Starting phenix.real_space_refine
on Tue Feb 11 00:22:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wb5_32395/02_2025/7wb5_32395.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.022
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      15      5.16       5
     C    2077      2.51       5
     N     533      2.21       5
     O     631      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 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: 3256
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 928
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 928
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "L"
      Number of atoms: 824
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 824
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100}
    Chain: "R"
      Number of atoms: 1465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 183, 1465
          Classifications: {'peptide': 183}
          Link IDs: {'PTRANS': 9, 'TRANS': 173}
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.42, per 1000 atoms: 1.05
  Number of scatterers: 3256
  At special positions: 0
  Unit cell: (72.36, 88.56, 72.36, 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      15     16.00
     O     631      8.00
     N     533      7.00
     C    2077      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.02

  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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
      " NAG A   2 " - " BMA A   3 "
    NAG-ASN
      " NAG A   1 " - " ASN R 343 "
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 358.3 milliseconds
  

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  746

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 12 sheets defined
      4.4% alpha, 25.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.45
  Creating SS restraints...
    Processing helix  chain 'R' and resid 349 through 353
    Processing helix  chain 'R' and resid 364 through 370
      removed outlier: 4.598A  pdb=" N   LEU R 368 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'H' and resid 5 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.682A  pdb=" N   LYS H  12 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'H' and resid 46 through 47
      removed outlier: 3.906A  pdb=" N   THR H 113 " --> pdb=" O   TYR H  94 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 49 through 51
      removed outlier: 3.533A  pdb=" N   TRP H  50 " --> pdb=" O   THR H  59 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 68 through 70
    Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.846A  pdb=" N   ILE L  21 " --> pdb=" O   LEU L  73 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   LEU L  73 " --> pdb=" O   ILE L  21 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   SER L  63 " --> pdb=" O   THR L  74 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13
      removed outlier: 3.595A  pdb=" N   LEU L  11 " --> pdb=" O   LYS L 103 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   GLU L 105 " --> pdb=" O   LEU L  11 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 53 through 54
      removed outlier: 3.572A  pdb=" N   GLN L  53 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   LEU L  46 " --> pdb=" O   GLN L  37 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   GLN L  37 " --> pdb=" O   LEU L  46 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.884A  pdb=" N   ILE R 434 " --> pdb=" O   VAL R 511 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   CYS R 432 " --> pdb=" O   LEU R 513 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'R' and resid 354 through 358
    Processing sheet with id=AB2, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB3, first strand: chain 'R' and resid 473 through 474

    73 hydrogen bonds defined for protein.
    171 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: 0.84

