Starting phenix.real_space_refine
on Tue Feb 13 14:24:31 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dlk_27504/02_2024/8dlk_27504.pdb"
  }
  resolution = 3.04
  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=  -0.001 sd=   0.033
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      37      5.16       5
     C    4191      2.51       5
     N    1077      2.21       5
     O    1249      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "B TYR  380": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "B TYR  449": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 6554
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1594
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 27, 'TRANS': 568}
    Chain: "B"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 4.19, per 1000 atoms: 0.64
  Number of scatterers: 6554
  At special positions: 0
  Unit cell: (78, 84, 122, 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      37     16.00
     O    1249      8.00
     N    1077      7.00
     C    4191      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 133 " - pdb=" SG  CYS E 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E 530 " - pdb=" SG  CYS E 542 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG B1301 " - " ASN B 343 "
      " NAG E 701 " - " ASN E  53 "
      " NAG E 702 " - " ASN E  90 "
      " NAG E 703 " - " ASN E 103 "
      " NAG E 704 " - " ASN E 322 "
      " NAG E 705 " - " ASN E 432 "
      " NAG E 706 " - " ASN E 546 "
  Time building additional restraints: 2.36
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1500

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.77
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
    Processing helix  chain 'B' and resid 383 through 387
      removed outlier: 3.504A  pdb=" N   LYS B 386 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.653A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.714A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
    Processing helix  chain 'E' and resid 82 through 83
      No H-bonds generated for 'chain 'E' and resid 82 through 83'
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.747A  pdb=" N   GLU E  87 " --> pdb=" O   PRO E  84 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 90 through 101
    Processing helix  chain 'E' and resid 103 through 108
      removed outlier: 4.089A  pdb=" N   VAL E 107 " --> pdb=" O   GLY E 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 109 through 129
    Processing helix  chain 'E' and resid 147 through 155
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.681A  pdb=" N   VAL E 185 " --> pdb=" O   GLU E 181 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 198 through 205
    Processing helix  chain 'E' and resid 206 through 208
      No H-bonds generated for 'chain 'E' and resid 206 through 208'
    Processing helix  chain 'E' and resid 218 through 252
      removed outlier: 3.754A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.457A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLU E 232 " --> pdb=" O   HIS E 228 " (cutoff:3.500A)
      Proline residue:  E 235  - end of helix
    Processing helix  chain 'E' and resid 265 through 267
      No H-bonds generated for 'chain 'E' and resid 265 through 267'
    Processing helix  chain 'E' and resid 275 through 279
      removed outlier: 3.819A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 301
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.550A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.668A  pdb=" N   TYR E 385 " --> pdb=" O   TYR E 381 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 386 through 388
      No H-bonds generated for 'chain 'E' and resid 386 through 388'
    Processing helix  chain 'E' and resid 389 through 393
    Processing helix  chain 'E' and resid 397 through 413
      removed outlier: 4.281A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.529A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.326A  pdb=" N   PHE E 452 " --> pdb=" O   GLY E 448 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 469 through 471
      No H-bonds generated for 'chain 'E' and resid 469 through 471'
    Processing helix  chain 'E' and resid 472 through 484
    Processing helix  chain 'E' and resid 499 through 502
      removed outlier: 3.652A  pdb=" N   SER E 502 " --> pdb=" O   ASP E 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 499 through 502'
    Processing helix  chain 'E' and resid 503 through 508
    Processing helix  chain 'E' and resid 512 through 533
      removed outlier: 4.465A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   PHE E 523 " --> pdb=" O   THR E 519 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 538 through 542
    Processing helix  chain 'E' and resid 547 through 559
      removed outlier: 3.873A  pdb=" N   MET E 557 " --> pdb=" O   LYS E 553 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 565 through 574
    Processing helix  chain 'E' and resid 581 through 588
    Processing helix  chain 'E' and resid 588 through 599
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.961A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'E' and resid 131 through 132
      removed outlier: 3.670A  pdb=" N   LEU E 142 " --> pdb=" O   VAL E 132 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 262 through 263
      removed outlier: 6.081A  pdb=" N   LEU E 262 " --> pdb=" O   VAL E 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 347 through 352
      removed outlier: 6.381A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    322 hydrogen bonds defined for protein.
