Starting phenix.real_space_refine
on Fri Oct 10 10:59:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ix3_35788/10_2025/8ix3_35788.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ix3_35788/10_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_35788/10_2025/8ix3_35788.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ix3_35788/10_2025/8ix3_35788.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ix3_35788/10_2025/8ix3_35788.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ix3_35788/10_2025/8ix3_35788.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.00, per 1000 atoms: 0.30
  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: 0.27
  Conformation dependent library (CDL) restraints added in 112.7 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.08
  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: 0.32

  Time building geometry restraints manager: 0.39 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:             11.510
  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:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     4.920
  Find NCS groups from input model:        0.010
  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:1.080
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.630
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.003   0.000   ARG G 346 
 TYR   0.013   0.002   TYR G 453 
 PHE   0.012   0.002   PHE H  27 
 TRP   0.008   0.002   TRP G 436 
 HIS   0.004   0.001   HIS H  35 

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

*********************** 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  : 0.077 
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: 0.0710
  time to fit residues: 9.8585
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  : 0.089 
-------------------------------------------------------------------------------
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 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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
H 111 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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.133437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.113591 restraints weight = 5669.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116399 restraints weight = 3613.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.118241 restraints weight = 2636.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.119603 restraints weight = 2118.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.120747 restraints weight = 1796.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.1970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   3434  Z= 0.217
  Angle     :  0.651   6.599   4672  Z= 0.350
  Chirality :  0.046   0.173    493
  Planarity :  0.005   0.036    607
  Dihedral  :  7.038  78.765    477
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 14.17 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.35), residues: 420
  helix: -4.66 (0.48), residues: 20
  sheet: -1.61 (0.47), residues: 114
  loop : -2.42 (0.30), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  72 
 TYR   0.027   0.002   TYR L  49 
 PHE   0.012   0.002   PHE H  27 
 TRP   0.013   0.002   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00513 ( 3429)
  covalent geometry    : angle       0.64776 ( 4662)
  SS BOND              : bond        0.00430 (    5)
  SS BOND              : angle       1.59800 (   10)
  hydrogen bonds       : bond        0.04318 (   76)
  hydrogen bonds       : angle       5.69231 (  234)

*********************** 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  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7888 (m-30) cc_final: 0.7212 (m-30)
REVERT: L   36 TYR cc_start: 0.9263 (m-80) cc_final: 0.8919 (m-80)
REVERT: H   47 TRP cc_start: 0.8504 (t60) cc_final: 0.8059 (t60)
REVERT: G  406 GLU cc_start: 0.7996 (pt0) cc_final: 0.7760 (pt0)
REVERT: G  471 GLU cc_start: 0.7587 (tp30) cc_final: 0.7336 (mm-30)
REVERT: G  474 GLN cc_start: 0.6973 (tp-100) cc_final: 0.6505 (pp30)
  outliers start: 20
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0657
  time to fit residues: 8.3104
Evaluate side-chains
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
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 32 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0370
   chunk 3 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 = 0.3509 r_free = 0.3509 target = 0.133745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.112626 restraints weight = 5658.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.115742 restraints weight = 3462.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.118018 restraints weight = 2470.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.119483 restraints weight = 1926.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.120515 restraints weight = 1609.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2449

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= 0.179
  Angle     :  0.635   6.765   4672  Z= 0.333
  Chirality :  0.045   0.149    493
  Planarity :  0.004   0.034    607
  Dihedral  :  6.765  76.012    477
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.61 %
    Favored  : 77.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.03 (0.36), residues: 420
  helix: -5.22 (0.19), residues: 20
  sheet: -1.33 (0.48), residues: 112
  loop : -2.18 (0.32), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  65 
 TYR   0.027   0.002   TYR L  49 
 PHE   0.011   0.001   PHE G 377 
 TRP   0.012   0.001   TRP G 436 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 3429)
  covalent geometry    : angle       0.63233 ( 4662)
  SS BOND              : bond        0.00333 (    5)
  SS BOND              : angle       1.47247 (   10)
  hydrogen bonds       : bond        0.03884 (   76)
  hydrogen bonds       : angle       5.02212 (  234)

*********************** 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: 15
    poor density    : 85
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7969 (m-30) cc_final: 0.7191 (m-30)
REVERT: L   36 TYR cc_start: 0.9271 (m-80) cc_final: 0.8863 (m-80)
REVERT: H   47 TRP cc_start: 0.8442 (t60) cc_final: 0.8016 (t60)
REVERT: G  379 CYS cc_start: 0.6780 (m) cc_final: 0.6410 (m)
  outliers start: 15
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0665
  time to fit residues: 7.6003
Evaluate side-chains
  84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 74
  time to evaluate  : 0.109 
-------------------------------------------------------------------------------
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  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 32 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0020
   chunk 37 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0070
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.5608

