Starting phenix.real_space_refine
on Fri Dec 27 21:15:26 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.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/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dln_27507/12_2024/8dln_27507.cif"
  }
  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=   0.031
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    4190      2.51       5
     N    1078      2.21       5
     O    1248      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6553
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1593
          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: 4.82, per 1000 atoms: 0.74
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (77, 85, 123, 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    1248      8.00
     N    1078      7.00
     C    4190      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG 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: 1.64
  Conformation dependent library (CDL) restraints added in 1.0 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:
      38 helices and 7 sheets defined
      57.0% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.403A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.725A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 3.697A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.563A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.727A  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: 4.072A  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: 3.732A  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: 3.762A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.743A  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: 3.795A  pdb=" N   TYR E 279 " --> pdb=" O   THR E 276 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 293 through 300
    Processing helix  chain 'E' and resid 303 through 318
    Processing helix  chain 'E' and resid 324 through 331
      removed outlier: 3.585A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.693A  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: 4.294A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.947A  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: 3.526A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.318A  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: 3.665A  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: 4.425A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.618A  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: 3.877A  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: 3.985A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.814A  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: 3.790A  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: 6.052A  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: 6.363A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    912 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: 1.88

  Time building geometry restraints manager: 1.92 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: 2079
        1.35 -     1.47: 1795
        1.47 -     1.60: 2804
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6736
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.460 -0.054 2.00e-02 2.50e+03 7.23e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.452 -0.046 2.00e-02 2.50e+03 5.26e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.72e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.65e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.449 -0.043 2.00e-02 2.50e+03 4.53e+00
  ... (remaining 6731 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.00: 8794
        2.00 -     4.00: 314
        4.00 -     6.00: 35
        6.00 -     8.00: 7
        8.00 -    10.00: 5
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  123.90  -10.00 1.80e+00 3.09e-01 3.09e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.36  128.33   -5.97 1.42e+00 4.96e-01 1.77e+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  123.02   -8.62 2.30e+00 1.89e-01 1.41e+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  116.03   -3.43 1.00e+00 1.00e+00 1.18e+01
  angle pdb=" C   TYR B 495 "
        pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     110.78  105.54    5.24 1.60e+00 3.91e-01 1.07e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 3688
       17.19 -    34.37: 310
       34.37 -    51.55: 44
       51.55 -    68.74: 12
       68.74 -    85.92: 11
  Dihedral angle restraints: 4065
    sinusoidal: 1726
      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  -46.48  -39.52     1      1.00e+01 1.00e-02 2.19e+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   14.60   64.40     1      2.00e+01 2.50e-03 1.36e+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 -130.75    8.15     0      2.50e+00 1.60e-01 1.06e+01
  ... (remaining 4062 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 701
       0.052 -    0.105: 197
       0.105 -    0.157: 64
       0.157 -    0.209: 14
       0.209 -    0.261: 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 1.71e+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   -2.38   -0.25 2.00e-01 2.50e+01 1.55e+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    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 495 "   -0.030 2.00e-02 2.50e+03   1.88e-02 7.09e+00
        pdb=" CG  TYR B 495 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 495 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 495 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 495 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 495 "   -0.006 2.00e-02 2.50e+03
        pdb=" OH  TYR B 495 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.043 5.00e-02 4.00e+02   6.41e-02 6.58e+00
        pdb=" N   PRO E 590 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.043 5.00e-02 4.00e+02   6.39e-02 6.53e+00
        pdb=" N   PRO E 500 "    0.110 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1941
        2.82 -     3.34: 5987
        3.34 -     3.86: 11373
        3.86 -     4.38: 12873
        4.38 -     4.90: 22360
  Nonbonded interactions: 54534
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.303 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.330 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.351 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.366 3.120
  ... (remaining 54529 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 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:             2.780
  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:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.730
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.930
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
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   0.064   6736  Z= 0.344
  Angle     :  0.860  10.004   9155  Z= 0.481
  Chirality :  0.056   0.261    978
  Planarity :  0.007   0.064   1177
  Dihedral  : 13.351  85.924   2547
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 2.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  3.57 %
    Favored  : 96.14 %
  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: -0.21 (0.26), residues: 793
  helix:  0.33 (0.22), residues: 387
  sheet:  1.07 (0.72), residues: 43
  loop : -0.73 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E  69 
 HIS   0.007   0.001   HIS E  34 
 PHE   0.027   0.003   PHE E 369 
 TYR   0.043   0.002   TYR B 495 
 ARG   0.011   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
  118 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 116
  time to evaluate  : 0.812 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8276 (m-30) cc_final: 0.7950 (m-30)
REVERT: E  143 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8945 (mp)
REVERT: E  562 LYS cc_start: 0.9196 (tttt) cc_final: 0.8983 (tttp)
REVERT: E  589 GLU cc_start: 0.7916 (tp30) cc_final: 0.7473 (tp30)
  outliers start: 2
  outliers final: 0
  residues processed: 117
  average time/residue: 0.2650
  time to fit residues: 38.5269
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  143 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.6980
   chunk 59 optimal weight:    0.0070
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   overall best weight:    0.6598

