Starting phenix.real_space_refine
on Wed Jul 23 13:38:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ix3_35788/07_2025/8ix3_35788.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.008
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      14      5.16       5
     C    2130      2.51       5
     N     562      2.21       5
     O     633      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3339
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "L"
      Number of atoms: 821
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 821
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 971
          Classifications: {'peptide': 125}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 122}
    Chain: "G"
      Number of atoms: 1547
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1547
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
  Time building chain proxies: 9.57, per 1000 atoms: 2.87
  Number of scatterers: 3339
  At special positions: 0
  Unit cell: (61.462, 87.136, 87.914, 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      14     16.00
     O     633      8.00
     N     562      7.00
     C    2130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 336 " - pdb=" SG  CYS G 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 480 " - pdb=" SG  CYS G 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: 0.71
  Conformation dependent library (CDL) restraints added in 377.3 milliseconds
  

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  776

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 9 sheets defined
      3.5% alpha, 31.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'H' and resid 87 through 91
      removed outlier: 3.565A  pdb=" N   ASP H  90 " --> pdb=" O   GLY H  87 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   THR H  91 " --> pdb=" O   VAL H  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 87 through 91'
    Processing helix  chain 'G' and resid 366 through 370
      removed outlier: 3.840A  pdb=" N   TYR G 369 " --> pdb=" O   SER G 366 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 406 through 410
      removed outlier: 3.579A  pdb=" N   GLN G 409 " --> pdb=" O   GLU G 406 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.650A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ILE L  75 " --> pdb=" O   VAL L  19 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12
      removed outlier: 6.639A  pdb=" N   LEU L  11 " --> pdb=" O   ASP L 105 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ILE L  48 " --> pdb=" O   TRP L  35 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLN L  37 " --> pdb=" O   VAL L  46 " (cutoff:3.500A)
      removed outlier: 5.987A  pdb=" N   VAL L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 7
      removed outlier: 3.859A  pdb=" N   ASP H  73 " --> pdb=" O   SER H  78 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 59 through 60
      removed outlier: 5.252A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   MET H  34 " --> pdb=" O   THR H  51 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   TYR H 114 " --> pdb=" O   LYS H  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 59 through 60
      removed outlier: 5.252A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   MET H  34 " --> pdb=" O   THR H  51 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   VAL H  97 " --> pdb=" O   HIS H  35 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   ILE H 119 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 376 through 379
    Processing sheet with id=AA7, first strand: chain 'G' and resid 376 through 379
    Processing sheet with id=AA8, first strand: chain 'G' and resid 452 through 454
    Processing sheet with id=AA9, first strand: chain 'G' and resid 473 through 474

    96 hydrogen bonds defined for protein.
    234 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: 0.87

  Time building geometry restraints manager: 0.86 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: 927
        1.33 -     1.45: 702
        1.45 -     1.57: 1784
        1.57 -     1.69: 0
        1.69 -     1.81: 16
  Bond restraints: 3429
  Sorted by residual:
  bond pdb=" C   ALA G 520 "
       pdb=" N   PRO G 521 "
    ideal  model  delta    sigma   weight residual
    1.336  1.387 -0.051 1.20e-02 6.94e+03 1.79e+01
  bond pdb=" C   CYS G 336 "
       pdb=" N   PRO G 337 "
    ideal  model  delta    sigma   weight residual
    1.333  1.354 -0.020 1.01e-02 9.80e+03 4.09e+00
  bond pdb=" C   ALA H  40 "
       pdb=" N   PRO H  41 "
    ideal  model  delta    sigma   weight residual
    1.335  1.356 -0.021 1.28e-02 6.10e+03 2.80e+00
  bond pdb=" C   SER H 104 "
       pdb=" O   SER H 104 "
