Starting phenix.real_space_refine
on Wed Mar  5 20:03:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wsc_32753/03_2025/7wsc_32753.cif"
  }
  resolution = 3.78
  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=   0.019
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    2156      2.51       5
     N     563      2.21       5
     O     635      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-5624/modules/chem_data/mon_lib"
  Total number of atoms: 3369
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "R"
      Number of atoms: 1504
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1504
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 1024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1024
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 2, 'TRANS': 124}
    Chain: "L"
      Number of atoms: 813
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 813
          Classifications: {'peptide': 108}
          Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.49, per 1000 atoms: 1.04
  Number of scatterers: 3369
  At special positions: 0
  Unit cell: (63.13, 87.74, 74.9, 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     635      8.00
     N     563      7.00
     C    2156      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.02
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.01
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  42 " - pdb=" SG  CYS L 112 " 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
    BETA1-4
      " NAG A   1 " - " NAG A   2 "
    NAG-ASN
      " NAG A   1 " - " ASN R 343 "
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 365.9 milliseconds
  

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  766

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 6 sheets defined
      9.2% alpha, 21.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'R' and resid 338 through 344
    Processing helix  chain 'R' and resid 364 through 369
      removed outlier: 3.593A  pdb=" N   TYR R 369 " --> pdb=" O   SER R 366 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 388
      removed outlier: 4.117A  pdb=" N   ASN R 388 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 405 through 407
      No H-bonds generated for 'chain 'R' and resid 405 through 407'
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'H' and resid 106 through 110
      removed outlier: 3.870A  pdb=" N   ASP H 109 " --> pdb=" O   ARG H 106 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   THR H 110 " --> pdb=" O   VAL H 107 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 106 through 110'
    Processing helix  chain 'L' and resid 103 through 107
    Processing sheet with id=AA1, first strand: chain 'R' and resid 354 through 358
      removed outlier: 3.915A  pdb=" N   ASN R 354 " --> pdb=" O   SER R 399 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER R 399 " --> pdb=" O   ASN R 354 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   LYS R 356 " --> pdb=" O   ALA R 397 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA R 397 " --> pdb=" O   LYS R 356 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   VAL R 512 " --> pdb=" O   ASP R 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'R' and resid 452 through 453
    Processing sheet with id=AA3, first strand: chain 'H' and resid 22 through 26
      removed outlier: 3.861A  pdb=" N   LEU H  37 " --> pdb=" O   MET H 102 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 65 through 70
      removed outlier: 6.433A  pdb=" N   TRP H  55 " --> pdb=" O   VAL H  67 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   LEU H  69 " --> pdb=" O   ILE H  53 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE H  53 " --> pdb=" O   LEU H  69 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL H 112 " --> pdb=" O   GLN H  58 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   VAL H 144 " --> pdb=" O   ALA H 111 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 24 through 26
      removed outlier: 3.736A  pdb=" N   THR L  24 " --> pdb=" O   ARG L  43 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 69 through 70
      removed outlier: 3.554A  pdb=" N   ILE L 109 " --> pdb=" O   GLN L  62 " (cutoff:3.500A)

    74 hydrogen bonds defined for protein.
