Starting phenix.real_space_refine
on Tue Feb 11 12:45:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ekd_28199/02_2025/8ekd_28199.cif"
  }
  resolution = 3.6
  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=   0.003 sd=   0.278
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3152 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      13      5.16       5
     C    2075      2.51       5
     N     540      2.21       5
     O     611      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 3239
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "E"
      Number of atoms: 968
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 968
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 120}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "F"
      Number of atoms: 857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 111, 857
          Classifications: {'peptide': 111}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105}
    Chain: "G"
      Number of atoms: 1400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 174, 1400
          Classifications: {'peptide': 174}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 10, 'TRANS': 163}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 5
          Unresolved non-hydrogen chiralities: 3
    Chain: "G"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 4.18, per 1000 atoms: 1.29
  Number of scatterers: 3239
  At special positions: 0
  Unit cell: (94.462, 60.818, 80.228, 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      13     16.00
     O     611      8.00
     N     540      7.00
     C    2075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  98 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  23 " - pdb=" SG  CYS F  94 " distance=2.03
    Simple disulfide: pdb=" SG  CYS G 379 " - pdb=" SG  CYS G 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG G 601 " - " ASN G 343 "
  Time building additional restraints: 0.69
  Conformation dependent library (CDL) restraints added in 426.2 milliseconds
  

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 7 sheets defined
      6.6% alpha, 24.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'E' and resid 64 through 67
    Processing helix  chain 'G' and resid 337 through 343
    Processing helix  chain 'G' and resid 365 through 371
      removed outlier: 3.907A  pdb=" N   TYR G 369 " --> pdb=" O   TYR G 365 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 405 through 407
      No H-bonds generated for 'chain 'G' and resid 405 through 407'
    Processing helix  chain 'G' and resid 416 through 421
      removed outlier: 3.549A  pdb=" N   TYR G 421 " --> pdb=" O   ASN G 417 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.506A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER E   7 " --> pdb=" O   SER E  21 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   TYR E  82 " --> pdb=" O   SER E  73 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12
    Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62
      removed outlier: 7.212A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7
      removed outlier: 3.506A  pdb=" N   ASN F  22 " --> pdb=" O   SER F   7 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 12
      removed outlier: 3.644A  pdb=" N   GLU F 110 " --> pdb=" O   LEU F  11 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   LEU F  39 " --> pdb=" O   TYR F  55 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   TYR F  55 " --> pdb=" O   LEU F  39 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   TRP F  41 " --> pdb=" O   LEU F  53 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 354 through 356
      removed outlier: 3.503A  pdb=" N   TYR G 396 " --> pdb=" O   SER G 514 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP G 398 " --> pdb=" O   VAL G 512 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 452 through 454

    71 hydrogen bonds defined for protein.
    189 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: 0.75

  Time building geometry restraints manager: 0.80 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: 893
        1.33 -     1.45: 677
        1.45 -     1.57: 1735
        1.57 -     1.69: 1
        1.69 -     1.81: 17
  Bond restraints: 3323
  Sorted by residual:
  bond pdb=" N   GLN G 474 "
       pdb=" CA  GLN G 474 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.22e-02 6.72e+03 7.66e+00
  bond pdb=" CB  PRO G 507 "
       pdb=" CG  PRO G 507 "
    ideal  model  delta    sigma   weight residual
    1.492  1.630 -0.138 5.00e-02 4.00e+02 7.65e+00
  bond pdb=" CA  SER G 459 "
       pdb=" CB  SER G 459 "
    ideal  model  delta    sigma   weight residual
    1.527  1.487  0.040 1.44e-02 4.82e+03 7.58e+00
  bond pdb=" N   LYS G 458 "
       pdb=" CA  LYS G 458 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.21e-02 6.83e+03 7.41e+00