    ideal  model  delta    sigma   weight residual
    1.236  1.220  0.016 9.60e-03 1.09e+04 2.76e+00
  bond pdb=" C   SER H 100 "
       pdb=" O   SER H 100 "
    ideal  model  delta    sigma   weight residual
    1.235  1.211  0.024 1.43e-02 4.89e+03 2.75e+00
  ... (remaining 3424 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 4563
        2.46 -     4.92: 84
        4.92 -     7.37: 7
        7.37 -     9.83: 6
        9.83 -    12.29: 2
  Bond angle restraints: 4662
  Sorted by residual:
  angle pdb=" N   SER H 104 "
        pdb=" CA  SER H 104 "
        pdb=" C   SER H 104 "
      ideal   model   delta    sigma   weight residual
     108.24  120.53  -12.29 1.32e+00 5.74e-01 8.67e+01
  angle pdb=" N   ASP H 103 "
        pdb=" CA  ASP H 103 "
        pdb=" C   ASP H 103 "
      ideal   model   delta    sigma   weight residual
     112.93  123.63  -10.70 1.33e+00 5.65e-01 6.47e+01
  angle pdb=" N   SER H 105 "
        pdb=" CA  SER H 105 "
        pdb=" C   SER H 105 "
      ideal   model   delta    sigma   weight residual
     111.28  119.24   -7.96 1.09e+00 8.42e-01 5.33e+01
  angle pdb=" N   TYR H 102 "
        pdb=" CA  TYR H 102 "
        pdb=" C   TYR H 102 "
      ideal   model   delta    sigma   weight residual
     111.28  118.65   -7.37 1.09e+00 8.42e-01 4.58e+01
  angle pdb=" N   GLY H 106 "
        pdb=" CA  GLY H 106 "
        pdb=" C   GLY H 106 "
      ideal   model   delta    sigma   weight residual
     112.73  119.23   -6.50 1.20e+00 6.94e-01 2.94e+01
  ... (remaining 4657 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.73: 1779
       16.73 -    33.46: 175
       33.46 -    50.19: 30
       50.19 -    66.92: 10
       66.92 -    83.65: 5
  Dihedral angle restraints: 1999
    sinusoidal: 771
      harmonic: 1228
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.76  -58.76     1      1.00e+01 1.00e-02 4.62e+01
  dihedral pdb=" CA  CYS G 361 "
           pdb=" C   CYS G 361 "
           pdb=" N   VAL G 362 "
           pdb=" CA  VAL G 362 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.31   28.69     0      5.00e+00 4.00e-02 3.29e+01
  dihedral pdb=" CA  PRO G 337 "
           pdb=" C   PRO G 337 "
           pdb=" N   PHE G 338 "
           pdb=" CA  PHE G 338 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  ... (remaining 1996 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 429
       0.085 -    0.171: 57
       0.171 -    0.256: 5
       0.256 -    0.341: 0
       0.341 -    0.427: 2
  Chirality restraints: 493
  Sorted by residual:
  chirality pdb=" CA  ASP H 103 "
            pdb=" N   ASP H 103 "
            pdb=" C   ASP H 103 "
            pdb=" CB  ASP H 103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.08    0.43 2.00e-01 2.50e+01 4.55e+00
  chirality pdb=" CA  TYR H 102 "
            pdb=" N   TYR H 102 "
            pdb=" C   TYR H 102 "
            pdb=" CB  TYR H 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.24e+00
  chirality pdb=" CA  SER H 100 "
            pdb=" N   SER H 100 "
            pdb=" C   SER H 100 "
            pdb=" CB  SER H 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.25e+00
  ... (remaining 490 not shown)

  Planarity restraints: 607
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 411 "    0.037 5.00e-02 4.00e+02   5.51e-02 4.86e+00
        pdb=" N   PRO G 412 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO G 412 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO G 412 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN H  13 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.07e+00
        pdb=" N   PRO H  14 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO H  14 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO H  14 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP H  99 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.06e+00
        pdb=" C   ASP H  99 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASP H  99 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   SER H 100 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 604 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 822
        2.79 -     3.32: 2663
        3.32 -     3.84: 5249
        3.84 -     4.37: 5705
        4.37 -     4.90: 10347
  Nonbonded interactions: 24786
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP G 398 "
            pdb=" OH  TYR G 423 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ASN G 439 "
            pdb=" OG  SER G 443 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NH1 ARG G 457 "
            pdb=" OD2 ASP G 467 "
     model   vdw
     2.346 3.120
  nonbonded pdb=" NH2 ARG G 454 "
            pdb=" O   SER G 469 "
     model   vdw
     2.371 3.120