    183 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: 0.77

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 532
        1.26 -     1.40: 979
        1.40 -     1.54: 1912
        1.54 -     1.68: 17
        1.68 -     1.82: 18
  Bond restraints: 3458
  Sorted by residual:
  bond pdb=" CA  TYR R 380 "
       pdb=" C   TYR R 380 "
    ideal  model  delta    sigma   weight residual
    1.524  1.395  0.129 1.35e-02 5.49e+03 9.08e+01
  bond pdb=" C   PHE R 377 "
       pdb=" O   PHE R 377 "
    ideal  model  delta    sigma   weight residual
    1.235  1.116  0.120 1.26e-02 6.30e+03 9.01e+01
  bond pdb=" C   VAL R 382 "
       pdb=" O   VAL R 382 "
    ideal  model  delta    sigma   weight residual
    1.236  1.153  0.083 1.03e-02 9.43e+03 6.47e+01
  bond pdb=" CB  TYR R 380 "
       pdb=" CG  TYR R 380 "
    ideal  model  delta    sigma   weight residual
    1.512  1.341  0.171 2.20e-02 2.07e+03 6.07e+01
  bond pdb=" CA  ALA R 475 "
       pdb=" C   ALA R 475 "
    ideal  model  delta    sigma   weight residual
    1.523  1.436  0.088 1.25e-02 6.40e+03 4.91e+01
  ... (remaining 3453 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.03: 4634
        6.03 -    12.06: 48
       12.06 -    18.09: 10
       18.09 -    24.12: 1
       24.12 -    30.15: 2
  Bond angle restraints: 4695
  Sorted by residual:
  angle pdb=" N   GLY R 482 "
        pdb=" CA  GLY R 482 "
        pdb=" C   GLY R 482 "
      ideal   model   delta    sigma   weight residual
     113.18   85.51   27.67 2.37e+00 1.78e-01 1.36e+02
  angle pdb=" C   PHE R 490 "
        pdb=" N   PRO R 491 "
        pdb=" CA  PRO R 491 "
      ideal   model   delta    sigma   weight residual
     119.84  132.96  -13.12 1.25e+00 6.40e-01 1.10e+02
  angle pdb=" N   PHE R 486 "
        pdb=" CA  PHE R 486 "
        pdb=" C   PHE R 486 "
      ideal   model   delta    sigma   weight residual
     111.04   95.20   15.84 1.55e+00 4.16e-01 1.04e+02
  angle pdb=" N   ALA R 475 "
        pdb=" CA  ALA R 475 "
        pdb=" C   ALA R 475 "
      ideal   model   delta    sigma   weight residual
     107.98   89.55   18.43 1.88e+00 2.83e-01 9.61e+01
  angle pdb=" CA  PRO L  37 "
        pdb=" N   PRO L  37 "
        pdb=" CD  PRO L  37 "
      ideal   model   delta    sigma   weight residual
     112.00   98.55   13.45 1.40e+00 5.10e-01 9.23e+01
  ... (remaining 4690 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.87: 1778
       15.87 -    31.73: 183
       31.73 -    47.60: 60
       47.60 -    63.46: 15
       63.46 -    79.32: 8
  Dihedral angle restraints: 2044
    sinusoidal: 827
      harmonic: 1217
  Sorted by residual:
  dihedral pdb=" CB  CYS R 391 "
           pdb=" SG  CYS R 391 "
           pdb=" SG  CYS R 525 "
           pdb=" CB  CYS R 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -6.68  -79.32     1      1.00e+01 1.00e-02 7.82e+01
  dihedral pdb=" N   CYS R 488 "
           pdb=" C   CYS R 488 "
           pdb=" CA  CYS R 488 "
           pdb=" CB  CYS R 488 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  106.51   16.29     0      2.50e+00 1.60e-01 4.25e+01
  dihedral pdb=" CA  ARG H  71 "
           pdb=" C   ARG H  71 "
           pdb=" N   TYR H  72 "
           pdb=" CA  TYR H  72 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.47   29.53     0      5.00e+00 4.00e-02 3.49e+01
  ... (remaining 2041 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.158: 476
       0.158 -    0.317: 11
       0.317 -    0.475: 6
       0.475 -    0.633: 4
       0.633 -    0.791: 2
  Chirality restraints: 499
  Sorted by residual:
  chirality pdb=" CA  CYS R 379 "
            pdb=" N   CYS R 379 "
            pdb=" C   CYS R 379 "
            pdb=" CB  CYS R 379 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.72    0.79 2.00e-01 2.50e+01 1.57e+01
  chirality pdb=" CA  ASN R 477 "
            pdb=" N   ASN R 477 "
            pdb=" C   ASN R 477 "
            pdb=" CB  ASN R 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.85    0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" CB  VAL R 483 "
            pdb=" CA  VAL R 483 "
            pdb=" CG1 VAL R 483 "
            pdb=" CG2 VAL R 483 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.06   -0.57 2.00e-01 2.50e+01 8.19e+00
  ... (remaining 496 not shown)

  Planarity restraints: 605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R 490 "   -0.119 5.00e-02 4.00e+02   1.69e-01 4.60e+01
        pdb=" N   PRO R 491 "    0.291 5.00e-02 4.00e+02
        pdb=" CA  PRO R 491 "   -0.111 5.00e-02 4.00e+02
        pdb=" CD  PRO R 491 "   -0.061 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU R 368 "   -0.032 2.00e-02 2.50e+03   6.42e-02 4.12e+01