  bond pdb=" N   TYR G 473 "
       pdb=" CA  TYR G 473 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.032 1.31e-02 5.83e+03 5.91e+00
  ... (remaining 3318 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 4357
        2.23 -     4.46: 121
        4.46 -     6.69: 19
        6.69 -     8.91: 7
        8.91 -    11.14: 2
  Bond angle restraints: 4506
  Sorted by residual:
  angle pdb=" N   GLN G 474 "
        pdb=" CA  GLN G 474 "
        pdb=" C   GLN G 474 "
      ideal   model   delta    sigma   weight residual
     110.28  121.42  -11.14 1.48e+00 4.57e-01 5.67e+01
  angle pdb=" CA  PRO G 507 "
        pdb=" N   PRO G 507 "
        pdb=" CD  PRO G 507 "
      ideal   model   delta    sigma   weight residual
     112.00  103.04    8.96 1.40e+00 5.10e-01 4.09e+01
  angle pdb=" C   THR G 470 "
        pdb=" CA  THR G 470 "
        pdb=" CB  THR G 470 "
      ideal   model   delta    sigma   weight residual
     111.22  103.83    7.39 1.23e+00 6.61e-01 3.61e+01
  angle pdb=" CA  ALA G 475 "
        pdb=" C   ALA G 475 "
        pdb=" N   GLY G 476 "
      ideal   model   delta    sigma   weight residual
     119.63  114.99    4.64 8.10e-01 1.52e+00 3.28e+01
  angle pdb=" C   SER G 459 "
        pdb=" N   ASN G 460 "
        pdb=" CA  ASN G 460 "
      ideal   model   delta    sigma   weight residual
     120.82  112.85    7.97 1.41e+00 5.03e-01 3.19e+01
  ... (remaining 4501 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.36: 1670
       21.36 -    42.72: 236
       42.72 -    64.07: 26
       64.07 -    85.43: 9
       85.43 -   106.79: 8
  Dihedral angle restraints: 1949
    sinusoidal: 769
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  98 "
           pdb=" CB  CYS E  98 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   44.64   48.36     1      1.00e+01 1.00e-02 3.22e+01
  dihedral pdb=" CA  PRO F  65 "
           pdb=" C   PRO F  65 "
           pdb=" N   ASP F  66 "
           pdb=" CA  ASP F  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.07  -20.93     0      5.00e+00 4.00e-02 1.75e+01
  dihedral pdb=" C2  NAG G 601 "
           pdb=" C3  NAG G 601 "
           pdb=" C4  NAG G 601 "
           pdb=" O4  NAG G 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     175.11   68.32  106.79     1      3.00e+01 1.11e-03 1.37e+01
  ... (remaining 1946 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 356
       0.045 -    0.091: 83
       0.091 -    0.136: 25
       0.136 -    0.182: 3
       0.182 -    0.227: 6
  Chirality restraints: 473
  Sorted by residual:
  chirality pdb=" CB  ILE E  51 "
            pdb=" CA  ILE E  51 "
            pdb=" CG1 ILE E  51 "
            pdb=" CG2 ILE E  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  THR G 470 "
            pdb=" N   THR G 470 "
            pdb=" C   THR G 470 "
            pdb=" CB  THR G 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.75   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ARG G 457 "
            pdb=" N   ARG G 457 "
            pdb=" C   ARG G 457 "
            pdb=" CB  ARG G 457 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.19 2.00e-01 2.50e+01 9.50e-01
  ... (remaining 470 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER G 383 "   -0.079 5.00e-02 4.00e+02   1.17e-01 2.18e+01
        pdb=" N   PRO G 384 "    0.202 5.00e-02 4.00e+02
        pdb=" CA  PRO G 384 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO G 384 "   -0.062 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN F  48 "   -0.054 5.00e-02 4.00e+02   8.05e-02 1.04e+01
        pdb=" N   PRO F  49 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO F  49 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO F  49 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU G 471 "   -0.015 2.00e-02 2.50e+03   3.16e-02 9.99e+00
        pdb=" C   GLU G 471 "    0.055 2.00e-02 2.50e+03
        pdb=" O   GLU G 471 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   ILE G 472 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 256
        2.73 -     3.27: 3328
        3.27 -     3.82: 5704
        3.82 -     4.36: 6739
        4.36 -     4.90: 11108
  Nonbonded interactions: 27135
  Sorted by model distance:
  nonbonded pdb=" O   PRO F   8 "
            pdb=" OG1 THR F 107 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O   PRO G 479 "
            pdb=" SG  CYS G 480 "
     model   vdw
     2.195 3.400
  nonbonded pdb=" OH  TYR E 106 "
            pdb=" O   TYR F  97 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OE1 GLU G 406 "
            pdb=" NE2 GLN G 409 "
     model   vdw
     2.205 3.120
  nonbonded pdb=" O   GLY E 116 "
            pdb=" OG  SER F  62 "
     model   vdw
     2.239 3.040
  ... (remaining 27130 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:             0.120
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.070