  nonbonded pdb=" O   SER L   7 "
            pdb=" OG1 THR L  22 "
     model   vdw
     2.380 3.040
  ... (remaining 24781 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:             37.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     19.740
  Find NCS groups from input model:        0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6602
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      :  0.005   0.051   3434  Z= 0.273
  Angle     :  0.924  12.290   4672  Z= 0.571
  Chirality :  0.062   0.427    493
  Planarity :  0.007   0.055    607
  Dihedral  : 14.179  83.646   1208
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  6.94 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -4.10 (0.32), residues: 420
  helix: -5.14 (0.19), residues: 20
  sheet: -2.03 (0.45), residues: 120
  loop : -3.04 (0.27), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP G 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.012   0.002   PHE H  27 
 TYR   0.013   0.002   TYR G 453 
 ARG   0.003   0.000   ARG G 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30932 (   76)
  hydrogen bonds       : angle      10.31312 (  234)
  SS BOND              : bond        0.00507 (    5)
  SS BOND              : angle       1.61187 (   10)
  covalent geometry    : bond        0.00516 ( 3429)
  covalent geometry    : angle       0.92172 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 117
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7689 (m-30) cc_final: 0.6842 (m-30)
REVERT: L   37 GLN cc_start: 0.7695 (tt0) cc_final: 0.6433 (tt0)
REVERT: L   45 LYS cc_start: 0.7666 (mmtm) cc_final: 0.7450 (mmtm)
REVERT: L   81 GLU cc_start: 0.8783 (pt0) cc_final: 0.8336 (tm-30)
REVERT: H   18 LEU cc_start: 0.7235 (tt) cc_final: 0.7016 (tt)
REVERT: H   47 TRP cc_start: 0.7622 (t60) cc_final: 0.7306 (t60)
REVERT: H   83 MET cc_start: 0.7212 (ptp) cc_final: 0.6949 (ptp)
REVERT: H  111 ASN cc_start: 0.8113 (p0) cc_final: 0.7850 (p0)
REVERT: G  390 LEU cc_start: 0.8615 (mp) cc_final: 0.8167 (mp)
REVERT: G  406 GLU cc_start: 0.8606 (pt0) cc_final: 0.8360 (pt0)
REVERT: G  457 ARG cc_start: 0.7239 (ttt90) cc_final: 0.6900 (ttt90)
REVERT: G  460 ASN cc_start: 0.8182 (m-40) cc_final: 0.7903 (m-40)
REVERT: G  467 ASP cc_start: 0.7802 (t0) cc_final: 0.6906 (p0)
REVERT: G  471 GLU cc_start: 0.7827 (tp30) cc_final: 0.7438 (mm-30)
REVERT: G  474 GLN cc_start: 0.5260 (tp40) cc_final: 0.4755 (mm-40)
REVERT: G  498 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6781 (ttm-80)
  outliers start: 2
  outliers final: 2
  residues processed: 117
  average time/residue: 0.1783
  time to fit residues: 24.8344
Evaluate side-chains
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 87
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
L  37 GLN
H  84 ASN
G 409 GLN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 474 GLN
G 506 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.133545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.113654 restraints weight = 5577.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.116457 restraints weight = 3569.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.118356 restraints weight = 2617.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3434  Z= 0.209
  Angle     :  0.645   6.314   4672  Z= 0.346
  Chirality :  0.046   0.173    493
  Planarity :  0.005   0.036    607
  Dihedral  :  7.011  78.824    477
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 14.72 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -3.31 (0.35), residues: 420
  helix: -4.66 (0.47), residues: 20
  sheet: -1.60 (0.47), residues: 114
  loop : -2.41 (0.30), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.012   0.002   PHE H  27 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.003   0.001   ARG H  72 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (   76)
  hydrogen bonds       : angle       5.61753 (  234)
  SS BOND              : bond        0.00421 (    5)
  SS BOND              : angle       1.54950 (   10)
  covalent geometry    : bond        0.00495 ( 3429)
  covalent geometry    : angle       0.64192 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7923 (m-30) cc_final: 0.7204 (m-30)
REVERT: L   36 TYR cc_start: 0.9263 (m-80) cc_final: 0.8867 (m-80)
REVERT: H   47 TRP cc_start: 0.8499 (t60) cc_final: 0.8054 (t60)
REVERT: G  406 GLU cc_start: 0.8031 (pt0) cc_final: 0.7785 (pt0)
REVERT: G  471 GLU cc_start: 0.7599 (tp30) cc_final: 0.7366 (mm-30)
REVERT: G  474 GLN cc_start: 0.7157 (tp-100) cc_final: 0.6567 (pp30)
  outliers start: 20
  outliers final: 11
  residues processed: 103
  average time/residue: 0.1458
  time to fit residues: 18.2440
Evaluate side-chains
  90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  394 ASN