        pdb=" C   LEU R 368 "    0.111 2.00e-02 2.50e+03
        pdb=" O   LEU R 368 "   -0.042 2.00e-02 2.50e+03
        pdb=" N   TYR R 369 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN R 477 "    0.032 2.00e-02 2.50e+03   6.34e-02 4.02e+01
        pdb=" C   ASN R 477 "   -0.110 2.00e-02 2.50e+03
        pdb=" O   ASN R 477 "    0.043 2.00e-02 2.50e+03
        pdb=" N   LYS R 478 "    0.035 2.00e-02 2.50e+03
  ... (remaining 602 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 9
        2.26 -     2.92: 1670
        2.92 -     3.58: 4936
        3.58 -     4.24: 7946
        4.24 -     4.90: 13267
  Nonbonded interactions: 27828
  Sorted by model distance:
  nonbonded pdb=" O   TYR R 473 "
            pdb=" O   CYS R 488 "
     model   vdw
     1.600 3.040
  nonbonded pdb=" OG1 THR L  33 "
            pdb=" OE2 GLU L  36 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" O   ASN R 477 "
            pdb=" ND2 ASN R 477 "
     model   vdw
     2.084 3.120
  nonbonded pdb=" OG  SER H  36 "
            pdb=" O   MET H 102 "
     model   vdw
     2.088 3.040
  nonbonded pdb=" OD1 ASP H  73 "
            pdb=" OG  SER H  75 "
     model   vdw
     2.118 3.040
  ... (remaining 27823 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:             4.290
  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:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.560
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.013   0.171   3458  Z= 0.821
  Angle     :  1.667  30.153   4695  Z= 0.880
  Chirality :  0.101   0.791    499
  Planarity :  0.012   0.169    604
  Dihedral  : 15.341  79.299   1263
  Min Nonbonded Distance : 1.600

Molprobity Statistics.
  All-atom Clashscore : 41.09
  Ramachandran Plot:
    Outliers :  3.62 %
    Allowed  : 14.73 %
    Favored  : 81.64 %
  Rotamer:
    Outliers :  4.99 %
    Allowed  :  1.94 %
    Favored  : 93.07 %
  Cbeta Deviations :  1.31 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.09 (0.39), residues: 414
  helix: -5.03 (0.30), residues: 12
  sheet: -2.57 (0.41), residues: 129
  loop : -2.82 (0.37), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP L  59 
 HIS   0.015   0.005   HIS H  54 
 PHE   0.056   0.004   PHE R 490 
 TYR   0.023   0.002   TYR H  51 
 ARG   0.039   0.002   ARG R 493 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.398 
Fit side-chains
REVERT: R  377 PHE cc_start: 0.8354 (OUTLIER) cc_final: 0.7889 (m-80)
REVERT: R  423 TYR cc_start: 0.7992 (t80) cc_final: 0.7695 (t80)
REVERT: R  455 LEU cc_start: 0.7505 (pt) cc_final: 0.7293 (pt)
REVERT: R  486 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6242 (t80)
REVERT: L   32 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7557 (p)
REVERT: L   50 GLN cc_start: 0.7708 (tm-30) cc_final: 0.7213 (tm-30)
REVERT: L  111 TYR cc_start: 0.8367 (m-80) cc_final: 0.7826 (m-80)
  outliers start: 18
  outliers final: 9
  residues processed: 131
  average time/residue: 0.1596
  time to fit residues: 25.3612
Evaluate side-chains
  103 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  474 GLN
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  480 CYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  486 PHE
Chi-restraints excluded: chain R residue  487 ASN
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  493 ARG
Chi-restraints excluded: chain L residue   32 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 11 optimal weight:    6.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
R 474 GLN
** H  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 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 = 0.3843 r_free = 0.3843 target = 0.139927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.115312 restraints weight = 5825.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.119304 restraints weight = 3388.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.122043 restraints weight = 2336.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7838
moved from start:          0.2022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.105   3458  Z= 0.423
  Angle     :  0.991  13.883   4695  Z= 0.492
  Chirality :  0.056   0.373    499
  Planarity :  0.010   0.149    604
  Dihedral  : 10.162  86.175    542
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 24.72
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  : 12.80 %
    Favored  : 86.47 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 14.40 %
    Favored  : 79.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.66 (0.39), residues: 414
  helix: -3.30 (1.06), residues: 12
  sheet: -2.49 (0.40), residues: 128