  Process input model:                     14.030
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
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   0.138   3323  Z= 0.334
  Angle     :  0.883  11.143   4506  Z= 0.531
  Chirality :  0.049   0.227    473
  Planarity :  0.009   0.117    580
  Dihedral  : 19.664 106.791   1196
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 21.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 38.94 %
    Favored  : 59.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.40), residues: 399
  helix: -0.53 (1.97), residues: 7
  sheet: -1.25 (0.46), residues: 120
  loop : -1.07 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP E 121 
 HIS   0.002   0.001   HIS G 505 
 PHE   0.008   0.001   PHE E 118 
 TYR   0.017   0.002   TYR E 105 
 ARG   0.009   0.001   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5854 (pm20) cc_final: 0.5353 (pm20)
  outliers start: 6
  outliers final: 5
  residues processed: 100
  average time/residue: 0.1794
  time to fit residues: 21.1478
Evaluate side-chains
  102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   37 ASN
Chi-restraints excluded: chain G residue  357 ARG
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain G residue  457 ARG
Chi-restraints excluded: chain G residue  459 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.0870
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0000
   chunk 31 optimal weight:    0.5980
   chunk 12 optimal weight:    9.9990
   chunk 19 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.4964

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  96 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.184489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.155347 restraints weight = 4155.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.160263 restraints weight = 2258.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163676 restraints weight = 1522.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6337
moved from start:          0.1340

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3323  Z= 0.211
  Angle     :  0.674   7.169   4506  Z= 0.345
  Chirality :  0.046   0.252    473
  Planarity :  0.007   0.075    580
  Dihedral  :  8.949  56.402    489
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 30.09 %
    Favored  : 64.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.40), residues: 399
  helix: -0.49 (1.97), residues: 7
  sheet: -1.32 (0.47), residues: 113
  loop : -0.99 (0.36), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.007   0.001   PHE G 497 
 TYR   0.014   0.002   TYR E 105 
 ARG   0.004   0.001   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4360 (OUTLIER) cc_final: 0.3319 (m-80)
REVERT: E  112 GLU cc_start: 0.5541 (pm20) cc_final: 0.5156 (pm20)
REVERT: F   67 ARG cc_start: 0.5653 (ptt-90) cc_final: 0.5071 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7548 (tmt170) cc_final: 0.7289 (tmm-80)
REVERT: G  406 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.6837 (mm-30)
REVERT: G  429 PHE cc_start: 0.7561 (OUTLIER) cc_final: 0.7178 (p90)
REVERT: G  459 SER cc_start: 0.8414 (t) cc_final: 0.7810 (p)
  outliers start: 20
  outliers final: 9
  residues processed: 110
  average time/residue: 0.1626
  time to fit residues: 21.3722
Evaluate side-chains
  105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  109 VAL
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  429 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 34 optimal weight:    3.9990
   chunk 26 optimal weight:    0.4980
   chunk 4 optimal weight:    6.9990
   chunk 37 optimal weight:    0.3980
   chunk 17 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
F  85 GLN
F  96 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.183014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153646 restraints weight = 4103.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.158756 restraints weight = 2178.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.162171 restraints weight = 1462.198|
|-----------------------------------------------------------------------------|
r_work (final): 0.3835
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3323  Z= 0.273
  Angle     :  0.671   6.163   4506  Z= 0.344
  Chirality :  0.045   0.262    473
  Planarity :  0.006   0.061    580
  Dihedral  :  6.159  52.392    476
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.51 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 31.27 %
    Favored  : 61.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.40), residues: 399
  helix: -0.34 (1.97), residues: 7
  sheet: -0.85 (0.48), residues: 115
  loop : -1.05 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.026   0.002   PHE E 118 
 TYR   0.014   0.002   TYR F  42 
 ARG   0.002   0.000   ARG E  50 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4668 (OUTLIER) cc_final: 0.3692 (m-80)
