= 0.391
  Chirality :  0.048   0.166    499
  Planarity :  0.005   0.036    594
  Dihedral  :  7.512  55.944    489
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.74 %
    Favored  : 84.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.50 (0.39), residues: 417
  helix: -3.35 (0.68), residues: 35
  sheet:  0.09 (0.45), residues: 138
  loop : -1.30 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.021   0.002   PHE C  98 
 TYR   0.020   0.002   TYR A 365 
 ARG   0.005   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  403 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7155 (ttp-110)
REVERT: A  406 GLU cc_start: 0.8439 (pt0) cc_final: 0.7438 (pt0)
REVERT: A  467 ASP cc_start: 0.7645 (t0) cc_final: 0.6458 (p0)
REVERT: A  468 ILE cc_start: 0.9157 (pt) cc_final: 0.8931 (pt)
REVERT: A  484 GLU cc_start: 0.8117 (pm20) cc_final: 0.7913 (pm20)
REVERT: B   36 TRP cc_start: 0.9012 (m100) cc_final: 0.8083 (m-10)
REVERT: B   48 MET cc_start: 0.8115 (mtp) cc_final: 0.7512 (mtm)
REVERT: B   96 MET cc_start: 0.8112 (mtp) cc_final: 0.7785 (mmm)
REVERT: B  105 GLN cc_start: 0.8725 (tt0) cc_final: 0.8146 (pt0)
  outliers start: 11
  outliers final: 9
  residues processed: 104
  average time/residue: 0.1745
  time to fit residues: 21.6924
Evaluate side-chains
  95 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0670
   chunk 30 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7522

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

Flipped N/Q/H residues before XYZ refinement:
** C   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.115645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.103587 restraints weight = 8474.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.106508 restraints weight = 4342.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.108446 restraints weight = 2649.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3558
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3388  Z= 0.223
  Angle     :  0.640   6.674   4605  Z= 0.342
  Chirality :  0.045   0.160    499
  Planarity :  0.005   0.046    594
  Dihedral  :  6.872  55.792    489
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 9.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 15.79 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.25 %