    918 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: 1.63

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2081
        1.35 -     1.47: 1806
        1.47 -     1.60: 2792
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.462 -0.056 2.00e-02 2.50e+03 7.91e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.36e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.454 -0.048 2.00e-02 2.50e+03 5.80e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.448 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.31e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
       97.58 -   104.89: 155
      104.89 -   112.19: 3134
      112.19 -   119.49: 2365
      119.49 -   126.79: 3371
      126.79 -   134.09: 131
  Bond angle restraints: 9156
  Sorted by residual:
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.21   -5.85 1.42e+00 4.96e-01 1.70e+01
  angle pdb=" CA  CYS E 141 "
        pdb=" CB  CYS E 141 "
        pdb=" SG  CYS E 141 "
      ideal   model   delta    sigma   weight residual
     114.40  122.71   -8.31 2.30e+00 1.89e-01 1.31e+01
  angle pdb=" CA  ASN E 437 "
        pdb=" CB  ASN E 437 "
        pdb=" CG  ASN E 437 "
      ideal   model   delta    sigma   weight residual
     112.60  116.07   -3.47 1.00e+00 1.00e+00 1.20e+01
  angle pdb=" N   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" C   TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.32  104.85    5.47 1.59e+00 3.96e-01 1.18e+01
  angle pdb=" CA  ASN B 360 "
        pdb=" CB  ASN B 360 "
        pdb=" CG  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     112.60  115.83   -3.23 1.00e+00 1.00e+00 1.04e+01
  ... (remaining 9151 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.01: 3688
       17.01 -    34.03: 303
       34.03 -    51.04: 51
       51.04 -    68.06: 12
       68.06 -    85.07: 12
  Dihedral angle restraints: 4066
    sinusoidal: 1727
      harmonic: 2339
  Sorted by residual:
  dihedral pdb=" CB  CYS E 133 "
           pdb=" SG  CYS E 133 "
           pdb=" SG  CYS E 141 "
           pdb=" CB  CYS E 141 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.29  -41.71     1      1.00e+01 1.00e-02 2.43e+01
  dihedral pdb=" SG  CYS B 391 "
           pdb=" CB  CYS B 525 "
           pdb=" SG  CYS B 525 "
           pdb=" CA  CYS B 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   16.72   62.28     1      2.00e+01 2.50e-03 1.28e+01
  dihedral pdb=" C   ASN B 360 "
           pdb=" N   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -130.83    8.23     0      2.50e+00 1.60e-01 1.08e+01
  ... (remaining 4063 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 688
       0.053 -    0.105: 213
       0.105 -    0.158: 63
       0.158 -    0.211: 12
       0.211 -    0.263: 2
  Chirality restraints: 978
  Sorted by residual:
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  VAL E 581 "
            pdb=" CA  VAL E 581 "
            pdb=" CG1 VAL E 581 "
            pdb=" CG2 VAL E 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  ASN E 437 "
            pdb=" N   ASN E 437 "
            pdb=" C   ASN E 437 "
            pdb=" CB  ASN E 437 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.20 2.00e-01 2.50e+01 9.54e-01
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 145 "   -0.049 5.00e-02 4.00e+02   7.34e-02 8.62e+00
        pdb=" N   PRO E 146 "    0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO E 146 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO E 146 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.047 5.00e-02 4.00e+02   7.06e-02 7.97e+00
        pdb=" N   PRO E 590 "    0.122 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "    0.013 2.00e-02 2.50e+03   2.71e-02 7.32e+00
        pdb=" C   ARG E 169 "   -0.047 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "    0.017 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.83: 2062
        2.83 -     3.35: 6013
        3.35 -     3.87: 11403
        3.87 -     4.38: 12820
        4.38 -     4.90: 22189
  Nonbonded interactions: 54487
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.319 2.440
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.323 2.440
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.338 2.440
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.347 2.520
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.351 2.520
  ... (remaining 54482 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
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:             3.360
  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:          13.390
  Check model and map are aligned:         0.090
  Set scattering table:                    0.060
  Process input model:                     21.750
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.590
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8444
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   6737  Z= 0.338