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 39 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 4 optimal weight:    0.6980
   chunk 19 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
G 409 GLN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.134550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.114558 restraints weight = 5490.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.117385 restraints weight = 3533.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.119339 restraints weight = 2589.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3434  Z= 0.172
  Angle     :  0.629   6.575   4672  Z= 0.330
  Chirality :  0.045   0.149    493
  Planarity :  0.004   0.033    607
  Dihedral  :  6.728  75.851    477
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 19.44 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.99 (0.36), residues: 420
  helix: -5.22 (0.19), residues: 20
  sheet: -1.31 (0.48), residues: 112
  loop : -2.14 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 436 
 HIS   0.002   0.001   HIS H  35 
 PHE   0.011   0.001   PHE G 377 
 TYR   0.028   0.002   TYR L  49 
 ARG   0.003   0.000   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (   76)
  hydrogen bonds       : angle       4.98683 (  234)
  SS BOND              : bond        0.00311 (    5)
  SS BOND              : angle       1.43832 (   10)
  covalent geometry    : bond        0.00411 ( 3429)
  covalent geometry    : angle       0.62624 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.390 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7902 (m-30) cc_final: 0.7183 (m-30)
REVERT: L   36 TYR cc_start: 0.9259 (m-80) cc_final: 0.8969 (m-80)
REVERT: H   47 TRP cc_start: 0.8455 (t60) cc_final: 0.8068 (t60)
REVERT: H   83 MET cc_start: 0.7768 (ptp) cc_final: 0.7510 (ptp)
REVERT: G  379 CYS cc_start: 0.6712 (m) cc_final: 0.6342 (m)
REVERT: G  403 ARG cc_start: 0.8168 (mtt-85) cc_final: 0.7721 (mtm-85)
REVERT: G  406 GLU cc_start: 0.7854 (pt0) cc_final: 0.7645 (pt0)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 0.1474
  time to fit residues: 16.8758
Evaluate side-chains
  87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  394 ASN
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 21 optimal weight:    0.8980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.132436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.112237 restraints weight = 5697.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.115087 restraints weight = 3645.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117115 restraints weight = 2663.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   3434  Z= 0.217
  Angle     :  0.668   8.131   4672  Z= 0.349
  Chirality :  0.046   0.154    493
  Planarity :  0.004   0.033    607
  Dihedral  :  6.654  71.930    477
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.33 %
    Favored  : 91.67 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 20.28 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.88 (0.38), residues: 420
  helix: -4.62 (0.50), residues: 26
  sheet: -1.11 (0.49), residues: 112
  loop : -2.09 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.014   0.002   PHE G 377 
 TYR   0.025   0.002   TYR L  49 
 ARG   0.003   0.000   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04053 (   76)
  hydrogen bonds       : angle       4.89718 (  234)
  SS BOND              : bond        0.00430 (    5)
  SS BOND              : angle       1.50369 (   10)
  covalent geometry    : bond        0.00516 ( 3429)
  covalent geometry    : angle       0.66539 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.901 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7908 (m-30) cc_final: 0.7159 (m-30)
REVERT: H   47 TRP cc_start: 0.8431 (t60) cc_final: 0.8019 (t60)
REVERT: G  379 CYS cc_start: 0.6729 (m) cc_final: 0.6406 (m)
REVERT: G  471 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7033 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 93
  average time/residue: 0.2132
  time to fit residues: 24.5177
Evaluate side-chains
  92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  394 ASN
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0770
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
L  37 GLN
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.113928 restraints weight = 5706.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116875 restraints weight = 3668.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.118929 restraints weight = 2672.665|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8098
moved from start:          0.3107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3434  Z= 0.164