-------------------------------------------------------------------------------
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 = 0.3522 r_free = 0.3522 target = 0.134657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.113480 restraints weight = 5630.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.116462 restraints weight = 3519.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.118789 restraints weight = 2551.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.120226 restraints weight = 1994.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.121108 restraints weight = 1681.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8018
moved from start:          0.2765

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= 0.161
  Angle     :  0.631   8.386   4672  Z= 0.325
  Chirality :  0.045   0.148    493
  Planarity :  0.004   0.033    607
  Dihedral  :  6.500  73.942    477
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 21.94 %
    Favored  : 74.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.81 (0.37), residues: 420
  helix: -4.45 (0.63), residues: 20
  sheet: -1.08 (0.49), residues: 112
  loop : -2.12 (0.33), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  65 
 TYR   0.025   0.002   TYR L  49 
 PHE   0.010   0.001   PHE G 377 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3429)
  covalent geometry    : angle       0.62902 ( 4662)
  SS BOND              : bond        0.00332 (    5)
  SS BOND              : angle       1.21480 (   10)
  hydrogen bonds       : bond        0.03762 (   76)
  hydrogen bonds       : angle       4.81293 (  234)

*********************** 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
  97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7941 (m-30) cc_final: 0.7113 (m-30)
REVERT: L   37 GLN cc_start: 0.8835 (tt0) cc_final: 0.8581 (mt0)
REVERT: G  379 CYS cc_start: 0.6729 (m) cc_final: 0.6348 (m)
REVERT: G  406 GLU cc_start: 0.7817 (pt0) cc_final: 0.7594 (tt0)
  outliers start: 12
  outliers final: 10
  residues processed: 92
  average time/residue: 0.0653
  time to fit residues: 7.3742
Evaluate side-chains
  89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
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  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 39 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   chunk 22 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 37 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:
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 = 0.3514 r_free = 0.3514 target = 0.134282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.114027 restraints weight = 5628.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.116912 restraints weight = 3596.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.118922 restraints weight = 2629.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.120208 restraints weight = 2090.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.121279 restraints weight = 1773.542|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2963

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= 0.165
  Angle     :  0.628   7.824   4672  Z= 0.325
  Chirality :  0.045   0.143    493
  Planarity :  0.004   0.033    607
  Dihedral  :  6.334  70.987    477
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 21.94 %
    Favored  : 74.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.68 (0.38), residues: 420
  helix: -4.56 (0.53), residues: 26
  sheet: -0.94 (0.50), residues: 112
  loop : -1.97 (0.34), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  16 
 TYR   0.029   0.002   TYR L  49 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3429)
  covalent geometry    : angle       0.62663 ( 4662)
  SS BOND              : bond        0.00317 (    5)
  SS BOND              : angle       1.21354 (   10)
  hydrogen bonds       : bond        0.03678 (   76)
  hydrogen bonds       : angle       4.76263 (  234)

*********************** 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
  99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7880 (m-30) cc_final: 0.7121 (m-30)
REVERT: H   47 TRP cc_start: 0.8524 (t60) cc_final: 0.8112 (t60)
REVERT: G  379 CYS cc_start: 0.6667 (m) cc_final: 0.6366 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 94
  average time/residue: 0.0641
  time to fit residues: 7.3639
Evaluate side-chains
  92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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  394 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0370
   chunk 37 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0000
   chunk 12 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.4862

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

Flipped N/Q/H residues before XYZ refinement:
L  37 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 = 0.3540 r_free = 0.3540 target = 0.136439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.115840 restraints weight = 5591.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.118820 restraints weight = 3505.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.120955 restraints weight = 2533.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.122464 restraints weight = 1996.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.123373 restraints weight = 1673.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3212

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3434  Z= 0.147
  Angle     :  0.629   8.662   4672  Z= 0.320
  Chirality :  0.044   0.142    493
  Planarity :  0.004   0.033    607
  Dihedral  :  6.068  65.388    477
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 22.22 %
    Favored  : 73.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.49 (0.39), residues: 420
  helix: -4.53 (0.55), residues: 26
  sheet: -0.93 (0.49), residues: 113
  loop : -1.76 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  65 
 TYR   0.027   0.002   TYR L  49 
 PHE   0.011   0.001   PHE L  62 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3429)
  covalent geometry    : angle       0.62716 ( 4662)
  SS BOND              : bond        0.00297 (    5)
  SS BOND              : angle       1.10515 (   10)
  hydrogen bonds       : bond        0.03472 (   76)
  hydrogen bonds       : angle       4.56781 (  234)