  loop : -2.46 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP L  59 
 HIS   0.009   0.003   HIS H  54 
 PHE   0.025   0.003   PHE R 486 
 TYR   0.023   0.002   TYR H  51 
 ARG   0.009   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  374 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6056 (p90)
REVERT: R  377 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7777 (m-80)
REVERT: R  423 TYR cc_start: 0.8188 (t80) cc_final: 0.7878 (t80)
REVERT: R  472 ILE cc_start: 0.3328 (OUTLIER) cc_final: 0.3094 (mm)
REVERT: L   26 SER cc_start: 0.6961 (OUTLIER) cc_final: 0.6670 (p)
REVERT: L   28 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7214 (tt)
REVERT: L   50 GLN cc_start: 0.7883 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: L  111 TYR cc_start: 0.8453 (m-80) cc_final: 0.7703 (m-80)
  outliers start: 23
  outliers final: 14
  residues processed: 116
  average time/residue: 0.1495
  time to fit residues: 21.2435
Evaluate side-chains
  116 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  358 ILE
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  472 ILE
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  480 CYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  488 CYS
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  493 ARG
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   28 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 32 optimal weight:    0.8980
   chunk 37 optimal weight:    0.9990
   chunk 14 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** H  32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  25 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 = 0.3874 r_free = 0.3874 target = 0.141744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.117544 restraints weight = 5680.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121628 restraints weight = 3295.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124518 restraints weight = 2268.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093   3458  Z= 0.303
  Angle     :  0.859  13.533   4695  Z= 0.430
  Chirality :  0.051   0.182    499
  Planarity :  0.008   0.139    604
  Dihedral  :  8.346  58.764    534
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 19.86
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.63 %
    Favored  : 88.89 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 17.73 %
    Favored  : 75.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.31 (0.40), residues: 414
  helix: -3.32 (0.99), residues: 12
  sheet: -2.48 (0.41), residues: 130
  loop : -2.06 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP L  59 
 HIS   0.005   0.002   HIS H  54 
 PHE   0.014   0.002   PHE H  48 
 TYR   0.019   0.002   TYR H  51 
 ARG   0.006   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  377 PHE cc_start: 0.8256 (OUTLIER) cc_final: 0.7599 (m-80)
REVERT: R  423 TYR cc_start: 0.8095 (t80) cc_final: 0.7737 (t80)
REVERT: H   72 TYR cc_start: 0.7100 (p90) cc_final: 0.6651 (p90)
REVERT: H  134 TYR cc_start: 0.8738 (p90) cc_final: 0.8043 (p90)
REVERT: L   28 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7171 (tt)
REVERT: L   42 CYS cc_start: 0.6196 (m) cc_final: 0.5933 (m)
REVERT: L   50 GLN cc_start: 0.8073 (tm-30) cc_final: 0.7325 (tm-30)
REVERT: L   52 ASN cc_start: 0.8552 (p0) cc_final: 0.8077 (p0)
REVERT: L   62 GLN cc_start: 0.8751 (pt0) cc_final: 0.8518 (pt0)
REVERT: L   74 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8413 (tt)
REVERT: L  111 TYR cc_start: 0.8253 (m-80) cc_final: 0.7665 (m-80)
  outliers start: 24
  outliers final: 14
  residues processed: 124
  average time/residue: 0.1375
  time to fit residues: 20.9729
Evaluate side-chains
  118 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 101
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   28 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 24 optimal weight:    0.4980
   chunk 14 optimal weight:    8.9990
   chunk 31 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
H  32 GLN
L  25 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.141758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.117400 restraints weight = 5818.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.121593 restraints weight = 3307.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.124428 restraints weight = 2241.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3640
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.087   3458  Z= 0.318
  Angle     :  0.830  13.845   4695  Z= 0.412
  Chirality :  0.049   0.168    499
  Planarity :  0.007   0.133    604
  Dihedral  :  7.811  55.244    527
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 17.89