  Angle     :  0.636   7.467   4672  Z= 0.329
  Chirality :  0.045   0.146    493
  Planarity :  0.004   0.035    607
  Dihedral  :  6.342  66.802    477
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.94 %
    Favored  : 73.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.65 (0.39), residues: 420
  helix: -4.58 (0.53), residues: 26
  sheet: -0.95 (0.50), residues: 112
  loop : -1.91 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.009   0.001   PHE G 377 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.003   0.000   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (   76)
  hydrogen bonds       : angle       4.84222 (  234)
  SS BOND              : bond        0.00337 (    5)
  SS BOND              : angle       1.21792 (   10)
  covalent geometry    : bond        0.00388 ( 3429)
  covalent geometry    : angle       0.63466 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7889 (m-30) cc_final: 0.7093 (m-30)
  outliers start: 15
  outliers final: 13
  residues processed: 97
  average time/residue: 0.2429
  time to fit residues: 29.2194
Evaluate side-chains
  91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  394 ASN
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0010
   chunk 21 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.133741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.113449 restraints weight = 5734.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.116518 restraints weight = 3601.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.118718 restraints weight = 2579.490|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3434  Z= 0.175
  Angle     :  0.655   8.880   4672  Z= 0.338
  Chirality :  0.045   0.147    493
  Planarity :  0.004   0.034    607
  Dihedral  :  6.154  59.380    477
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 12.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 22.50 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.49 (0.39), residues: 420
  helix: -4.54 (0.56), residues: 26
  sheet: -0.90 (0.50), residues: 112
  loop : -1.77 (0.35), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.009   0.001   PHE G 377 
 TYR   0.028   0.002   TYR L  49 
 ARG   0.006   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03849 (   76)
  hydrogen bonds       : angle       4.75975 (  234)
  SS BOND              : bond        0.00348 (    5)
  SS BOND              : angle       1.68877 (   10)
  covalent geometry    : bond        0.00417 ( 3429)
  covalent geometry    : angle       0.65069 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7875 (m-30) cc_final: 0.7045 (m-30)
REVERT: L   81 GLU cc_start: 0.8745 (pp20) cc_final: 0.8529 (pp20)
REVERT: H   47 TRP cc_start: 0.8512 (t60) cc_final: 0.8183 (t60)
REVERT: G  471 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7162 (mm-30)
  outliers start: 18
  outliers final: 15
  residues processed: 89
  average time/residue: 0.2220
  time to fit residues: 25.0598
Evaluate side-chains
  93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  367 VAL
Chi-restraints excluded: chain G residue  394 ASN
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  415 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 23 optimal weight:    0.0020
   chunk 37 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0060
   chunk 5 optimal weight:    0.7980
   chunk 24 optimal weight:    0.2980
   chunk 29 optimal weight:    0.7980
   overall best weight:    0.2162

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

Flipped N/Q/H residues before XYZ refinement:
L   6 GLN
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.138135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.117669 restraints weight = 5517.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.120970 restraints weight = 3403.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.123053 restraints weight = 2406.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3434  Z= 0.112
  Angle     :  0.609   9.366   4672  Z= 0.308
  Chirality :  0.044   0.149    493
  Planarity :  0.004   0.034    607
  Dihedral  :  5.508  49.108    477
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.33 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.27 (0.39), residues: 420
  helix: -4.53 (0.54), residues: 26
  sheet: -0.77 (0.49), residues: 112
  loop : -1.58 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.005   0.001   PHE G 400 
 TYR   0.027   0.001   TYR L  49 
 ARG   0.007   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03313 (   76)
  hydrogen bonds       : angle       4.39224 (  234)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       1.12225 (   10)
  covalent geometry    : bond        0.00262 ( 3429)