  Time building geometry restraints manager: 0.97 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: 734
        1.33 -     1.45: 857
        1.45 -     1.57: 1735
        1.57 -     1.69: 1
        1.69 -     1.82: 18
  Bond restraints: 3345
  Sorted by residual:
  bond pdb=" CA  SER R 438 "
       pdb=" CB  SER R 438 "
    ideal  model  delta    sigma   weight residual
    1.528  1.475  0.053 1.35e-02 5.49e+03 1.53e+01
  bond pdb=" CA  SER R 349 "
       pdb=" CB  SER R 349 "
    ideal  model  delta    sigma   weight residual
    1.529  1.467  0.062 1.64e-02 3.72e+03 1.43e+01
  bond pdb=" N   LEU R 452 "
       pdb=" CA  LEU R 452 "
    ideal  model  delta    sigma   weight residual
    1.452  1.495 -0.043 1.22e-02 6.72e+03 1.23e+01
  bond pdb=" N   VAL R 433 "
       pdb=" CA  VAL R 433 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.041 1.25e-02 6.40e+03 1.07e+01
  bond pdb=" N   LYS R 378 "
       pdb=" CA  LYS R 378 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.041 1.29e-02 6.01e+03 1.03e+01
  ... (remaining 3340 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 4160
        2.59 -     5.17: 364
        5.17 -     7.76: 19
        7.76 -    10.34: 3
       10.34 -    12.93: 2
  Bond angle restraints: 4548
  Sorted by residual:
  angle pdb=" CA  PRO L  80 "
        pdb=" N   PRO L  80 "
        pdb=" CD  PRO L  80 "
      ideal   model   delta    sigma   weight residual
     112.00   99.07   12.93 1.40e+00 5.10e-01 8.52e+01
  angle pdb=" CA  TRP R 436 "
        pdb=" CB  TRP R 436 "
        pdb=" CG  TRP R 436 "
      ideal   model   delta    sigma   weight residual
     113.60  123.83  -10.23 1.90e+00 2.77e-01 2.90e+01
  angle pdb=" CA  PHE R 400 "
        pdb=" CB  PHE R 400 "
        pdb=" CG  PHE R 400 "
      ideal   model   delta    sigma   weight residual
     113.80  118.30   -4.50 1.00e+00 1.00e+00 2.03e+01
  angle pdb=" N   PRO L  80 "
        pdb=" CD  PRO L  80 "
        pdb=" CG  PRO L  80 "
      ideal   model   delta    sigma   weight residual
     103.20   96.90    6.30 1.50e+00 4.44e-01 1.77e+01
  angle pdb=" N   LEU R 387 "
        pdb=" CA  LEU R 387 "
        pdb=" C   LEU R 387 "
      ideal   model   delta    sigma   weight residual
     114.75  109.56    5.19 1.26e+00 6.30e-01 1.69e+01
  ... (remaining 4543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.52: 1718
       21.52 -    43.04: 173
       43.04 -    64.55: 66
       64.55 -    86.07: 12
       86.07 -   107.59: 12
  Dihedral angle restraints: 1981
    sinusoidal: 801
      harmonic: 1180
  Sorted by residual:
  dihedral pdb=" CA  VAL L  29 "
           pdb=" C   VAL L  29 "
           pdb=" N   SER L  30 "
           pdb=" CA  SER L  30 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -139.90  -40.10     0      5.00e+00 4.00e-02 6.43e+01
  dihedral pdb=" CA  PHE H 106 "
           pdb=" C   PHE H 106 "
           pdb=" N   ASP H 107 "
           pdb=" CA  ASP H 107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -146.68  -33.32     0      5.00e+00 4.00e-02 4.44e+01
  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  136.78  -43.78     1      1.00e+01 1.00e-02 2.67e+01
  ... (remaining 1978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.119: 417
       0.119 -    0.238: 63
       0.238 -    0.356: 5
       0.356 -    0.475: 0
       0.475 -    0.593: 2
  Chirality restraints: 487
  Sorted by residual:
  chirality pdb=" C1  NAG A   2 "
            pdb=" O4  NAG A   1 "
            pdb=" C2  NAG A   2 "
            pdb=" O5  NAG A   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-02 2.50e+03 6.89e+01
  chirality pdb=" C1  BMA A   3 "
            pdb=" O4  NAG A   2 "
            pdb=" C2  BMA A   3 "
            pdb=" O5  BMA A   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.29e+01
  chirality pdb=" C1  NAG A   1 "
            pdb=" ND2 ASN R 343 "
            pdb=" C2  NAG A   1 "
            pdb=" O5  NAG A   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.81   -0.59 2.00e-01 2.50e+01 8.81e+00
  ... (remaining 484 not shown)