  Angle     :  0.861   9.308   9156  Z= 0.481
  Chirality :  0.057   0.263    978
  Planarity :  0.007   0.073   1177
  Dihedral  : 13.416  85.073   2548
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.71 %
    Favored  : 97.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.00 (0.26), residues: 793
  helix:  0.45 (0.22), residues: 392
  sheet:  0.65 (0.65), residues: 53
  loop : -0.52 (0.30), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 566 
 HIS   0.004   0.001   HIS E 378 
 PHE   0.030   0.003   PHE E 369 
 TYR   0.037   0.002   TYR E 385 
 ARG   0.012   0.001   ARG E 460 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8470 (m-30) cc_final: 0.8183 (m-30)
REVERT: B  519 HIS cc_start: 0.8500 (m170) cc_final: 0.8233 (p90)
REVERT: E  564 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8614 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 97
  average time/residue: 0.2488
  time to fit residues: 30.6419
Evaluate side-chains
  55 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 54
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   34 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 59 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 46 optimal weight:    0.1980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
E 149 ASN
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.1798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6737  Z= 0.206
  Angle     :  0.537   6.483   9156  Z= 0.277
  Chirality :  0.040   0.141    978
  Planarity :  0.004   0.041   1177
  Dihedral  :  5.473  58.234   1015
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  7.71 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.06 (0.28), residues: 793
  helix:  1.42 (0.25), residues: 399
  sheet:  1.09 (0.74), residues: 42
  loop : -0.09 (0.31), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 369 
 ARG   0.004   0.000   ARG B 408 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 60
  time to evaluate  : 0.737 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8402 (m-30) cc_final: 0.8048 (m-30)
REVERT: B  519 HIS cc_start: 0.8529 (m170) cc_final: 0.8277 (p90)
REVERT: E  148 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8322 (mt)
REVERT: E  564 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8514 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 69
  average time/residue: 0.1894
  time to fit residues: 18.1339
Evaluate side-chains
  55 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  385 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 22 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    0.5980
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS
E 522 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2169

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6737  Z= 0.196
  Angle     :  0.510   5.558   9156  Z= 0.259
  Chirality :  0.040   0.135    978
  Planarity :  0.004   0.037   1177
  Dihedral  :  4.982  57.100   1013
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.14 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.29), residues: 793
  helix:  1.70 (0.26), residues: 397
  sheet:  1.21 (0.75), residues: 42
  loop :  0.20 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.017   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8409 (m-30) cc_final: 0.8047 (m-30)
REVERT: B  519 HIS cc_start: 0.8595 (m170) cc_final: 0.8284 (p90)
REVERT: E  249 MET cc_start: 0.9169 (ttt) cc_final: 0.8828 (tpp)
  outliers start: 10
  outliers final: 4
  residues processed: 56
  average time/residue: 0.2021
  time to fit residues: 15.5268
Evaluate side-chains
  46 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 7 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6737  Z= 0.206
  Angle     :  0.493   5.913   9156  Z= 0.253
  Chirality :  0.040   0.145    978
  Planarity :  0.004   0.036   1177
  Dihedral  :  4.759  57.346   1013
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.14 %
    Favored  : 89.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.29), residues: 793
  helix:  1.85 (0.26), residues: 397
  sheet:  1.33 (0.78), residues: 42
  loop :  0.29 (0.32), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 52
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8445 (m-30) cc_final: 0.8214 (m-30)
REVERT: B  484 GLU cc_start: 0.8208 (tt0) cc_final: 0.7964 (tt0)
REVERT: B  519 HIS cc_start: 0.8612 (m170) cc_final: 0.8206 (p90)
REVERT: E  114 LYS cc_start: 0.9469 (mmmt) cc_final: 0.9217 (pttm)
  outliers start: 10
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1919
  time to fit residues: 16.1025
Evaluate side-chains
  52 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 19 optimal weight:   10.0000
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    3.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8574
moved from start:          0.3201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.058   6737  Z= 0.626
  Angle     :  0.713   7.415   9156  Z= 0.371