  covalent geometry    : angle       0.60757 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7804 (m-30) cc_final: 0.6931 (m-30)
REVERT: L   22 THR cc_start: 0.7361 (p) cc_final: 0.7120 (t)
REVERT: L   81 GLU cc_start: 0.8840 (pp20) cc_final: 0.8582 (pp20)
REVERT: H   47 TRP cc_start: 0.8535 (t60) cc_final: 0.8152 (t60)
REVERT: G  403 ARG cc_start: 0.8140 (mtt-85) cc_final: 0.7459 (mtm-85)
REVERT: G  518 LEU cc_start: 0.4109 (OUTLIER) cc_final: 0.3884 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 100
  average time/residue: 0.2316
  time to fit residues: 28.3811
Evaluate side-chains
  99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue    5 VAL
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  120 LEU
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  392 PHE
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 474 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 = 0.3493 r_free = 0.3493 target = 0.132266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.111881 restraints weight = 5633.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.114700 restraints weight = 3653.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116750 restraints weight = 2688.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038   3434  Z= 0.235
  Angle     :  0.694   9.567   4672  Z= 0.359
  Chirality :  0.047   0.152    493
  Planarity :  0.004   0.035    607
  Dihedral  :  5.718  36.135    475
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.10 %
    Favored  : 91.90 %
  Rotamer:
    Outliers :  6.39 %
    Allowed  : 22.50 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.35 (0.40), residues: 420
  helix: -4.37 (0.70), residues: 20
  sheet: -0.89 (0.49), residues: 113
  loop : -1.72 (0.36), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP G 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.013   0.002   PHE G 377 
 TYR   0.026   0.002   TYR L  49 
 ARG   0.006   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (   76)
  hydrogen bonds       : angle       4.53265 (  234)
  SS BOND              : bond        0.00454 (    5)
  SS BOND              : angle       1.71440 (   10)
  covalent geometry    : bond        0.00558 ( 3429)
  covalent geometry    : angle       0.69009 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 81
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   22 THR cc_start: 0.7216 (p) cc_final: 0.7008 (t)
REVERT: H   47 TRP cc_start: 0.8648 (t60) cc_final: 0.8242 (t60)
REVERT: G  439 ASN cc_start: 0.9268 (t0) cc_final: 0.8888 (t0)
  outliers start: 23
  outliers final: 17
  residues processed: 96
  average time/residue: 0.2321
  time to fit residues: 29.2235
Evaluate side-chains
  98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  367 VAL
Chi-restraints excluded: chain G residue  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  464 PHE
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.3980
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 474 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 = 0.3488 r_free = 0.3488 target = 0.132263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.111270 restraints weight = 5714.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.114364 restraints weight = 3557.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.116584 restraints weight = 2555.718|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   3434  Z= 0.191
  Angle     :  0.704  13.338   4672  Z= 0.354
  Chirality :  0.046   0.148    493
  Planarity :  0.004   0.035    607
  Dihedral  :  5.654  33.347    475
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 22.78 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.38 (0.39), residues: 420
  helix: -4.55 (0.55), residues: 26
  sheet: -0.93 (0.49), residues: 113
  loop : -1.63 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 436 
 HIS   0.004   0.001   HIS H  35 
 PHE   0.010   0.001   PHE G 377 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.007   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03652 (   76)
  hydrogen bonds       : angle       4.50180 (  234)
  SS BOND              : bond        0.00376 (    5)
  SS BOND              : angle       1.51825 (   10)
  covalent geometry    : bond        0.00456 ( 3429)
  covalent geometry    : angle       0.70140 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   22 THR cc_start: 0.7287 (p) cc_final: 0.7067 (t)
REVERT: H   47 TRP cc_start: 0.8647 (t60) cc_final: 0.8178 (t60)
  outliers start: 18
  outliers final: 16
  residues processed: 95
  average time/residue: 0.2241
  time to fit residues: 26.5690
Evaluate side-chains
  100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  120 LEU