  Planarity restraints: 582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   2 "    0.304 2.00e-02 2.50e+03   2.62e-01 8.61e+02
        pdb=" C7  NAG A   2 "   -0.065 2.00e-02 2.50e+03
        pdb=" C8  NAG A   2 "    0.009 2.00e-02 2.50e+03
        pdb=" N2  NAG A   2 "   -0.453 2.00e-02 2.50e+03
        pdb=" O7  NAG A   2 "    0.205 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A   1 "   -0.292 2.00e-02 2.50e+03   2.51e-01 7.91e+02
        pdb=" C7  NAG A   1 "    0.068 2.00e-02 2.50e+03
        pdb=" C8  NAG A   1 "   -0.164 2.00e-02 2.50e+03
        pdb=" N2  NAG A   1 "    0.443 2.00e-02 2.50e+03
        pdb=" O7  NAG A   1 "   -0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN L  79 "   -0.111 5.00e-02 4.00e+02   1.57e-01 3.92e+01
        pdb=" N   PRO L  80 "    0.270 5.00e-02 4.00e+02
        pdb=" CA  PRO L  80 "   -0.083 5.00e-02 4.00e+02
        pdb=" CD  PRO L  80 "   -0.076 5.00e-02 4.00e+02
  ... (remaining 579 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 281
        2.73 -     3.27: 3255
        3.27 -     3.82: 5356
        3.82 -     4.36: 6706
        4.36 -     4.90: 11080
  Nonbonded interactions: 26678
  Sorted by model distance:
  nonbonded pdb=" O   ILE L  21 "
            pdb=" OG1 THR L  72 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OG  SER H   7 "
            pdb=" OG  SER H  21 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OE1 GLN H   6 "
            pdb=" OG1 THR H 113 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OG  SER L  26 "
            pdb=" OE1 GLN L  27 "
     model   vdw
     2.405 3.040
  nonbonded pdb=" O   VAL H  76 "
            pdb=" OG  SER H  77 "
     model   vdw
     2.421 3.040
  ... (remaining 26673 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.050
  Process input model:                     13.460
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
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      :  0.011   0.132   3345  Z= 0.690
  Angle     :  1.407  12.925   4548  Z= 0.926
  Chirality :  0.090   0.593    487
  Planarity :  0.018   0.262    581
  Dihedral  : 21.949 107.591   1220
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 18.30
  Ramachandran Plot:
    Outliers :  2.24 %
    Allowed  : 18.16 %
    Favored  : 79.60 %
  Rotamer:
    Outliers : 14.00 %
    Allowed  :  7.43 %
    Favored  : 78.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.52 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.90 (0.36), residues: 402
  helix: -4.22 (0.64), residues: 21
  sheet: -3.58 (0.39), residues: 121
  loop : -3.14 (0.35), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.092   0.006   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.023   0.003   PHE R 400 
 TYR   0.024   0.003   TYR L  49 
 ARG   0.007   0.001   ARG L  61 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 125
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
REVERT: H   83 ILE cc_start: 0.9173 (tt) cc_final: 0.8932 (tt)
REVERT: L   74 THR cc_start: 0.7091 (m) cc_final: 0.6553 (m)
REVERT: L   79 GLN cc_start: 0.8296 (mp10) cc_final: 0.7818 (mp10)
REVERT: R  369 TYR cc_start: 0.7978 (t80) cc_final: 0.7755 (t80)
REVERT: R  387 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8498 (tt)
REVERT: R  454 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7654 (mtp-110)
REVERT: R  493 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7989 (tm-30)
  outliers start: 49
  outliers final: 12
  residues processed: 150
  average time/residue: 0.1897
  time to fit residues: 33.2701
Evaluate side-chains
  122 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 107
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  410 ILE
Chi-restraints excluded: chain R residue  422 ASN
Chi-restraints excluded: chain R residue  425 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  454 ARG
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  493 GLN
Chi-restraints excluded: chain R residue  516 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 32 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 19 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 30 optimal weight:    0.4980
   chunk 11 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
H  35 ASN
H  82 GLN
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 481 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.139977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.117041 restraints weight = 5131.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.119418 restraints weight = 3322.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.121340 restraints weight = 2527.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   3345  Z= 0.261
  Angle     :  0.817   8.195   4548  Z= 0.416
  Chirality :  0.050   0.188    487
  Planarity :  0.007   0.084    581
  Dihedral  : 17.669  92.973    544
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.20 %
    Favored  : 89.30 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 18.00 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.48 (0.36), residues: 402
  helix: -3.44 (0.77), residues: 21
  sheet: -3.11 (0.42), residues: 114
  loop : -3.03 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.027   0.002   PHE R 515 
 TYR   0.019   0.002   TYR L  49 
 ARG   0.006   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   60 TYR cc_start: 0.8419 (m-80) cc_final: 0.8073 (m-10)
REVERT: L   79 GLN cc_start: 0.8421 (mp10) cc_final: 0.7700 (mp10)
REVERT: R  387 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8393 (tt)
REVERT: R  462 LYS cc_start: 0.8530 (pptt) cc_final: 0.8100 (ptmm)
REVERT: R  493 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7731 (tm-30)
REVERT: R  516 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7474 (pp20)
  outliers start: 27
  outliers final: 19
  residues processed: 123
  average time/residue: 0.1817
  time to fit residues: 26.2461
Evaluate side-chains
  120 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 98
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   82 GLN
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  422 ASN
Chi-restraints excluded: chain R residue  425 LEU
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Chi-restraints excluded: chain R residue  493 GLN
Chi-restraints excluded: chain R residue  495 TYR
Chi-restraints excluded: chain R residue  516 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 5 optimal weight:    0.2980
   chunk 21 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0470
   chunk 14 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 13 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4878