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.35 %
    Favored  : 88.16 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 20.22 %
    Favored  : 72.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.41), residues: 414
  helix: -3.32 (1.00), residues: 12
  sheet: -2.45 (0.41), residues: 130
  loop : -1.88 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP L  59 
 HIS   0.002   0.001   HIS H  54 
 PHE   0.012   0.002   PHE H  48 
 TYR   0.013   0.001   TYR H  51 
 ARG   0.005   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  377 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7588 (m-80)
REVERT: R  423 TYR cc_start: 0.8112 (t80) cc_final: 0.7797 (t80)
REVERT: H   72 TYR cc_start: 0.7124 (p90) cc_final: 0.6645 (p90)
REVERT: L   28 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7413 (tt)
REVERT: L   62 GLN cc_start: 0.8705 (pt0) cc_final: 0.8013 (pt0)
REVERT: L   74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8450 (tt)
REVERT: L  111 TYR cc_start: 0.8278 (m-80) cc_final: 0.7709 (m-80)
  outliers start: 25
  outliers final: 18
  residues processed: 119
  average time/residue: 0.1379
  time to fit residues: 20.5777
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 96
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   28 LEU
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 30 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0770
   chunk 4 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
R 450 ASN
H 103 ASN
** H 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.143403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.119448 restraints weight = 5757.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.123704 restraints weight = 3251.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.126658 restraints weight = 2190.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.083   3458  Z= 0.269
  Angle     :  0.811  13.841   4695  Z= 0.400
  Chirality :  0.047   0.167    499
  Planarity :  0.007   0.128    604
  Dihedral  :  7.479  50.893    527
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 17.29
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.14 %
    Favored  : 89.37 %
  Rotamer:
    Outliers :  6.37 %
    Allowed  : 22.44 %
    Favored  : 71.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.98 (0.42), residues: 414
  helix: -3.12 (1.04), residues: 12
  sheet: -2.39 (0.43), residues: 131
  loop : -1.73 (0.40), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP L  59 
 HIS   0.003   0.001   HIS H  54 
 PHE   0.014   0.002   PHE H 133 
 TYR   0.020   0.002   TYR L  56 
 ARG   0.006   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 104
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.8019 (t80) cc_final: 0.7714 (t80)
REVERT: R  489 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6954 (t80)
REVERT: H   32 GLN cc_start: 0.7179 (tp-100) cc_final: 0.6943 (mm-40)
REVERT: H   71 ARG cc_start: 0.7526 (mtt90) cc_final: 0.7172 (mtt90)
REVERT: H   72 TYR cc_start: 0.7153 (p90) cc_final: 0.6648 (p90)
REVERT: H  123 TYR cc_start: 0.8673 (p90) cc_final: 0.8355 (p90)
REVERT: L   50 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7529 (tm-30)
REVERT: L   62 GLN cc_start: 0.8606 (pt0) cc_final: 0.7991 (pt0)
REVERT: L   74 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8413 (tt)
REVERT: L  111 TYR cc_start: 0.8273 (m-80) cc_final: 0.7699 (m-80)
  outliers start: 23
  outliers final: 17
  residues processed: 113
  average time/residue: 0.1512
  time to fit residues: 20.8104
Evaluate side-chains
  117 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   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  62 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 = 0.3903 r_free = 0.3903 target = 0.144109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.119437 restraints weight = 5883.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123767 restraints weight = 3339.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126731 restraints weight = 2257.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   3458  Z= 0.304
  Angle     :  0.813  13.993   4695  Z= 0.400
  Chirality :  0.047   0.152    499
  Planarity :  0.007   0.124    604
  Dihedral  :  7.070  48.744    525
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.87 %
    Favored  : 88.65 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 23.55 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.41), residues: 414
  helix: -3.68 (0.70), residues: 18
  sheet: -2.20 (0.44), residues: 124
  loop : -1.73 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP L  59 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.012   0.002   PHE H  87 