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

Flipped N/Q/H residues before XYZ refinement:
E 374 HIS
E 552 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6736  Z= 0.193
  Angle     :  0.557   9.217   9155  Z= 0.285
  Chirality :  0.042   0.140    978
  Planarity :  0.005   0.041   1177
  Dihedral  :  5.206  49.543   1015
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  8.29 %
    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:  1.05 (0.28), residues: 793
  helix:  1.52 (0.25), residues: 383
  sheet:  0.87 (0.72), residues: 43
  loop : -0.15 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.016   0.001   PHE E 369 
 TYR   0.018   0.001   TYR B 495 
 ARG   0.005   0.000   ARG E 559 

*********************** 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
  76 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.879 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8218 (m-30) cc_final: 0.7722 (m-30)
REVERT: E  149 ASN cc_start: 0.9306 (m-40) cc_final: 0.9092 (m-40)
REVERT: E  152 MET cc_start: 0.8245 (mmp) cc_final: 0.7900 (mmt)
REVERT: E  249 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8689 (mtm)
REVERT: E  471 ASP cc_start: 0.8398 (p0) cc_final: 0.7975 (t0)
REVERT: E  474 MET cc_start: 0.8538 (mmt) cc_final: 0.8032 (mmt)
  outliers start: 6
  outliers final: 3
  residues processed: 73
  average time/residue: 0.2815
  time to fit residues: 25.8447
Evaluate side-chains
  64 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 60
  time to evaluate  : 0.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 71 optimal weight:    1.9990
   chunk 77 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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: 0.8512
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   6736  Z= 0.258
  Angle     :  0.552   9.157   9155  Z= 0.282
  Chirality :  0.042   0.134    978
  Planarity :  0.004   0.042   1177
  Dihedral  :  4.936  50.358   1013
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  8.43 %
    Favored  : 89.86 %
  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:  1.43 (0.29), residues: 793
  helix:  1.73 (0.26), residues: 389
  sheet:  0.74 (0.72), residues: 43
  loop :  0.20 (0.32), 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   0.016   0.001   PHE E 369 
 TYR   0.015   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
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   22 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8323 (tm-30)
REVERT: E  145 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8328 (tm-30)
REVERT: E  249 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8736 (mtm)
REVERT: E  471 ASP cc_start: 0.8423 (p0) cc_final: 0.7929 (t0)
  outliers start: 12
  outliers final: 4
  residues processed: 66
  average time/residue: 0.2554
  time to fit residues: 21.5863
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  458 LYS
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 48 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0270
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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: 0.8486
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6736  Z= 0.171
  Angle     :  0.507   7.409   9155  Z= 0.258
  Chirality :  0.040   0.129    978
  Planarity :  0.004   0.042   1177
  Dihedral  :  4.745  51.616   1013
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.00 %
    Favored  : 89.57 %
  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:  1.59 (0.29), residues: 793
  helix:  1.82 (0.26), residues: 389
  sheet:  0.73 (0.75), residues: 43
  loop :  0.35 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR B 495 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 58
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8211 (m-30) cc_final: 0.7733 (m-30)
REVERT: E   22 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8177 (tm-30)
REVERT: E   62 MET cc_start: 0.8988 (ttm) cc_final: 0.8539 (ttm)
REVERT: E  145 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: E  149 ASN cc_start: 0.9307 (m-40) cc_final: 0.9097 (m-40)
REVERT: E  152 MET cc_start: 0.8262 (mmp) cc_final: 0.7821 (mmt)
REVERT: E  249 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8683 (mtm)
REVERT: E  471 ASP cc_start: 0.8364 (p0) cc_final: 0.7883 (t0)
  outliers start: 10
  outliers final: 5
  residues processed: 65
  average time/residue: 0.2731
  time to fit residues: 22.5609
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  132 VAL
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 56 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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: 0.8520
moved from start:          0.2890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6736  Z= 0.264
  Angle     :  0.537   7.846   9155  Z= 0.275
  Chirality :  0.041   0.130    978
  Planarity :  0.004   0.042   1177
  Dihedral  :  4.822  52.056   1013
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.57 %
    Favored  : 89.29 %
  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:  1.64 (0.29), residues: 793
  helix:  1.80 (0.26), residues: 396
  sheet:  0.82 (0.76), residues: 43
  loop :  0.43 (0.32), residues: 354