REVERT: E  112 GLU cc_start: 0.5717 (pm20) cc_final: 0.5318 (pm20)
REVERT: F   59 GLU cc_start: 0.7060 (mm-30) cc_final: 0.6655 (tm-30)
REVERT: F   60 ARG cc_start: 0.5836 (ttm-80) cc_final: 0.5293 (tpp80)
REVERT: F   67 ARG cc_start: 0.6003 (ptt-90) cc_final: 0.5655 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7525 (tmt170) cc_final: 0.7302 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8035 (m-30) cc_final: 0.6874 (m-30)
REVERT: G  406 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7116 (mm-30)
REVERT: G  409 GLN cc_start: 0.6991 (mt0) cc_final: 0.6396 (tt0)
REVERT: G  429 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.6760 (p90)
REVERT: G  459 SER cc_start: 0.8373 (t) cc_final: 0.7935 (p)
  outliers start: 23
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1708
  time to fit residues: 23.4594
Evaluate side-chains
  112 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  473 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.3980
   chunk 7 optimal weight:    8.9990
   chunk 31 optimal weight:    0.6980
   chunk 3 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0010
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 2 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5186

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

Flipped N/Q/H residues before XYZ refinement:
E 123 GLN
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4133 r_free = 0.4133 target = 0.188204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.158976 restraints weight = 4127.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.164183 restraints weight = 2159.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.167469 restraints weight = 1440.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6335
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   3323  Z= 0.191
  Angle     :  0.629   6.413   4506  Z= 0.322
  Chirality :  0.044   0.187    473
  Planarity :  0.006   0.060    580
  Dihedral  :  5.464  37.713    476
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 14.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 31.56 %
    Favored  : 61.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.35 (0.41), residues: 399
  helix: -0.54 (1.84), residues: 7
  sheet: -0.65 (0.50), residues: 115
  loop : -1.04 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.020   0.001   PHE E 118 
 TYR   0.013   0.001   TYR E 105 
 ARG   0.002   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5469 (pm20) cc_final: 0.5063 (pm20)
REVERT: F   67 ARG cc_start: 0.5951 (ptt-90) cc_final: 0.5554 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7490 (tmt170) cc_final: 0.7201 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8110 (m-30) cc_final: 0.7593 (m-30)
REVERT: G  406 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7186 (mm-30)
REVERT: G  409 GLN cc_start: 0.6893 (mt0) cc_final: 0.6441 (tt0)
REVERT: G  429 PHE cc_start: 0.7353 (OUTLIER) cc_final: 0.6835 (p90)
REVERT: G  495 TYR cc_start: 0.4586 (OUTLIER) cc_final: 0.4177 (m-80)
  outliers start: 23
  outliers final: 11
  residues processed: 116
  average time/residue: 0.1731
  time to fit residues: 23.9083
Evaluate side-chains
  107 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 1 optimal weight:   30.0000
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 38 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
F  85 GLN
** F  96 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 = 0.4022 r_free = 0.4022 target = 0.178127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.149047 restraints weight = 4178.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.153734 restraints weight = 2277.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.156802 restraints weight = 1563.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6447
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   3323  Z= 0.282
  Angle     :  0.686   8.359   4506  Z= 0.346
  Chirality :  0.045   0.204    473
  Planarity :  0.006   0.058    580
  Dihedral  :  5.533  35.563    476
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 18.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.02 %
    Favored  : 93.98 %
  Rotamer:
    Outliers :  8.26 %
    Allowed  : 30.97 %
    Favored  : 60.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.41), residues: 399
  helix: -0.51 (1.81), residues: 7
  sheet: -0.62 (0.49), residues: 115
  loop : -1.05 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.021   0.002   PHE E 118 
 TYR   0.015   0.002   TYR G 380 
 ARG   0.003   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4506 (OUTLIER) cc_final: 0.3565 (m-80)
REVERT: E  112 GLU cc_start: 0.5676 (pm20) cc_final: 0.5268 (pm20)
REVERT: F   59 GLU cc_start: 0.7119 (mm-30) cc_final: 0.6683 (tm-30)