 TYR   0.018   0.001   TYR L  73 
 ARG   0.006   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.7998 (t80) cc_final: 0.7734 (t80)
REVERT: R  489 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.7109 (t80)
REVERT: H   72 TYR cc_start: 0.7216 (p90) cc_final: 0.6762 (p90)
REVERT: H  123 TYR cc_start: 0.8649 (p90) cc_final: 0.8311 (p90)
REVERT: L   50 GLN cc_start: 0.8107 (tm-30) cc_final: 0.7587 (tm-30)
REVERT: L   62 GLN cc_start: 0.8582 (pt0) cc_final: 0.8023 (pt0)
REVERT: L   74 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8506 (tt)
REVERT: L   78 ARG cc_start: 0.8408 (ptp90) cc_final: 0.8202 (ptp-170)
REVERT: L  111 TYR cc_start: 0.8262 (m-80) cc_final: 0.7699 (m-80)
  outliers start: 26
  outliers final: 22
  residues processed: 113
  average time/residue: 0.1435
  time to fit residues: 19.9277
Evaluate side-chains
  119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 95
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  118 GLU
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** L  62 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 = 0.3886 r_free = 0.3886 target = 0.142311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.117962 restraints weight = 5822.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.122174 restraints weight = 3341.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125153 restraints weight = 2268.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.3581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075   3458  Z= 0.305
  Angle     :  0.811  13.991   4695  Z= 0.400
  Chirality :  0.047   0.156    499
  Planarity :  0.007   0.121    604
  Dihedral  :  6.996  48.168    525
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.90 %
    Favored  : 89.61 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 24.38 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.41), residues: 414
  helix: -3.76 (0.67), residues: 18
  sheet: -2.17 (0.45), residues: 123
  loop : -1.71 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP L  59 
 HIS   0.001   0.001   HIS H  54 
 PHE   0.011   0.002   PHE H  87 
 TYR   0.019   0.001   TYR L  73 
 ARG   0.007   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 96
  time to evaluate  : 0.455 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.8039 (t80) cc_final: 0.7776 (t80)
REVERT: R  489 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.7114 (t80)
REVERT: H   72 TYR cc_start: 0.7294 (p90) cc_final: 0.6783 (p90)
REVERT: H  123 TYR cc_start: 0.8627 (p90) cc_final: 0.8352 (p90)
REVERT: L   50 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: L   62 GLN cc_start: 0.8582 (pt0) cc_final: 0.8092 (pt0)
REVERT: L   74 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8520 (tt)
REVERT: L  111 TYR cc_start: 0.8306 (m-80) cc_final: 0.7726 (m-80)
  outliers start: 27
  outliers final: 23
  residues processed: 107
  average time/residue: 0.1379
  time to fit residues: 18.3742
Evaluate side-chains
  113 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain R residue  524 VAL
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   89 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  118 GLU
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   26 SER
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  109 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 13 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0570
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5100

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

Flipped N/Q/H residues before XYZ refinement:
** L  62 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 = 0.3911 r_free = 0.3911 target = 0.144184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.120467 restraints weight = 5780.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.124764 restraints weight = 3233.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.127748 restraints weight = 2155.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074   3458  Z= 0.250
  Angle     :  0.799  13.930   4695  Z= 0.391
  Chirality :  0.047   0.149    499
  Planarity :  0.007   0.118    604
  Dihedral  :  6.818  47.160    525
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 16.83
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  :  9.66 %
    Favored  : 89.86 %
  Rotamer:
    Outliers :  6.93 %
    Allowed  : 24.93 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.93 (0.42), residues: 414
  helix: -3.58 (0.74), residues: 18
  sheet: -2.33 (0.43), residues: 133
  loop : -1.61 (0.41), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP L  59 
 HIS   0.002   0.001   HIS H  54 
 PHE   0.012   0.002   PHE L  95 