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: -1.26 (0.40), residues: 417
  helix: -3.01 (0.76), residues: 35
  sheet:  0.03 (0.41), residues: 150
  loop : -1.05 (0.40), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 436 
 HIS   0.002   0.002   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.015   0.002   TYR A 365 
 ARG   0.007   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7684 (m110) cc_final: 0.7311 (m110)
REVERT: A  467 ASP cc_start: 0.7380 (t0) cc_final: 0.6431 (p0)
REVERT: B   36 TRP cc_start: 0.9051 (m100) cc_final: 0.8187 (m-10)
REVERT: B   48 MET cc_start: 0.8103 (mtp) cc_final: 0.7385 (mtm)
REVERT: B   61 GLN cc_start: 0.8900 (pm20) cc_final: 0.8361 (pp30)
REVERT: B   96 MET cc_start: 0.8279 (mtp) cc_final: 0.7999 (mmm)
REVERT: B  105 GLN cc_start: 0.8691 (tt0) cc_final: 0.8252 (pt0)
REVERT: C   89 GLN cc_start: 0.8397 (tm-30) cc_final: 0.7496 (tm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 104
  average time/residue: 0.1777
  time to fit residues: 21.9341
Evaluate side-chains
  96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0270
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
C  55 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 = 0.117752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.105677 restraints weight = 8666.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108549 restraints weight = 4452.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110432 restraints weight = 2730.021|
|-----------------------------------------------------------------------------|
r_work (final): 0.3590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3388  Z= 0.179
  Angle     :  0.615   6.923   4605  Z= 0.326
  Chirality :  0.044   0.155    499
  Planarity :  0.005   0.045    594
  Dihedral  :  6.498  55.244    489
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 17.17 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -0.95 (0.41), residues: 417
  helix: -2.94 (0.76), residues: 35
  sheet:  0.13 (0.41), residues: 152
  loop : -0.73 (0.42), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 436 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.007   0.001   PHE A 464 
 TYR   0.017   0.001   TYR A 451 
 ARG   0.008   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7634 (m110) cc_final: 0.7197 (m110)
REVERT: A  406 GLU cc_start: 0.8399 (pt0) cc_final: 0.8196 (pt0)
REVERT: A  467 ASP cc_start: 0.6924 (t0) cc_final: 0.6353 (p0)
REVERT: B   36 TRP cc_start: 0.8983 (m100) cc_final: 0.8218 (m-10)
REVERT: B   48 MET cc_start: 0.8134 (mtp) cc_final: 0.7422 (mtm)
REVERT: B   96 MET cc_start: 0.8154 (mtp) cc_final: 0.7890 (mmm)
REVERT: B   99 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8491 (tmm-80)
REVERT: B  105 GLN cc_start: 0.8683 (tt0) cc_final: 0.8204 (pt0)
REVERT: C   31 ASN cc_start: 0.7849 (m-40) cc_final: 0.7185 (t0)
  outliers start: 15
  outliers final: 13
  residues processed: 98
  average time/residue: 0.1746
  time to fit residues: 20.4915
Evaluate side-chains
  96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue   99 ARG
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 519 HIS
** B  61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.098605 restraints weight = 8754.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.101357 restraints weight = 4556.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.103227 restraints weight = 2831.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7708
moved from start:          0.3995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051   3388  Z= 0.432
  Angle     :  0.747   7.528   4605  Z= 0.401
  Chirality :  0.047   0.201    499
  Planarity :  0.006   0.058    594
  Dihedral  :  7.342  57.872    489
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 14.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 15.79 %
    Favored  : 77.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.42 (0.40), residues: 417
  helix: -2.35 (0.85), residues: 35
  sheet: -0.13 (0.41), residues: 155
  loop : -1.28 (0.40), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.003   TRP A 353 
 HIS   0.010   0.006   HIS A 519 
 PHE   0.012   0.002   PHE A 347 
 TYR   0.017   0.002   TYR A 451 
 ARG   0.007   0.001   ARG B  94 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 82
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7696 (m110) cc_final: 0.7301 (m110)
REVERT: A  406 GLU cc_start: 0.8603 (pt0) cc_final: 0.8262 (pt0)
REVERT: A  467 ASP cc_start: 0.7392 (t0) cc_final: 0.6470 (p0)
REVERT: B   99 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8889 (tmm-80)
REVERT: B  100 ASP cc_start: 0.8666 (p0) cc_final: 0.8424 (p0)
REVERT: B  105 GLN cc_start: 0.8752 (tt0) cc_final: 0.8287 (pt0)
REVERT: C   61 ARG cc_start: 0.8672 (mmp80) cc_final: 0.8408 (mmp80)
REVERT: C   89 GLN cc_start: 0.8447 (tm-30) cc_final: 0.7802 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 97
  average time/residue: 0.1540
  time to fit residues: 18.2077
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue   99 ARG
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 30 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 16 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.114843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.102490 restraints weight = 8958.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.105383 restraints weight = 4629.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.107298 restraints weight = 2840.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.4252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3388  Z= 0.212
  Angle     :  0.642   7.847   4605  Z= 0.337
  Chirality :  0.045   0.192    499
  Planarity :  0.005   0.062    594
  Dihedral  :  6.695  55.673    489
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.84 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.25 (0.41), residues: 417
  helix: -2.62 (0.76), residues: 41
  sheet: -0.03 (0.41), residues: 155
  loop : -1.02 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 HIS   0.002   0.001   HIS A 519 
 PHE   0.008   0.001   PHE C  71 
 TYR   0.012   0.001   TYR A 451 
 ARG   0.008   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7637 (m110) cc_final: 0.7251 (m110)
REVERT: A  406 GLU cc_start: 0.8454 (pt0) cc_final: 0.8200 (pt0)
REVERT: A  423 TYR cc_start: 0.7648 (t80) cc_final: 0.7414 (t80)
REVERT: A  467 ASP cc_start: 0.7342 (t0) cc_final: 0.6351 (p0)
REVERT: B   36 TRP cc_start: 0.9173 (m100) cc_final: 0.8840 (m-10)
REVERT: B   48 MET cc_start: 0.8280 (mtp) cc_final: 0.8043 (mtp)
REVERT: B   96 MET cc_start: 0.8446 (mmm) cc_final: 0.8208 (mmm)
REVERT: B  100 ASP cc_start: 0.8389 (p0) cc_final: 0.8011 (p0)
REVERT: B  105 GLN cc_start: 0.8757 (tt0) cc_final: 0.8219 (pt0)
REVERT: C   89 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7568 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 101
  average time/residue: 0.1435
  time to fit residues: 17.8232
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   97 VAL
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 1 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C   6 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.117020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.105024 restraints weight = 8630.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.107792 restraints weight = 4460.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.109645 restraints weight = 2755.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7576
moved from start:          0.4456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3388  Z= 0.173
  Angle     :  0.618   7.101   4605  Z= 0.325
  Chirality :  0.044   0.161    499
  Planarity :  0.005   0.058    594
  Dihedral  :  6.349  54.751    489
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 19.39 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.10 (0.41), residues: 417
  helix: -2.62 (0.75), residues: 41
  sheet:  0.05 (0.41), residues: 155
  loop : -0.87 (0.43), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.008   0.001   PHE C  62 
 TYR   0.010   0.001   TYR A 423 
 ARG   0.007   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7675 (m110) cc_final: 0.7288 (m110)
REVERT: A  406 GLU cc_start: 0.8434 (pt0) cc_final: 0.8213 (pt0)
REVERT: A  423 TYR cc_start: 0.7577 (t80) cc_final: 0.7375 (t80)
REVERT: A  467 ASP cc_start: 0.7237 (t0) cc_final: 0.6430 (p0)
REVERT: B   36 TRP cc_start: 0.9083 (m100) cc_final: 0.8768 (m-10)
REVERT: B   82 LEU cc_start: 0.7362 (OUTLIER) cc_final: 0.7057 (pp)
REVERT: B   96 MET cc_start: 0.8443 (mmm) cc_final: 0.8188 (mmm)
REVERT: B  100 ASP cc_start: 0.8052 (p0) cc_final: 0.7832 (p0)
REVERT: B  105 GLN cc_start: 0.8720 (tt0) cc_final: 0.8209 (pt0)
REVERT: C   31 ASN cc_start: 0.7729 (m-40) cc_final: 0.7132 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1488
  time to fit residues: 18.0389
Evaluate side-chains
  91 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0170
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   chunk 34 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.2026