*********************** 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
  102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7879 (m-30) cc_final: 0.7067 (m-30)
REVERT: L   22 THR cc_start: 0.7324 (p) cc_final: 0.7074 (t)
REVERT: H   47 TRP cc_start: 0.8503 (t60) cc_final: 0.8134 (t60)
  outliers start: 16
  outliers final: 12
  residues processed: 97
  average time/residue: 0.0572
  time to fit residues: 6.9584
Evaluate side-chains
  94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
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   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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0770
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.5740

-------------------------------------------------------------------------------
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 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 487 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.134023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.112492 restraints weight = 5716.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.115726 restraints weight = 3535.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.117983 restraints weight = 2515.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.119576 restraints weight = 1961.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.120765 restraints weight = 1646.301|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3434  Z= 0.165
  Angle     :  0.641   8.834   4672  Z= 0.329
  Chirality :  0.045   0.144    493
  Planarity :  0.004   0.034    607
  Dihedral  :  5.956  58.552    477
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.44 %
    Allowed  : 23.89 %
    Favored  : 71.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.48 (0.39), residues: 420
  helix: -4.51 (0.57), residues: 26
  sheet: -0.96 (0.48), residues: 113
  loop : -1.73 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  65 
 TYR   0.027   0.002   TYR L  49 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.012   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 3429)
  covalent geometry    : angle       0.63697 ( 4662)
  SS BOND              : bond        0.00388 (    5)
  SS BOND              : angle       1.72283 (   10)
  hydrogen bonds       : bond        0.03630 (   76)
  hydrogen bonds       : angle       4.51507 (  234)

*********************** 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
  100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7892 (m-30) cc_final: 0.7058 (m-30)
REVERT: L   22 THR cc_start: 0.7328 (p) cc_final: 0.7077 (t)
REVERT: H   47 TRP cc_start: 0.8617 (t60) cc_final: 0.8222 (t60)
REVERT: G  439 ASN cc_start: 0.9301 (t0) cc_final: 0.8908 (t0)
REVERT: G  471 GLU cc_start: 0.7653 (mm-30) cc_final: 0.7140 (mm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0562
  time to fit residues: 6.7729
Evaluate side-chains
  97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
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  120 LEU
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  402 ILE
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 11 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0980
   chunk 10 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 38 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.4358

-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.134987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.115191 restraints weight = 5628.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.118183 restraints weight = 3578.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.120130 restraints weight = 2574.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.121641 restraints weight = 2050.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.122723 restraints weight = 1704.734|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
moved from start:          0.3610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3434  Z= 0.141
  Angle     :  0.624   9.225   4672  Z= 0.317
  Chirality :  0.044   0.143    493
  Planarity :  0.004   0.034    607
  Dihedral  :  5.586  47.039    477
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.90 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 22.50 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.39 (0.39), residues: 420
  helix: -4.52 (0.56), residues: 26
  sheet: -0.94 (0.47), residues: 113
  loop : -1.63 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  65 
 TYR   0.027   0.001   TYR L  49 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 3429)
  covalent geometry    : angle       0.62073 ( 4662)
  SS BOND              : bond        0.00317 (    5)
  SS BOND              : angle       1.43843 (   10)
  hydrogen bonds       : bond        0.03398 (   76)
  hydrogen bonds       : angle       4.35084 (  234)

*********************** 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
  102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7691 (m-30) cc_final: 0.7044 (m-30)
REVERT: L   22 THR cc_start: 0.7265 (p) cc_final: 0.7045 (t)
REVERT: H   47 TRP cc_start: 0.8550 (t60) cc_final: 0.8184 (t60)
REVERT: H   83 MET cc_start: 0.7529 (ptp) cc_final: 0.7286 (ptp)
REVERT: G  439 ASN cc_start: 0.9242 (t0) cc_final: 0.8879 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 97
  average time/residue: 0.0575
  time to fit residues: 6.8244
Evaluate side-chains
  96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
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    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  109 ILE
Chi-restraints excluded: chain H residue  123 VAL
Chi-restraints excluded: chain G residue  349 SER
Chi-restraints excluded: chain G residue  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
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 0 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 12 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0070
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.4398

-------------------------------------------------------------------------------
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**
** G 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 519 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.134801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.114056 restraints weight = 5729.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.117267 restraints weight = 3526.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.119569 restraints weight = 2493.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.121132 restraints weight = 1927.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.122272 restraints weight = 1591.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3434  Z= 0.142
  Angle     :  0.623   9.551   4672  Z= 0.317
  Chirality :  0.044   0.141    493
  Planarity :  0.004   0.034    607
  Dihedral  :  5.454  38.270    477
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 21.67 %
    Favored  : 73.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.31 (0.39), residues: 420
  helix: -4.52 (0.56), residues: 26
  sheet: -0.93 (0.48), residues: 113
  loop : -1.55 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  65 
 TYR   0.028   0.002   TYR L  49 
 PHE   0.012   0.001   PHE L  62 
 TRP   0.011   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3429)
  covalent geometry    : angle       0.62028 ( 4662)
  SS BOND              : bond        0.00283 (    5)
  SS BOND              : angle       1.30381 (   10)
  hydrogen bonds       : bond        0.03376 (   76)
  hydrogen bonds       : angle       4.26438 (  234)