REVERT: F   67 ARG cc_start: 0.6160 (ptt-90) cc_final: 0.5906 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7549 (tmt170) cc_final: 0.7235 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8180 (m-30) cc_final: 0.7563 (m-30)
REVERT: G  406 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7189 (mm-30)
REVERT: G  409 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6511 (tt0)
REVERT: G  429 PHE cc_start: 0.7515 (OUTLIER) cc_final: 0.6777 (p90)
REVERT: G  495 TYR cc_start: 0.4447 (OUTLIER) cc_final: 0.3880 (m-80)
REVERT: G  501 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.5889 (m-10)
  outliers start: 28
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1733
  time to fit residues: 23.5826
Evaluate side-chains
  118 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue   64 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  401 VAL
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  456 PHE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Chi-restraints excluded: chain G residue  501 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 1 optimal weight:   20.0000
   chunk 3 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4117 r_free = 0.4117 target = 0.186538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156987 restraints weight = 4219.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.162101 restraints weight = 2209.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.165441 restraints weight = 1479.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
moved from start:          0.2436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3323  Z= 0.215
  Angle     :  0.662   8.415   4506  Z= 0.332
  Chirality :  0.043   0.190    473
  Planarity :  0.006   0.059    580
  Dihedral  :  5.268  31.914    476
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 32.15 %
    Favored  : 61.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.41), residues: 399
  helix: -0.22 (1.91), residues: 7
  sheet: -0.53 (0.49), residues: 115
  loop : -1.01 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.017   0.001   PHE E 118 
 TYR   0.013   0.002   TYR E 105 
 ARG   0.003   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5278 (pm20) cc_final: 0.4907 (pm20)
REVERT: F   59 GLU cc_start: 0.6956 (mm-30) cc_final: 0.6613 (tm-30)
REVERT: F   67 ARG cc_start: 0.6044 (ptt-90) cc_final: 0.5834 (ptt-90)
REVERT: G  356 LYS cc_start: 0.8512 (mptt) cc_final: 0.8306 (mptt)
REVERT: G  357 ARG cc_start: 0.7445 (tmt170) cc_final: 0.7152 (tmm-80)
REVERT: G  398 ASP cc_start: 0.8078 (m-30) cc_final: 0.7538 (m-30)
REVERT: G  406 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7196 (mm-30)
REVERT: G  409 GLN cc_start: 0.6922 (OUTLIER) cc_final: 0.6402 (tt0)
REVERT: G  429 PHE cc_start: 0.7435 (OUTLIER) cc_final: 0.6859 (p90)
REVERT: G  495 TYR cc_start: 0.4201 (OUTLIER) cc_final: 0.3920 (m-80)
  outliers start: 23
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1719
  time to fit residues: 23.4423
Evaluate side-chains
  114 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 37 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 23 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4093 r_free = 0.4093 target = 0.184327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.154719 restraints weight = 4154.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.159736 restraints weight = 2206.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.162930 restraints weight = 1496.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6404
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3323  Z= 0.240
  Angle     :  0.683   8.752   4506  Z= 0.342
  Chirality :  0.044   0.212    473
  Planarity :  0.006   0.061    580
  Dihedral  :  5.256  29.632    476
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  8.26 %
    Allowed  : 29.79 %
    Favored  : 61.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.41), residues: 399
  helix:  0.10 (2.02), residues: 7
  sheet: -0.47 (0.49), residues: 115
  loop : -1.01 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.031   0.002   PHE E 118 
 TYR   0.016   0.002   TYR G 380 
 ARG   0.003   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   82 TYR cc_start: 0.4489 (OUTLIER) cc_final: 0.3558 (m-80)
REVERT: E  112 GLU cc_start: 0.5552 (pm20) cc_final: 0.5180 (pm20)
REVERT: F   60 ARG cc_start: 0.5985 (ttm-80) cc_final: 0.5664 (tpp80)
REVERT: F   67 ARG cc_start: 0.6170 (ptt-90) cc_final: 0.5960 (ptt-90)
REVERT: G  357 ARG cc_start: 0.7532 (tmt170) cc_final: 0.7299 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5549 (p90)
REVERT: G  398 ASP cc_start: 0.8106 (m-30) cc_final: 0.7606 (m-30)
REVERT: G  406 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7240 (mm-30)
REVERT: G  409 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6415 (tt0)
REVERT: G  429 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6747 (p90)