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

Flipped N/Q/H residues before XYZ refinement:
H  82 GLN
** L  89 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 = 0.3814 r_free = 0.3814 target = 0.142991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.119362 restraints weight = 5008.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.122062 restraints weight = 3175.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123796 restraints weight = 2368.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7652
moved from start:          0.2793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3345  Z= 0.230
  Angle     :  0.751   9.809   4548  Z= 0.373
  Chirality :  0.049   0.224    487
  Planarity :  0.006   0.077    581
  Dihedral  : 14.689  79.900    538
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  : 10.95 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 19.14 %
    Favored  : 74.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.37), residues: 402
  helix: -3.75 (0.69), residues: 21
  sheet: -2.43 (0.46), residues: 114
  loop : -2.88 (0.34), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.025   0.002   PHE R 515 
 TYR   0.020   0.002   TYR H 105 
 ARG   0.004   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   31 ASP cc_start: 0.7750 (t70) cc_final: 0.7548 (m-30)
REVERT: H   60 TYR cc_start: 0.8309 (m-80) cc_final: 0.8058 (m-10)
REVERT: L   79 GLN cc_start: 0.8457 (mp10) cc_final: 0.8028 (mp10)
REVERT: L  100 GLN cc_start: 0.7351 (tm-30) cc_final: 0.7135 (tm-30)
REVERT: R  386 LYS cc_start: 0.4603 (pttt) cc_final: 0.3238 (pttt)
REVERT: R  387 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8296 (tt)
REVERT: R  462 LYS cc_start: 0.8480 (pptt) cc_final: 0.8091 (ptmm)
REVERT: R  466 ARG cc_start: 0.7439 (OUTLIER) cc_final: 0.7235 (ptm-80)
REVERT: R  493 GLN cc_start: 0.8075 (tm-30) cc_final: 0.7459 (tm-30)
  outliers start: 24
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1729
  time to fit residues: 25.8605
Evaluate side-chains
  119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 98
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  107 ASP
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  430 THR
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 8 optimal weight:    0.4980
   chunk 14 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 414 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 = 0.3792 r_free = 0.3792 target = 0.140393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.116924 restraints weight = 5090.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.119798 restraints weight = 3978.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.120645 restraints weight = 2600.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.3052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3345  Z= 0.287
  Angle     :  0.749   8.292   4548  Z= 0.378
  Chirality :  0.048   0.246    487
  Planarity :  0.006   0.085    581
  Dihedral  : 12.320  66.482    526
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.70 %
    Favored  : 89.80 %
  Rotamer:
    Outliers :  8.86 %
    Allowed  : 20.57 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.06 (0.37), residues: 402
  helix: -3.60 (0.82), residues: 19
  sheet: -2.50 (0.45), residues: 119
  loop : -2.87 (0.34), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.004   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.020   0.002   PHE R 392 
 TYR   0.023   0.002   TYR R 380 
 ARG   0.008   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: H   34 MET cc_start: 0.8891 (tpp) cc_final: 0.8628 (tpp)
REVERT: H   60 TYR cc_start: 0.8465 (m-80) cc_final: 0.8119 (m-10)
REVERT: L   62 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7070 (p90)
REVERT: L   79 GLN cc_start: 0.8452 (mp10) cc_final: 0.8034 (mp10)
REVERT: L  100 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7182 (tm-30)
REVERT: R  386 LYS cc_start: 0.4437 (pttt) cc_final: 0.3192 (pttt)
REVERT: R  387 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: R  409 GLN cc_start: 0.8339 (mt0) cc_final: 0.7897 (mt0)
REVERT: R  466 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6277 (ptp-110)
REVERT: R  493 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7485 (tm-30)
  outliers start: 31
  outliers final: 20
  residues processed: 114
  average time/residue: 0.1810
  time to fit residues: 24.2947
Evaluate side-chains
  113 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 90
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  443 SER
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 7 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 450 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.142377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.119063 restraints weight = 5097.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122579 restraints weight = 4067.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.123258 restraints weight = 2516.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.3343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3345  Z= 0.238