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   0.014   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  67 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.668 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8179 (m-30) cc_final: 0.7670 (m-30)
REVERT: E   62 MET cc_start: 0.9027 (ttm) cc_final: 0.8587 (ttm)
REVERT: E  152 MET cc_start: 0.8344 (mmp) cc_final: 0.8002 (mmm)
REVERT: E  249 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.8716 (mtm)
  outliers start: 8
  outliers final: 5
  residues processed: 63
  average time/residue: 0.2632
  time to fit residues: 21.2087
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 40 optimal weight:    0.5980
   chunk 73 optimal weight:    0.7980
   chunk 8 optimal weight:    0.2980
   chunk 43 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.5980

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.2963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6736  Z= 0.176
  Angle     :  0.509   6.698   9155  Z= 0.259
  Chirality :  0.040   0.127    978
  Planarity :  0.003   0.041   1177
  Dihedral  :  4.694  53.082   1013
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  9.71 %
    Favored  : 89.14 %
  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:  1.73 (0.29), residues: 793
  helix:  1.83 (0.25), residues: 402
  sheet:  0.87 (0.78), residues: 43
  loop :  0.50 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.011   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.849 
Fit side-chains
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8139 (m-30) cc_final: 0.7661 (m-30)
REVERT: E  249 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8704 (mtm)
REVERT: E  471 ASP cc_start: 0.8706 (p0) cc_final: 0.8034 (t0)
  outliers start: 8
  outliers final: 5
  residues processed: 61
  average time/residue: 0.2793
  time to fit residues: 21.9175
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 43 optimal weight:    6.9990
   chunk 64 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 47 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9180

-------------------------------------------------------------------------------
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: 0.8514
moved from start:          0.3073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6736  Z= 0.231
  Angle     :  0.538   6.750   9155  Z= 0.274
  Chirality :  0.041   0.199    978
  Planarity :  0.004   0.040   1177
  Dihedral  :  4.729  52.909   1013
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 7.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.43 %
    Favored  : 88.29 %
  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 (0.29), residues: 793
  helix:  1.84 (0.25), residues: 402
  sheet:  0.90 (0.78), residues: 43
  loop :  0.53 (0.33), residues: 348

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   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 MET cc_start: 0.8729 (ttt) cc_final: 0.8459 (ttm)
REVERT: E  152 MET cc_start: 0.8251 (mmp) cc_final: 0.7634 (mmt)
REVERT: E  249 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8664 (mtm)
REVERT: E  291 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8950 (mt)
REVERT: E  471 ASP cc_start: 0.8731 (p0) cc_final: 0.8028 (t0)
  outliers start: 9
  outliers final: 5
  residues processed: 61
  average time/residue: 0.2799
  time to fit residues: 21.7226
Evaluate side-chains
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.822 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  291 ILE
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0770
   chunk 70 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.6938