REVERT: G  495 TYR cc_start: 0.4439 (OUTLIER) cc_final: 0.4058 (m-80)
REVERT: G  501 TYR cc_start: 0.6442 (OUTLIER) cc_final: 0.5948 (m-10)
  outliers start: 28
  outliers final: 16
  residues processed: 115
  average time/residue: 0.1801
  time to fit residues: 24.5261
Evaluate side-chains
  117 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   82 TYR
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain E residue  105 TYR
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  406 GLU
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Chi-restraints excluded: chain G residue  501 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 1 optimal weight:   30.0000
   chunk 31 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0570
   chunk 25 optimal weight:    2.9990
   chunk 10 optimal weight:    0.2980
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4147 r_free = 0.4147 target = 0.189630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.160231 restraints weight = 4095.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165309 restraints weight = 2144.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.168636 restraints weight = 1449.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6315
moved from start:          0.2740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3323  Z= 0.187
  Angle     :  0.664   8.567   4506  Z= 0.330
  Chirality :  0.043   0.204    473
  Planarity :  0.006   0.062    580
  Dihedral  :  4.945  25.823    476
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 15.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  6.78 %
    Allowed  : 30.97 %
    Favored  : 62.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.41), residues: 399
  helix: -0.03 (1.98), residues: 7
  sheet: -0.40 (0.49), residues: 115
  loop : -0.99 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.029   0.001   PHE E 118 
 TYR   0.011   0.001   TYR E 120 
 ARG   0.003   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5385 (pm20) cc_final: 0.5049 (pm20)
REVERT: F   60 ARG cc_start: 0.6014 (ttm-80) cc_final: 0.5760 (tpp80)
REVERT: G  357 ARG cc_start: 0.7490 (tmt170) cc_final: 0.7181 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.5516 (p90)
REVERT: G  396 TYR cc_start: 0.6500 (m-10) cc_final: 0.6269 (m-10)
REVERT: G  429 PHE cc_start: 0.7232 (OUTLIER) cc_final: 0.6674 (p90)
REVERT: G  495 TYR cc_start: 0.4643 (OUTLIER) cc_final: 0.4374 (m-80)
  outliers start: 23
  outliers final: 14
  residues processed: 112
  average time/residue: 0.1704
  time to fit residues: 22.6757
Evaluate side-chains
  110 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   10 SER
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue  101 LEU
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 32 optimal weight:    3.9990
   chunk 12 optimal weight:    8.9990
   chunk 33 optimal weight:    0.0970
   chunk 10 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 7 optimal weight:    8.9990
   overall best weight:    1.1180

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

Flipped N/Q/H residues before XYZ refinement:
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.184744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.154938 restraints weight = 4138.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.159877 restraints weight = 2169.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.162932 restraints weight = 1472.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3323  Z= 0.270
  Angle     :  0.724   9.230   4506  Z= 0.358
  Chirality :  0.044   0.239    473
  Planarity :  0.006   0.062    580
  Dihedral  :  5.200  25.678    476
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 19.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  6.49 %
    Allowed  : 31.27 %
    Favored  : 62.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.41), residues: 399
  helix:  0.20 (2.01), residues: 7
  sheet: -0.49 (0.48), residues: 115
  loop : -1.03 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.031   0.002   PHE E 118 
 TYR   0.016   0.002   TYR E 105 
 ARG   0.002   0.000   ARG G 403 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5545 (pm20) cc_final: 0.5226 (pm20)
REVERT: F   20 THR cc_start: 0.7628 (OUTLIER) cc_final: 0.7209 (p)
REVERT: F   60 ARG cc_start: 0.5966 (ttm-80) cc_final: 0.5705 (tpp80)
REVERT: G  357 ARG cc_start: 0.7461 (tmt170) cc_final: 0.7063 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6689 (OUTLIER) cc_final: 0.5536 (p90)
REVERT: G  398 ASP cc_start: 0.8156 (m-30) cc_final: 0.7572 (m-30)
REVERT: G  429 PHE cc_start: 0.7342 (OUTLIER) cc_final: 0.6663 (p90)
REVERT: G  458 LYS cc_start: 0.7000 (mmtt) cc_final: 0.6746 (mmtt)
REVERT: G  495 TYR cc_start: 0.4566 (OUTLIER) cc_final: 0.4033 (m-80)
  outliers start: 22
  outliers final: 15
  residues processed: 115
  average time/residue: 0.1831
  time to fit residues: 24.7230