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  367 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  518 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 17 optimal weight:    0.4980
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 32 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 28 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 474 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 = 0.3492 r_free = 0.3492 target = 0.132679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.111997 restraints weight = 5613.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.115068 restraints weight = 3469.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.117269 restraints weight = 2477.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3295
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3434  Z= 0.171
  Angle     :  0.701  13.176   4672  Z= 0.354
  Chirality :  0.046   0.145    493
  Planarity :  0.004   0.035    607
  Dihedral  :  5.561  28.607    475
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.86 %
    Favored  : 92.14 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 22.50 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.32 (0.40), residues: 420
  helix: -4.55 (0.55), residues: 26
  sheet: -0.85 (0.49), residues: 111
  loop : -1.60 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.009   0.001   PHE G 377 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.007   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03523 (   76)
  hydrogen bonds       : angle       4.37405 (  234)
  SS BOND              : bond        0.00330 (    5)
  SS BOND              : angle       1.35927 (   10)
  covalent geometry    : bond        0.00408 ( 3429)
  covalent geometry    : angle       0.69871 ( 4662)

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

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

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  840 Ramachandran restraints generated.
    420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7811 (m-30) cc_final: 0.7010 (m-30)
REVERT: L   22 THR cc_start: 0.7240 (p) cc_final: 0.7037 (t)
REVERT: H   47 TRP cc_start: 0.8628 (t60) cc_final: 0.8193 (t60)
REVERT: G  406 GLU cc_start: 0.8050 (pt0) cc_final: 0.7630 (tt0)
REVERT: G  471 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7322 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 91
  average time/residue: 0.1848
  time to fit residues: 21.3137
Evaluate side-chains
  97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue    4 LEU
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   91 THR
Chi-restraints excluded: chain H residue   97 VAL
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain H residue  109 ILE
Chi-restraints excluded: chain H residue  120 LEU
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  367 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  415 THR
Chi-restraints excluded: chain G residue  464 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 39 optimal weight:    0.3980
   chunk 26 optimal weight:    0.3980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
H 111 ASN
** G 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 474 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 = 0.3484 r_free = 0.3484 target = 0.132066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.111062 restraints weight = 5700.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.114199 restraints weight = 3523.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.116408 restraints weight = 2518.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.3921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3434  Z= 0.182
  Angle     :  0.710  13.468   4672  Z= 0.358
  Chirality :  0.046   0.146    493
  Planarity :  0.004   0.032    607
  Dihedral  :  5.527  24.697    475
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 22.22 %
    Favored  : 72.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    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: -2.33 (0.39), residues: 420
  helix: -4.56 (0.54), residues: 26
  sheet: -0.92 (0.48), residues: 111
  loop : -1.57 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 
 PHE   0.010   0.001   PHE G 377 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.007   0.001   ARG H  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03533 (   76)
  hydrogen bonds       : angle       4.36179 (  234)
  SS BOND              : bond        0.00346 (    5)
  SS BOND              : angle       1.41435 (   10)
  covalent geometry    : bond        0.00436 ( 3429)
  covalent geometry    : angle       0.70800 ( 4662)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3248.86 seconds
wall clock time: 61 minutes 6.26 seconds (3666.26 seconds total)