-------------------------------------------------------------------------------
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: 0.8501
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6736  Z= 0.193
  Angle     :  0.520   6.585   9155  Z= 0.265
  Chirality :  0.041   0.172    978
  Planarity :  0.003   0.042   1177
  Dihedral  :  4.679  53.722   1013
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.43 %
    Favored  : 88.29 %
  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:  1.70 (0.29), residues: 793
  helix:  1.74 (0.25), residues: 411
  sheet:  0.84 (0.77), residues: 43
  loop :  0.53 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 

*********************** 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
  65 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  152 MET cc_start: 0.8194 (mmp) cc_final: 0.7649 (mmt)
REVERT: E  249 MET cc_start: 0.9035 (OUTLIER) cc_final: 0.8691 (mtm)
REVERT: E  471 ASP cc_start: 0.8708 (p0) cc_final: 0.8054 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 60
  average time/residue: 0.2613
  time to fit residues: 20.1646
Evaluate side-chains
  62 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 64 optimal weight:    0.1980
   chunk 67 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 45 optimal weight:    0.7980
   chunk 35 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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: 0.8496
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6736  Z= 0.184
  Angle     :  0.541  11.508   9155  Z= 0.270
  Chirality :  0.041   0.151    978
  Planarity :  0.003   0.041   1177
  Dihedral  :  4.633  53.946   1013
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.71 %
    Favored  : 88.29 %
  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:  1.75 (0.30), residues: 793
  helix:  1.80 (0.25), residues: 410
  sheet:  0.85 (0.77), residues: 43
  loop :  0.54 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.012   0.001   TYR E 385 
 ARG   0.002   0.000   ARG E 559 

*********************** 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
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 54
  time to evaluate  : 0.828 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  471 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8604 (mm-30)
REVERT: E  152 MET cc_start: 0.8184 (mmp) cc_final: 0.7653 (mmt)
REVERT: E  249 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8663 (mtm)
REVERT: E  471 ASP cc_start: 0.8671 (p0) cc_final: 0.8010 (t0)
  outliers start: 7
  outliers final: 6
  residues processed: 57
  average time/residue: 0.2746
  time to fit residues: 20.0235
Evaluate side-chains
  60 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue   91 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 66 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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: 0.8525
moved from start:          0.3241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6736  Z= 0.271
  Angle     :  0.576  10.935   9155  Z= 0.289
  Chirality :  0.042   0.149    978
  Planarity :  0.004   0.041   1177
  Dihedral  :  4.805  53.328   1013
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 11.29 %
    Favored  : 87.71 %
  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:  1.76 (0.29), residues: 793
  helix:  1.82 (0.25), residues: 402
  sheet:  0.70 (0.75), residues: 43
  loop :  0.58 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 357 

********************** 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
  63 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  471 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8561 (mm-30)
REVERT: E  152 MET cc_start: 0.8279 (mmp) cc_final: 0.7760 (mmt)
REVERT: E  249 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8667 (mtm)
REVERT: E  471 ASP cc_start: 0.8684 (p0) cc_final: 0.8059 (t0)
  outliers start: 7
  outliers final: 5
  residues processed: 59
  average time/residue: 0.2857
  time to fit residues: 21.5685
Evaluate side-chains
  59 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   29 LEU
Chi-restraints excluded: chain E residue  249 MET
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  474 MET
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  579 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   overall best weight:    0.9380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.067465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.051231 restraints weight = 19043.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.2862 rms_B_bonded: 3.25
r_work: 0.2713 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8656
moved from start:          0.3259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6736  Z= 0.236
  Angle     :  0.559  10.916   9155  Z= 0.280
  Chirality :  0.041   0.145    978
  Planarity :  0.003   0.041   1177
  Dihedral  :  4.790  53.739   1013
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 11.14 %
    Favored  : 88.00 %
  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:  1.66 (0.29), residues: 793
  helix:  1.74 (0.25), residues: 410
  sheet:  0.66 (0.75), residues: 43
  loop :  0.51 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.004   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 559 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1665.05 seconds
wall clock time: 31 minutes 16.55 seconds (1876.55 seconds total)