  Chirality :  0.048   0.190    978
  Planarity :  0.004   0.040   1177
  Dihedral  :  5.525  57.403   1013
  Min Nonbonded Distance : 2.182

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.71 %
    Favored  : 87.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.29), residues: 793
  helix:  1.55 (0.26), residues: 390
  sheet:  0.63 (0.71), residues: 53
  loop :  0.29 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.029   0.002   PHE E 400 
 TYR   0.027   0.002   TYR E 385 
 ARG   0.006   0.001   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.783 
Fit side-chains
REVERT: B  405 ASP cc_start: 0.8496 (m-30) cc_final: 0.8225 (m-30)
REVERT: B  442 ASP cc_start: 0.9084 (m-30) cc_final: 0.8802 (m-30)
REVERT: B  519 HIS cc_start: 0.8728 (m170) cc_final: 0.8313 (p90)
REVERT: E  114 LYS cc_start: 0.9563 (mmmt) cc_final: 0.9277 (mmmt)
REVERT: E  190 MET cc_start: 0.8797 (tmm) cc_final: 0.8466 (tmm)
REVERT: E  291 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8869 (mt)
  outliers start: 15
  outliers final: 8
  residues processed: 59
  average time/residue: 0.1678
  time to fit residues: 14.2690
Evaluate side-chains
  52 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 43
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  333 THR
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  610 TRP
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 35 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   chunk 8 optimal weight:    0.0670
   chunk 43 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.5318

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6737  Z= 0.175
  Angle     :  0.507   7.893   9156  Z= 0.259
  Chirality :  0.040   0.160    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.766  56.610   1013
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 11.43 %
    Favored  : 87.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.61 (0.30), residues: 793
  helix:  1.87 (0.26), residues: 389
  sheet:  0.50 (0.70), residues: 53
  loop :  0.36 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 168 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 365 
 ARG   0.004   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 53
  time to evaluate  : 1.030 
Fit side-chains
REVERT: B  442 ASP cc_start: 0.9015 (m-30) cc_final: 0.8782 (m-30)
REVERT: B  519 HIS cc_start: 0.8723 (m170) cc_final: 0.8288 (p90)
REVERT: E   82 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8343 (mtm)
REVERT: E  190 MET cc_start: 0.8784 (tmm) cc_final: 0.8480 (tmm)
  outliers start: 9
  outliers final: 6
  residues processed: 58
  average time/residue: 0.2241
  time to fit residues: 18.7114
Evaluate side-chains
  54 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   82 MET
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Chi-restraints excluded: chain E residue  613 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 35 optimal weight:    0.5980
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 14 optimal weight:    4.9990
   overall best weight:    0.7782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6737  Z= 0.206
  Angle     :  0.517   7.385   9156  Z= 0.266
  Chirality :  0.041   0.152    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.658  57.371   1013
  Min Nonbonded Distance : 2.243

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.29 %
    Favored  : 86.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.30), residues: 793
  helix:  1.98 (0.26), residues: 388
  sheet:  0.42 (0.70), residues: 53
  loop :  0.52 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.013   0.001   TYR B 365 
 ARG   0.003   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 0.890 
Fit side-chains
REVERT: B  442 ASP cc_start: 0.9029 (m-30) cc_final: 0.8714 (m-30)
REVERT: B  519 HIS cc_start: 0.8752 (m170) cc_final: 0.8263 (p90)
REVERT: E  190 MET cc_start: 0.8818 (tmm) cc_final: 0.8509 (tmm)
REVERT: E  383 MET cc_start: 0.9276 (mtm) cc_final: 0.8952 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1918
  time to fit residues: 14.8792
Evaluate side-chains
  53 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  471 ASP
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 59 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
E  81 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066   6737  Z= 0.360
  Angle     :  0.590   9.908   9156  Z= 0.304
  Chirality :  0.043   0.147    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.923  57.440   1013
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.71 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.30), residues: 793
  helix:  1.85 (0.26), residues: 387
  sheet:  0.17 (0.69), residues: 55
  loop :  0.59 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.018   0.001   PHE E 369 
 TYR   0.019   0.001   TYR E 385 
 ARG   0.004   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.795 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8451 (mmmm) cc_final: 0.8031 (mmtm)