  Angle     :  0.719   8.785   4548  Z= 0.362
  Chirality :  0.047   0.201    487
  Planarity :  0.006   0.080    581
  Dihedral  : 10.274  50.287    525
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 10.20 %
    Favored  : 89.55 %
  Rotamer:
    Outliers :  8.29 %
    Allowed  : 22.29 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.37), residues: 402
  helix: -3.65 (0.82), residues: 19
  sheet: -2.54 (0.44), residues: 122
  loop : -2.77 (0.34), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.003   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.013   0.001   PHE R 515 
 TYR   0.023   0.002   TYR R 380 
 ARG   0.005   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.401 
Fit side-chains
REVERT: H   43 GLN cc_start: 0.7103 (mp10) cc_final: 0.6684 (mp10)
REVERT: H   60 TYR cc_start: 0.8419 (m-80) cc_final: 0.8170 (m-10)
REVERT: H  102 TRP cc_start: 0.7887 (t-100) cc_final: 0.7623 (t-100)
REVERT: L   62 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7072 (p90)
REVERT: L   79 GLN cc_start: 0.8476 (mp10) cc_final: 0.7993 (mp10)
REVERT: L  100 GLN cc_start: 0.7434 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: R  386 LYS cc_start: 0.4318 (pttt) cc_final: 0.3127 (pttt)
REVERT: R  387 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8319 (tt)
REVERT: R  408 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.8064 (ptm160)
REVERT: R  493 GLN cc_start: 0.8092 (tm-30) cc_final: 0.7457 (tm-30)
  outliers start: 29
  outliers final: 22
  residues processed: 117
  average time/residue: 0.1850
  time to fit residues: 25.5517
Evaluate side-chains
  118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   82 GLN
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Chi-restraints excluded: chain R residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 25 optimal weight:    0.0170
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 10 optimal weight:    0.2980
   chunk 17 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
H  82 GLN
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 422 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.143168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.119603 restraints weight = 5137.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.122988 restraints weight = 3636.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.123803 restraints weight = 2388.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.3612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3345  Z= 0.218
  Angle     :  0.740  11.593   4548  Z= 0.366
  Chirality :  0.047   0.198    487
  Planarity :  0.006   0.078    581
  Dihedral  :  9.432  52.093    523
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.71 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  8.29 %
    Allowed  : 22.29 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.88 (0.37), residues: 402
  helix: -3.28 (0.92), residues: 19
  sheet: -2.40 (0.48), residues: 108
  loop : -2.76 (0.33), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.011   0.001   PHE R 515 
 TYR   0.021   0.002   TYR H  80 
 ARG   0.005   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 GLN cc_start: 0.7082 (mp10) cc_final: 0.6588 (mp10)
REVERT: H   60 TYR cc_start: 0.8374 (m-80) cc_final: 0.8105 (m-10)
REVERT: H  102 TRP cc_start: 0.7766 (t-100) cc_final: 0.7350 (t-100)
REVERT: H  109 TRP cc_start: 0.7441 (OUTLIER) cc_final: 0.7123 (p90)
REVERT: L   62 PHE cc_start: 0.7934 (OUTLIER) cc_final: 0.7056 (p90)
REVERT: L   79 GLN cc_start: 0.8491 (mp10) cc_final: 0.7995 (mp10)
REVERT: L  100 GLN cc_start: 0.7408 (tm-30) cc_final: 0.7206 (tm-30)
REVERT: R  386 LYS cc_start: 0.4189 (pttt) cc_final: 0.3014 (pttt)
REVERT: R  387 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8235 (tt)
REVERT: R  408 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8313 (ptm160)
REVERT: R  418 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: R  453 TYR cc_start: 0.8659 (p90) cc_final: 0.8275 (p90)
REVERT: R  454 ARG cc_start: 0.7879 (mtp180) cc_final: 0.7441 (mtp85)
REVERT: R  467 ASP cc_start: 0.6869 (p0) cc_final: 0.6261 (p0)
REVERT: R  493 GLN cc_start: 0.8116 (tm-30) cc_final: 0.7554 (tm-30)
  outliers start: 29
  outliers final: 19
  residues processed: 115
  average time/residue: 0.1920
  time to fit residues: 26.0416
Evaluate side-chains
  118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  108 VAL
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  418 ILE
Chi-restraints excluded: chain R residue  434 ILE
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 38 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 18 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6038