 TYR   0.020   0.001   TYR L  73 
 ARG   0.007   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.7988 (t80) cc_final: 0.7672 (t80)
REVERT: R  489 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.7137 (t80)
REVERT: H  123 TYR cc_start: 0.8606 (p90) cc_final: 0.8388 (p90)
REVERT: L   50 GLN cc_start: 0.8071 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: L   62 GLN cc_start: 0.8534 (pt0) cc_final: 0.8063 (pt0)
REVERT: L   74 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: L  111 TYR cc_start: 0.8267 (m-80) cc_final: 0.7651 (m-80)
  outliers start: 25
  outliers final: 20
  residues processed: 109
  average time/residue: 0.1730
  time to fit residues: 22.6540
Evaluate side-chains
  113 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   24 THR
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 38 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 29 optimal weight:    0.6980
   chunk 37 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** L  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.143928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120766 restraints weight = 5672.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124706 restraints weight = 3350.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.127538 restraints weight = 2302.237|
|-----------------------------------------------------------------------------|
r_work (final): 0.3697
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.3938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3458  Z= 0.274
  Angle     :  0.804  13.824   4695  Z= 0.398
  Chirality :  0.047   0.165    499
  Planarity :  0.007   0.116    604
  Dihedral  :  6.800  47.115    525
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 17.74
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 11.84 %
    Favored  : 87.68 %
  Rotamer:
    Outliers :  7.48 %
    Allowed  : 24.93 %
    Favored  : 67.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.42), residues: 414
  helix: -3.61 (0.72), residues: 18
  sheet: -2.15 (0.44), residues: 131
  loop : -1.67 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP L  59 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.025   0.002   PHE H 133 
 TYR   0.020   0.002   TYR L  73 
 ARG   0.007   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.7997 (t80) cc_final: 0.7702 (t80)
REVERT: R  434 ILE cc_start: 0.8961 (mt) cc_final: 0.8610 (tt)
REVERT: R  489 TYR cc_start: 0.7393 (OUTLIER) cc_final: 0.7098 (t80)
REVERT: L   50 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7698 (tm-30)
REVERT: L   62 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (pt0)
REVERT: L   74 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8486 (tt)
REVERT: L  111 TYR cc_start: 0.8186 (m-80) cc_final: 0.7696 (m-80)
  outliers start: 27
  outliers final: 22
  residues processed: 109
  average time/residue: 0.1367
  time to fit residues: 18.4117
Evaluate side-chains
  119 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  118 GLU
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   62 GLN
Chi-restraints excluded: chain L residue   74 LEU
Chi-restraints excluded: chain L residue  109 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 9 optimal weight:    0.8980
   chunk 23 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0770
   chunk 39 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
R 487 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.144464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.120986 restraints weight = 5821.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.125113 restraints weight = 3399.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.128026 restraints weight = 2322.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   3458  Z= 0.262
  Angle     :  0.808  13.933   4695  Z= 0.400
  Chirality :  0.047   0.191    499
  Planarity :  0.007   0.115    604
  Dihedral  :  6.837  46.980    525
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 10.39 %
    Favored  : 89.13 %
  Rotamer:
    Outliers :  6.65 %
    Allowed  : 24.93 %
    Favored  : 68.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.84 (0.42), residues: 414
  helix: -3.57 (0.74), residues: 18
  sheet: -2.08 (0.45), residues: 131
  loop : -1.68 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP L  59 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.023   0.002   PHE H 133 
 TYR   0.020   0.001   TYR L  73 
 ARG   0.008   0.001   ARG H  91 

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

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

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  828 Ramachandran restraints generated.