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.113477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.101201 restraints weight = 8773.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.104034 restraints weight = 4584.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.105903 restraints weight = 2856.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.4453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   3388  Z= 0.298
  Angle     :  0.670   6.814   4605  Z= 0.360
  Chirality :  0.045   0.150    499
  Planarity :  0.005   0.055    594
  Dihedral  :  6.808  56.648    489
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  5.54 %
    Allowed  : 18.01 %
    Favored  : 76.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.15 (0.41), residues: 417
  helix: -2.49 (0.82), residues: 35
  sheet: -0.03 (0.41), residues: 149
  loop : -0.94 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  47 
 HIS   0.003   0.002   HIS A 519 
 PHE   0.009   0.002   PHE B  54 
 TYR   0.013   0.002   TYR B  95 
 ARG   0.006   0.001   ARG B  50 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 79
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7669 (m110) cc_final: 0.7335 (m110)
REVERT: A  406 GLU cc_start: 0.8532 (pt0) cc_final: 0.8155 (pt0)
REVERT: A  467 ASP cc_start: 0.7348 (t0) cc_final: 0.6425 (p0)
REVERT: B   82 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7166 (pp)
REVERT: B  100 ASP cc_start: 0.8268 (p0) cc_final: 0.8016 (p0)
REVERT: B  105 GLN cc_start: 0.8696 (tt0) cc_final: 0.8244 (pt0)
REVERT: C   61 ARG cc_start: 0.8548 (mmp80) cc_final: 0.8209 (mmp80)
REVERT: C   89 GLN cc_start: 0.8244 (tm-30) cc_final: 0.7756 (tm-30)
  outliers start: 20
  outliers final: 18
  residues processed: 91
  average time/residue: 0.1352
  time to fit residues: 15.4340
Evaluate side-chains
  98 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  395 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue   70 THR
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue   72 THR
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    0.0020
   chunk 16 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 36 optimal weight:    0.1980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.3988

-------------------------------------------------------------------------------
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 = 0.3693 r_free = 0.3693 target = 0.117115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.104961 restraints weight = 8609.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107807 restraints weight = 4402.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.109668 restraints weight = 2686.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.4646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3388  Z= 0.173
  Angle     :  0.629   7.182   4605  Z= 0.332
  Chirality :  0.044   0.152    499
  Planarity :  0.005   0.058    594
  Dihedral  :  6.297  54.457    489
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 19.39 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.10 (0.41), residues: 417
  helix: -2.73 (0.68), residues: 47
  sheet:  0.10 (0.41), residues: 148
  loop : -0.79 (0.43), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.001   HIS A 519 
 PHE   0.010   0.001   PHE C  62 
 TYR   0.017   0.001   TYR B  32 
 ARG   0.010   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7740 (m110) cc_final: 0.7356 (m110)
REVERT: A  403 ARG cc_start: 0.7981 (ttp80) cc_final: 0.7634 (ttp80)
REVERT: A  406 GLU cc_start: 0.8468 (pt0) cc_final: 0.8104 (pt0)
REVERT: A  467 ASP cc_start: 0.7423 (t0) cc_final: 0.6528 (p0)
REVERT: B   36 TRP cc_start: 0.9067 (m100) cc_final: 0.8763 (m-10)
REVERT: B   82 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7086 (pp)
REVERT: B   90 TYR cc_start: 0.8349 (m-80) cc_final: 0.8101 (m-80)
REVERT: B   96 MET cc_start: 0.8427 (mmm) cc_final: 0.8124 (mmm)
REVERT: B  100 ASP cc_start: 0.8078 (p0) cc_final: 0.7803 (p0)
REVERT: B  105 GLN cc_start: 0.8661 (tt0) cc_final: 0.8182 (pt0)
REVERT: C   31 ASN cc_start: 0.7647 (m-40) cc_final: 0.7104 (t0)
REVERT: C   89 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7639 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 93
  average time/residue: 0.1329
  time to fit residues: 15.4960
Evaluate side-chains
  96 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  402 ILE
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 37 optimal weight:    6.9990
   chunk 10 optimal weight:    0.0570
   chunk 16 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0870
   chunk 25 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   overall best weight:    0.3876