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 409 GLN
** R 414 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 = 0.3810 r_free = 0.3810 target = 0.142074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118203 restraints weight = 5042.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.121765 restraints weight = 4109.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.122417 restraints weight = 2545.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3575
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.3758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   3345  Z= 0.247
  Angle     :  0.737  10.504   4548  Z= 0.368
  Chirality :  0.047   0.160    487
  Planarity :  0.006   0.079    581
  Dihedral  :  8.962  53.940    523
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 17.51
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.96 %
    Favored  : 90.80 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 21.71 %
    Favored  : 70.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.86 (0.38), residues: 402
  helix: -3.25 (0.98), residues: 19
  sheet: -2.71 (0.41), residues: 130
  loop : -2.51 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.003   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.010   0.001   PHE R 515 
 TYR   0.022   0.002   TYR H 105 
 ARG   0.003   0.001   ARG R 403 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 GLN cc_start: 0.7201 (mp10) cc_final: 0.6669 (mp10)
REVERT: H   60 TYR cc_start: 0.8398 (m-80) cc_final: 0.7963 (m-10)
REVERT: H   69 VAL cc_start: 0.8389 (t) cc_final: 0.8015 (t)
REVERT: H  102 TRP cc_start: 0.7750 (t-100) cc_final: 0.7493 (t-100)
REVERT: H  109 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.7217 (p90)
REVERT: L   62 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7131 (p90)
REVERT: L   79 GLN cc_start: 0.8553 (mp10) cc_final: 0.8005 (mp10)
REVERT: L  100 GLN cc_start: 0.7426 (tm-30) cc_final: 0.7215 (tm-30)
REVERT: R  386 LYS cc_start: 0.4226 (pttt) cc_final: 0.3020 (pttt)
REVERT: R  387 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8179 (tt)
REVERT: R  408 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.8282 (ptm160)
REVERT: R  453 TYR cc_start: 0.8717 (p90) cc_final: 0.8355 (p90)
REVERT: R  454 ARG cc_start: 0.7766 (mtp180) cc_final: 0.7505 (mtp85)
REVERT: R  493 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7710 (tm-30)
  outliers start: 27
  outliers final: 18
  residues processed: 114
  average time/residue: 0.1905
  time to fit residues: 25.4650
Evaluate side-chains
  118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  345 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  455 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0770
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.3542