    414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 96
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: R  423 TYR cc_start: 0.7985 (t80) cc_final: 0.7686 (t80)
REVERT: R  434 ILE cc_start: 0.8954 (mt) cc_final: 0.8602 (tt)
REVERT: R  489 TYR cc_start: 0.7421 (OUTLIER) cc_final: 0.7125 (t80)
REVERT: L   50 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7656 (tm-30)
REVERT: L   62 GLN cc_start: 0.8582 (pt0) cc_final: 0.7975 (pt0)
REVERT: L   74 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8491 (tt)
REVERT: L  111 TYR cc_start: 0.8195 (m-80) cc_final: 0.7660 (m-80)
  outliers start: 24
  outliers final: 21
  residues processed: 107
  average time/residue: 0.1462
  time to fit residues: 19.3572
Evaluate side-chains
  115 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  374 PHE
Chi-restraints excluded: chain R residue  377 PHE
Chi-restraints excluded: chain R residue  395 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain R residue  478 LYS
Chi-restraints excluded: chain R residue  483 VAL
Chi-restraints excluded: chain R residue  487 ASN
Chi-restraints excluded: chain R residue  489 TYR
Chi-restraints excluded: chain H residue   24 VAL
Chi-restraints excluded: chain H residue   30 VAL
Chi-restraints excluded: chain H residue   51 TYR
Chi-restraints excluded: chain H residue   53 ILE
Chi-restraints excluded: chain H residue   56 VAL
Chi-restraints excluded: chain H residue   59 THR
Chi-restraints excluded: chain H residue   77 LYS
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  112 VAL
Chi-restraints excluded: chain H residue  120 ILE
Chi-restraints excluded: chain H residue  126 TYR
Chi-restraints excluded: chain H residue  142 THR
Chi-restraints excluded: chain L residue   22 VAL
Chi-restraints excluded: chain L residue   61 LEU
Chi-restraints excluded: chain L residue   74 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0770
   chunk 28 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    1.1944

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

Flipped N/Q/H residues before XYZ refinement:
R 487 ASN
L  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.140781 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.116608 restraints weight = 5870.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.120783 restraints weight = 3359.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.123725 restraints weight = 2283.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.3994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   3458  Z= 0.381
  Angle     :  0.844  13.693   4695  Z= 0.421
  Chirality :  0.048   0.206    499
  Planarity :  0.007   0.114    604
  Dihedral  :  7.049  47.986    525
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 19.26
  Ramachandran Plot:
    Outliers :  0.48 %
    Allowed  : 12.32 %
    Favored  : 87.20 %
  Rotamer:
    Outliers :  7.20 %
    Allowed  : 24.93 %
    Favored  : 67.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.41), residues: 414
  helix: -3.85 (0.63), residues: 18
  sheet: -2.18 (0.44), residues: 131
  loop : -1.77 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.003   TRP L  59 
 HIS   0.001   0.000   HIS H  54 
 PHE   0.023   0.002   PHE H 133 
 TYR   0.021   0.002   TYR H  78 
 ARG   0.007   0.001   ARG H  91 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1693.02 seconds
wall clock time: 30 minutes 3.99 seconds (1803.99 seconds total)