-------------------------------------------------------------------------------
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 = 0.3714 r_free = 0.3714 target = 0.118411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.106175 restraints weight = 8585.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108994 restraints weight = 4461.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.110828 restraints weight = 2752.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7551
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3388  Z= 0.174
  Angle     :  0.628   7.021   4605  Z= 0.329
  Chirality :  0.044   0.154    499
  Planarity :  0.005   0.051    594
  Dihedral  :  6.185  54.517    489
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.78 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.08 (0.41), residues: 417
  helix: -3.17 (0.65), residues: 41
  sheet:  0.09 (0.43), residues: 143
  loop : -0.71 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.011   0.001   PHE C  62 
 TYR   0.021   0.001   TYR B  32 
 ARG   0.010   0.001   ARG A 403 

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

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

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  834 Ramachandran restraints generated.
    417 Oldfield, 0 Emsley, 417 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  354 ASN cc_start: 0.7747 (m110) cc_final: 0.7359 (m110)
REVERT: A  403 ARG cc_start: 0.7909 (ttp80) cc_final: 0.7612 (ttp80)
REVERT: A  406 GLU cc_start: 0.8550 (pt0) cc_final: 0.8269 (pt0)
REVERT: A  420 ASP cc_start: 0.7831 (m-30) cc_final: 0.7120 (m-30)
REVERT: A  467 ASP cc_start: 0.7357 (t0) cc_final: 0.6490 (p0)
REVERT: B   36 TRP cc_start: 0.9038 (m100) cc_final: 0.8725 (m-10)
REVERT: B   82 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7023 (pp)
REVERT: B  100 ASP cc_start: 0.7994 (p0) cc_final: 0.7752 (p0)
REVERT: B  105 GLN cc_start: 0.8678 (tt0) cc_final: 0.8173 (pt0)
REVERT: C   31 ASN cc_start: 0.7599 (m-40) cc_final: 0.7114 (t0)
REVERT: C   36 TYR cc_start: 0.8745 (m-80) cc_final: 0.8136 (m-80)
  outliers start: 14
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1444
  time to fit residues: 16.5816
Evaluate side-chains
  93 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain B residue    5 VAL
Chi-restraints excluded: chain B residue   37 VAL
Chi-restraints excluded: chain B residue   52 ILE
Chi-restraints excluded: chain B residue   80 LEU
Chi-restraints excluded: chain B residue   82 LEU
Chi-restraints excluded: chain B residue  110 THR
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   37 GLN
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 26 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0670
   chunk 39 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0980
   chunk 38 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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 = 0.3711 r_free = 0.3711 target = 0.118365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.106128 restraints weight = 8733.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108907 restraints weight = 4534.003|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.110785 restraints weight = 2795.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.4934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3388  Z= 0.180
  Angle     :  0.624   6.086   4605  Z= 0.331
  Chirality :  0.044   0.155    499
  Planarity :  0.005   0.052    594
  Dihedral  :  6.142  54.394    489
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 21.05 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.09 %
    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: -1.06 (0.41), residues: 417
  helix: -3.12 (0.66), residues: 41
  sheet:  0.14 (0.43), residues: 143
  loop : -0.73 (0.42), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  47 
 HIS   0.001   0.000   HIS A 519 
 PHE   0.011   0.001   PHE C  62 
 TYR   0.019   0.001   TYR B  32 
 ARG   0.010   0.001   ARG A 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1567.23 seconds
wall clock time: 28 minutes 41.93 seconds (1721.93 seconds total)