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

Flipped N/Q/H residues before XYZ refinement:
** L  34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 437 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.137682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.114814 restraints weight = 5061.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.117990 restraints weight = 4260.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.118623 restraints weight = 2686.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.3503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.3698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   3345  Z= 0.418
  Angle     :  0.825  10.310   4548  Z= 0.418
  Chirality :  0.052   0.212    487
  Planarity :  0.006   0.078    581
  Dihedral  :  8.979  59.811    521
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 20.19
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  : 11.19 %
    Favored  : 88.56 %
  Rotamer:
    Outliers :  7.71 %
    Allowed  : 22.57 %
    Favored  : 69.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.00 (0.37), residues: 402
  helix: -3.08 (1.02), residues: 19
  sheet: -2.83 (0.42), residues: 124
  loop : -2.64 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.065   0.004   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.012   0.002   PHE R 515 
 TYR   0.027   0.003   TYR L  49 
 ARG   0.005   0.001   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
REVERT: H   43 GLN cc_start: 0.7211 (mp10) cc_final: 0.6763 (mp10)
REVERT: H   60 TYR cc_start: 0.8531 (m-80) cc_final: 0.8089 (m-10)
REVERT: H   69 VAL cc_start: 0.8464 (t) cc_final: 0.8039 (t)
REVERT: H  109 TRP cc_start: 0.7643 (OUTLIER) cc_final: 0.7074 (p90)
REVERT: L   62 PHE cc_start: 0.8059 (OUTLIER) cc_final: 0.7447 (p90)
REVERT: L   79 GLN cc_start: 0.8647 (mp10) cc_final: 0.8055 (mp10)
REVERT: L  100 GLN cc_start: 0.7435 (tm-30) cc_final: 0.7122 (tm-30)
REVERT: R  386 LYS cc_start: 0.4586 (pttt) cc_final: 0.3245 (pttt)
REVERT: R  387 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8386 (tt)
REVERT: R  408 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8180 (ptm160)
REVERT: R  453 TYR cc_start: 0.8740 (p90) cc_final: 0.8455 (p90)
REVERT: R  454 ARG cc_start: 0.7847 (mtp180) cc_final: 0.7428 (mtp180)
REVERT: R  493 GLN cc_start: 0.8046 (tm-30) cc_final: 0.7372 (tm-30)
  outliers start: 27
  outliers final: 21
  residues processed: 108
  average time/residue: 0.1907
  time to fit residues: 24.2768
Evaluate side-chains
  116 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   74 THR
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  436 TRP
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  452 LEU
Chi-restraints excluded: chain R residue  455 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 19 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0870
   chunk 3 optimal weight:    0.6980
   chunk 15 optimal weight:    0.5980
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** R 414 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 = 0.3923 r_free = 0.3923 target = 0.149417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.125032 restraints weight = 4963.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.127625 restraints weight = 3414.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.129358 restraints weight = 2650.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.3966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3345  Z= 0.235
  Angle     :  0.773  10.018   4548  Z= 0.389
  Chirality :  0.048   0.204    487
  Planarity :  0.006   0.080    581
  Dihedral  :  8.649  57.555    521
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.70 %
    Favored  : 90.05 %
  Rotamer:
    Outliers :  6.86 %
    Allowed  : 23.71 %
    Favored  : 69.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.76 (0.38), residues: 402
  helix: -3.33 (0.91), residues: 19
  sheet: -2.57 (0.42), residues: 122
  loop : -2.50 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.004   TRP H 109 
 HIS   0.001   0.001   HIS L  34 
 PHE   0.011   0.002   PHE H 106 
 TYR   0.024   0.002   TYR H 105 
 ARG   0.007   0.001   ARG H  65 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    2 VAL cc_start: 0.7568 (m) cc_final: 0.7341 (m)
REVERT: H   60 TYR cc_start: 0.8234 (m-80) cc_final: 0.7920 (m-10)
REVERT: H  109 TRP cc_start: 0.7081 (OUTLIER) cc_final: 0.6824 (p90)
REVERT: L   62 PHE cc_start: 0.7958 (OUTLIER) cc_final: 0.7217 (p90)
REVERT: L   79 GLN cc_start: 0.8553 (mp10) cc_final: 0.8049 (mp10)
REVERT: L  100 GLN cc_start: 0.7418 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: R  386 LYS cc_start: 0.4386 (pttt) cc_final: 0.3074 (pttt)
REVERT: R  387 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8191 (tt)
REVERT: R  408 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8221 (ptm-80)
REVERT: R  418 ILE cc_start: 0.8546 (tp) cc_final: 0.7849 (tp)
REVERT: R  453 TYR cc_start: 0.8687 (p90) cc_final: 0.8402 (p90)
REVERT: R  466 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6769 (mtm110)
REVERT: R  493 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7384 (tm-30)
  outliers start: 24
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1829
  time to fit residues: 23.0143
Evaluate side-chains
  114 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  109 TRP
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  466 ARG
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 5 optimal weight:    0.1980
   chunk 15 optimal weight:    0.0980
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 18 optimal weight:    0.7980
   chunk 8 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 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 = 0.3930 r_free = 0.3930 target = 0.150103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.126127 restraints weight = 4915.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.128704 restraints weight = 3370.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.130417 restraints weight = 2622.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.4058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3345  Z= 0.240
  Angle     :  0.751   9.797   4548  Z= 0.381
  Chirality :  0.048   0.202    487
  Planarity :  0.006   0.080    581
  Dihedral  :  8.255  50.879    521
  Min Nonbonded Distance : 2.316