*********************** 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
  104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 85
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7758 (m-30) cc_final: 0.7017 (m-30)
REVERT: L   22 THR cc_start: 0.7301 (p) cc_final: 0.7088 (t)
REVERT: H   47 TRP cc_start: 0.8575 (t60) cc_final: 0.8145 (t60)
REVERT: H   83 MET cc_start: 0.7494 (ptp) cc_final: 0.7272 (ptp)
REVERT: H  119 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8010 (tp)
REVERT: G  439 ASN cc_start: 0.9256 (t0) cc_final: 0.8872 (t0)
REVERT: G  471 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7147 (mm-30)
  outliers start: 19
  outliers final: 17
  residues processed: 96
  average time/residue: 0.0586
  time to fit residues: 7.0863
Evaluate side-chains
  101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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    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  109 ILE
Chi-restraints excluded: chain H residue  111 ASN
Chi-restraints excluded: chain H residue  119 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  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
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 16 optimal weight:    0.1980
   chunk 10 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0670
   chunk 2 optimal weight:    0.0270
   chunk 34 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 40 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.3376

-------------------------------------------------------------------------------
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 = 0.3512 r_free = 0.3512 target = 0.134570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.114897 restraints weight = 5599.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.117834 restraints weight = 3557.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.119695 restraints weight = 2567.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.121293 restraints weight = 2038.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.122399 restraints weight = 1688.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.3822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.124   3434  Z= 0.222
  Angle     :  1.278  59.199   4672  Z= 0.743
  Chirality :  0.048   0.399    493
  Planarity :  0.005   0.064    607
  Dihedral  :  5.500  38.212    477
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 14.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.39), residues: 420
  helix: -4.52 (0.56), residues: 26
  sheet: -0.91 (0.48), residues: 113
  loop : -1.54 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  65 
 TYR   0.026   0.002   TYR L  49 
 PHE   0.011   0.001   PHE L  62 
 TRP   0.010   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 3429)
  covalent geometry    : angle       1.27850 ( 4662)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       1.24304 (   10)
  hydrogen bonds       : bond        0.03367 (   76)
  hydrogen bonds       : angle       4.25944 (  234)

********************** 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
  101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.130 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   17 ASP cc_start: 0.7673 (m-30) cc_final: 0.7030 (m-30)
REVERT: H   47 TRP cc_start: 0.8557 (t60) cc_final: 0.8184 (t60)
REVERT: H   83 MET cc_start: 0.7579 (ptp) cc_final: 0.7353 (ptp)
REVERT: H  119 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8017 (tp)
REVERT: G  439 ASN cc_start: 0.9239 (t0) cc_final: 0.8871 (t0)
REVERT: G  471 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7040 (mm-30)
  outliers start: 18
  outliers final: 16
  residues processed: 93
  average time/residue: 0.0566
  time to fit residues: 6.5813
Evaluate side-chains
  95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
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    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  109 ILE
Chi-restraints excluded: chain H residue  119 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  392 PHE
Chi-restraints excluded: chain G residue  402 ILE
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 7 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 24 optimal weight:    0.2980
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 23 optimal weight:    0.2980
   chunk 0 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0070
   overall best weight:    0.3398

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

Flipped N/Q/H residues before XYZ refinement:
** H 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.134988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.115165 restraints weight = 5724.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.118135 restraints weight = 3620.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.120212 restraints weight = 2611.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.121555 restraints weight = 2047.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.122586 restraints weight = 1717.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8027
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.124   3434  Z= 0.222
  Angle     :  1.278  59.199   4672  Z= 0.743
  Chirality :  0.048   0.399    493
  Planarity :  0.005   0.064    607
  Dihedral  :  5.500  38.212    477
  Min Nonbonded Distance : 1.402

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.62 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.33 %
    Favored  : 71.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.29 (0.39), residues: 420
  helix: -4.52 (0.56), residues: 26
  sheet: -0.91 (0.48), residues: 113
  loop : -1.54 (0.36), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  65 
 TYR   0.026   0.002   TYR L  49 
 PHE   0.011   0.001   PHE L  62 
 TRP   0.010   0.001   TRP G 436 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 3429)
  covalent geometry    : angle       1.27850 ( 4662)
  SS BOND              : bond        0.00263 (    5)
  SS BOND              : angle       1.24304 (   10)
  hydrogen bonds       : bond        0.03367 (   76)
  hydrogen bonds       : angle       4.25944 (  234)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1040.01 seconds
wall clock time: 18 minutes 32.02 seconds (1112.02 seconds total)