Evaluate side-chains
  115 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   30 ARG
Chi-restraints excluded: chain E residue   32 VAL
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  480 CYS
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 1 optimal weight:   30.0000
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:    0.8980
   chunk 15 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 409 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.188158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.158009 restraints weight = 4080.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.163021 restraints weight = 2183.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.166074 restraints weight = 1485.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6391
moved from start:          0.2903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3323  Z= 0.231
  Angle     :  0.727   9.695   4506  Z= 0.357
  Chirality :  0.044   0.244    473
  Planarity :  0.006   0.062    580
  Dihedral  :  5.179  24.776    476
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 17.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  5.90 %
    Allowed  : 32.74 %
    Favored  : 61.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.41), residues: 399
  helix:  0.11 (1.99), residues: 7
  sheet: -0.52 (0.48), residues: 115
  loop : -1.05 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.003   TRP E 121 
 HIS   0.001   0.000   HIS G 505 
 PHE   0.029   0.002   PHE E 118 
 TYR   0.016   0.002   TYR E 105 
 ARG   0.003   0.000   ARG F  60 

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

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

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  798 Ramachandran restraints generated.
    399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  112 GLU cc_start: 0.5514 (pm20) cc_final: 0.5186 (pm20)
REVERT: F   20 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7154 (p)
REVERT: G  357 ARG cc_start: 0.7385 (tmt170) cc_final: 0.7057 (tmm-80)
REVERT: G  371 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5536 (p90)
REVERT: G  398 ASP cc_start: 0.8061 (m-30) cc_final: 0.7476 (m-30)
REVERT: G  429 PHE cc_start: 0.7284 (OUTLIER) cc_final: 0.6646 (p90)
REVERT: G  495 TYR cc_start: 0.4518 (OUTLIER) cc_final: 0.4042 (m-80)
  outliers start: 20
  outliers final: 14
  residues processed: 110
  average time/residue: 0.1678
  time to fit residues: 21.8271
Evaluate side-chains
  111 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   37 VAL
Chi-restraints excluded: chain E residue   86 ASN
Chi-restraints excluded: chain F residue    4 MET
Chi-restraints excluded: chain F residue   20 THR
Chi-restraints excluded: chain F residue   28 SER
Chi-restraints excluded: chain F residue   29 VAL
Chi-restraints excluded: chain F residue  111 ILE
Chi-restraints excluded: chain G residue  369 TYR
Chi-restraints excluded: chain G residue  371 PHE
Chi-restraints excluded: chain G residue  402 ILE
Chi-restraints excluded: chain G residue  403 ARG
Chi-restraints excluded: chain G residue  409 GLN
Chi-restraints excluded: chain G residue  410 ILE
Chi-restraints excluded: chain G residue  429 PHE
Chi-restraints excluded: chain G residue  434 ILE
Chi-restraints excluded: chain G residue  473 TYR
Chi-restraints excluded: chain G residue  480 CYS
Chi-restraints excluded: chain G residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 23 optimal weight:    0.0670
   chunk 38 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** F  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  96 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 = 0.4145 r_free = 0.4145 target = 0.189203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.160024 restraints weight = 4071.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.164927 restraints weight = 2154.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.168176 restraints weight = 1457.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6363
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3323  Z= 0.212
  Angle     :  0.724   9.914   4506  Z= 0.355
  Chirality :  0.044   0.240    473
  Planarity :  0.006   0.062    580
  Dihedral  :  5.064  23.318    476
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 17.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 32.45 %
    Favored  : 61.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.42), residues: 399
  helix: -0.02 (1.95), residues: 7
  sheet: -0.47 (0.48), residues: 115
  loop : -1.08 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP E 121 
 HIS   0.000   0.000   HIS G 505 
 PHE   0.028   0.001   PHE E 118 
 TYR   0.016   0.002   TYR E 105 
 ARG   0.003   0.000   ARG F  60 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1476.90 seconds
wall clock time: 27 minutes 5.58 seconds (1625.58 seconds total)