Molprobity Statistics.
  All-atom Clashscore : 17.35
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.45 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  6.00 %
    Allowed  : 24.86 %
    Favored  : 69.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.62 (0.37), residues: 402
  helix: -3.61 (0.85), residues: 18
  sheet: -2.52 (0.44), residues: 116
  loop : -2.37 (0.34), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.009   0.001   PHE L  83 
 TYR   0.024   0.002   TYR H 105 
 ARG   0.004   0.000   ARG L  18 

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

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

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  804 Ramachandran restraints generated.
    402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
REVERT: H   25 SER cc_start: 0.7630 (t) cc_final: 0.7236 (m)
REVERT: H   60 TYR cc_start: 0.8241 (m-80) cc_final: 0.8031 (m-10)
REVERT: H   69 VAL cc_start: 0.8347 (t) cc_final: 0.7980 (t)
REVERT: L   62 PHE cc_start: 0.8002 (OUTLIER) cc_final: 0.7254 (p90)
REVERT: L   79 GLN cc_start: 0.8522 (mp10) cc_final: 0.8025 (mp10)
REVERT: R  386 LYS cc_start: 0.4512 (pttt) cc_final: 0.3135 (pttt)
REVERT: R  387 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8141 (tt)
REVERT: R  408 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.8020 (ptm-80)
REVERT: R  453 TYR cc_start: 0.8726 (p90) cc_final: 0.8505 (p90)
REVERT: R  454 ARG cc_start: 0.7603 (mtp180) cc_final: 0.7392 (mtp85)
REVERT: R  493 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7444 (tm-30)
  outliers start: 21
  outliers final: 16
  residues processed: 109
  average time/residue: 0.1702
  time to fit residues: 22.0417
Evaluate side-chains
  112 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   18 VAL
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   83 ILE
Chi-restraints excluded: chain H residue  114 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   21 ILE
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   62 PHE
Chi-restraints excluded: chain L residue   73 LEU
Chi-restraints excluded: chain L residue   97 THR
Chi-restraints excluded: chain R residue  387 LEU
Chi-restraints excluded: chain R residue  398 ASP
Chi-restraints excluded: chain R residue  407 VAL
Chi-restraints excluded: chain R residue  408 ARG
Chi-restraints excluded: chain R residue  441 LEU
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 39
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 32 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    0.2980
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0370
   overall best weight:    0.4458

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

Flipped N/Q/H residues before XYZ refinement:
** L  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
R 474 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.151278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.127509 restraints weight = 4893.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.130114 restraints weight = 3345.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.131862 restraints weight = 2591.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3345  Z= 0.230
  Angle     :  0.765   9.495   4548  Z= 0.389
  Chirality :  0.048   0.193    487
  Planarity :  0.006   0.079    581
  Dihedral  :  7.798  51.360    517
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 16.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.71 %
    Favored  : 91.29 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 25.43 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.57 (0.38), residues: 402
  helix: -3.70 (0.79), residues: 18
  sheet: -2.42 (0.43), residues: 122
  loop : -2.34 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.070   0.004   TRP H 109 
 HIS   0.002   0.001   HIS L  34 
 PHE   0.027   0.002   PHE H 106 
 TYR   0.026   0.002   TYR H 105 
 ARG   0.005   0.001   ARG L  18 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1732.76 seconds
wall clock time: 31 minutes 37.14 seconds (1897.14 seconds total)