REVERT: B  442 ASP cc_start: 0.9057 (m-30) cc_final: 0.8736 (m-30)
REVERT: B  472 ILE cc_start: 0.9252 (mm) cc_final: 0.8816 (tp)
REVERT: B  519 HIS cc_start: 0.8744 (m170) cc_final: 0.8265 (p90)
REVERT: E  190 MET cc_start: 0.8804 (tmm) cc_final: 0.8487 (tmm)
REVERT: E  470 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8842 (mtpt)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.1913
  time to fit residues: 14.9006
Evaluate side-chains
  54 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  517 LEU
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  470 LYS
Chi-restraints excluded: chain E residue  471 ASP
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    2.9990
   chunk 64 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6737  Z= 0.214
  Angle     :  0.559  17.643   9156  Z= 0.278
  Chirality :  0.041   0.155    978
  Planarity :  0.004   0.033   1177
  Dihedral  :  4.642  56.817   1013
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 12.86 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.76 (0.30), residues: 793
  helix:  1.92 (0.26), residues: 388
  sheet:  0.17 (0.69), residues: 55
  loop :  0.62 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
REVERT: B  378 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8039 (mmtm)
REVERT: B  406 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: B  442 ASP cc_start: 0.9041 (m-30) cc_final: 0.8742 (m-30)
REVERT: B  472 ILE cc_start: 0.9236 (mm) cc_final: 0.8803 (tp)
REVERT: B  519 HIS cc_start: 0.8765 (m170) cc_final: 0.8216 (p90)
REVERT: E  190 MET cc_start: 0.8809 (tmm) cc_final: 0.8496 (tmm)
  outliers start: 6
  outliers final: 4
  residues processed: 55
  average time/residue: 0.1915
  time to fit residues: 14.8140
Evaluate side-chains
  53 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 49
  time to evaluate  : 0.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   chunk 62 optimal weight:    0.0870
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 66 optimal weight:    0.4980
   chunk 19 optimal weight:    0.0670
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0570
   overall best weight:    0.3014

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   6737  Z= 0.153
  Angle     :  0.542  15.843   9156  Z= 0.269
  Chirality :  0.040   0.159    978
  Planarity :  0.004   0.034   1177
  Dihedral  :  4.449  57.070   1013
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.14 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.30), residues: 793
  helix:  1.86 (0.27), residues: 396
  sheet:  0.58 (0.80), residues: 43
  loop :  0.54 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E  69 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.010   0.001   TYR B 365 
 ARG   0.002   0.000   ARG B 457 

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 52
  time to evaluate  : 0.773 
Fit side-chains
REVERT: B  378 LYS cc_start: 0.8354 (mmmm) cc_final: 0.7933 (mmtm)
REVERT: B  386 LYS cc_start: 0.8868 (pttp) cc_final: 0.8541 (pptt)
REVERT: B  406 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8148 (mt-10)
REVERT: B  472 ILE cc_start: 0.9205 (mm) cc_final: 0.8754 (tp)
REVERT: B  519 HIS cc_start: 0.8737 (m170) cc_final: 0.8198 (p90)
REVERT: E  190 MET cc_start: 0.8862 (tmm) cc_final: 0.8551 (tmm)
  outliers start: 6
  outliers final: 5
  residues processed: 55
  average time/residue: 0.1659
  time to fit residues: 13.3016
Evaluate side-chains
  53 residues out of total 700 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.764 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  471 ASP
Chi-restraints excluded: chain E residue  574 VAL
Chi-restraints excluded: chain E residue  611 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 26 optimal weight:    0.1980
   chunk 64 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9980
   chunk 55 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
E 586 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.063167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.047954 restraints weight = 20666.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.2823 rms_B_bonded: 3.51
r_work: 0.2669 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6737  Z= 0.197
  Angle     :  0.562  13.685   9156  Z= 0.279
  Chirality :  0.041   0.148    978
  Planarity :  0.004   0.035   1177
  Dihedral  :  4.455  57.202   1013
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 13.71 %
    Favored  : 85.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.30), residues: 793
  helix:  1.97 (0.27), residues: 389
  sheet:  0.61 (0.80), residues: 43
  loop :  0.66 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E 374 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.003   0.000   ARG B 457 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1667.74 seconds
wall clock time: 31 minutes 42.91 seconds (1902.91 seconds total)