Starting phenix.real_space_refine
on Tue Mar 11 21:31:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tez_25856/03_2025/7tez_25856.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.014
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    4186      2.51       5
     N    1082      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-5624/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: {'PCIS': 1, 'PTRANS': 26, '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: 4.97, per 1000 atoms: 0.76
  Number of scatterers: 6553
  At special positions: 0
  Unit cell: (81, 84, 121, 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    1082      7.00
     C    4186      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=2.02
    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: 1.46
  Conformation dependent library (CDL) restraints added in 870.2 milliseconds
  

  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:
      40 helices and 7 sheets defined
      57.8% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  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
    Processing helix  chain 'B' and resid 406 through 410
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.713A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.084A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU E  39 " --> pdb=" O   GLU E  35 " (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: 4.084A  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 146 through 155
      removed outlier: 3.970A  pdb=" N   ILE E 151 " --> pdb=" O   GLY E 147 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 157 through 194
      Proline residue:  E 178  - end of helix
      removed outlier: 3.694A  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: 3.745A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.845A  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: 3.766A  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: 3.558A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.667A  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: 4.292A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.901A  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: 3.514A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.312A  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: 3.596A  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: 4.494A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.650A  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: 3.829A  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: 4.013A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.839A  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: 3.811A  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: 6.093A  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: 6.377A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    323 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: 1.71

  Time building geometry restraints manager: 1.82 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2085
        1.34 -     1.47: 1765
        1.47 -     1.59: 2827
        1.59 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 6735
  Sorted by residual:
  bond pdb=" C1  NAG B1301 "
       pdb=" O5  NAG B1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.474 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.458 -0.052 2.00e-02 2.50e+03 6.63e+00
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.457 -0.051 2.00e-02 2.50e+03 6.50e+00
  bond pdb=" C1  NAG E 701 "
       pdb=" O5  NAG E 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.22e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.17e+00
  ... (remaining 6730 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 8789
        2.06 -     4.11: 320
        4.11 -     6.17: 32
        6.17 -     8.22: 8
        8.22 -    10.28: 3
  Bond angle restraints: 9152
  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  128.51   -6.15 1.42e+00 4.96e-01 1.87e+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  116.31   -3.71 1.00e+00 1.00e+00 1.38e+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  122.85   -8.45 2.30e+00 1.89e-01 1.35e+01
  angle pdb=" C   HIS E  34 "
        pdb=" N   GLU E  35 "
        pdb=" CA  GLU E  35 "
      ideal   model   delta    sigma   weight residual
     122.38  115.83    6.55 1.81e+00 3.05e-01 1.31e+01
  angle pdb=" CA  LYS E  31 "
        pdb=" CB  LYS E  31 "
        pdb=" CG  LYS E  31 "
      ideal   model   delta    sigma   weight residual
     114.10  120.95   -6.85 2.00e+00 2.50e-01 1.17e+01
  ... (remaining 9147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3676
       16.72 -    33.43: 308
       33.43 -    50.15: 56
       50.15 -    66.87: 16
       66.87 -    83.58: 12
  Dihedral angle restraints: 4068
    sinusoidal: 1730
      harmonic: 2338
  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  -48.44  -37.56     1      1.00e+01 1.00e-02 1.99e+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   16.07   62.93     1      2.00e+01 2.50e-03 1.31e+01
  dihedral pdb=" N   ASN B 360 "
           pdb=" C   ASN B 360 "
           pdb=" CA  ASN B 360 "
           pdb=" CB  ASN B 360 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.82   -8.02     0      2.50e+00 1.60e-01 1.03e+01
  ... (remaining 4065 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 726
       0.061 -    0.121: 205
       0.121 -    0.182: 38
       0.182 -    0.243: 6
       0.243 -    0.303: 2
  Chirality restraints: 977
  Sorted by residual:
  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   -2.33   -0.30 2.00e-01 2.50e+01 2.30e+00
  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    2.24    0.27 2.00e-01 2.50e+01 1.78e+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    0.21 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1185
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU E 589 "   -0.056 5.00e-02 4.00e+02   8.31e-02 1.11e+01
        pdb=" N   PRO E 590 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO E 590 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO E 590 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP E 499 "   -0.050 5.00e-02 4.00e+02   7.43e-02 8.82e+00
        pdb=" N   PRO E 500 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO E 500 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO E 500 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 478 "    0.041 5.00e-02 4.00e+02   6.19e-02 6.12e+00
        pdb=" N   PRO B 479 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "    0.034 5.00e-02 4.00e+02
  ... (remaining 1182 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 2097
        2.84 -     3.35: 5957
        3.35 -     3.87: 11286
        3.87 -     4.38: 12699
        4.38 -     4.90: 22030
  Nonbonded interactions: 54069
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.323 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.344 3.120
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.360 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.366 3.120
  ... (remaining 54064 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:             2.690
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.290
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
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      :  0.006   0.071   6735  Z= 0.357
  Angle     :  0.896  10.276   9152  Z= 0.510
  Chirality :  0.060   0.303    977
  Planarity :  0.008   0.083   1178
  Dihedral  : 13.451  83.585   2550
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  2.57 %
    Favored  : 96.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  0.05 (0.25), residues: 793
  helix:  0.58 (0.22), residues: 392
  sheet:  1.01 (0.72), residues: 43
  loop : -0.62 (0.28), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP E  69 
 HIS   0.013   0.002   HIS E  34 
 PHE   0.028   0.003   PHE E 369 
 TYR   0.041   0.003   TYR B 495 
 ARG   0.014   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
  153 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 148
  time to evaluate  : 0.800 
Fit side-chains
REVERT: B  417 LYS cc_start: 0.9093 (mmtt) cc_final: 0.8826 (mmtm)
REVERT: B  470 THR cc_start: 0.8859 (p) cc_final: 0.8567 (t)
REVERT: E  291 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8532 (tp)
REVERT: E  436 ILE cc_start: 0.9036 (mm) cc_final: 0.8812 (mt)
REVERT: E  475 LYS cc_start: 0.8613 (ttpp) cc_final: 0.8002 (tptp)
REVERT: E  483 GLU cc_start: 0.8717 (tp30) cc_final: 0.8452 (tp30)
  outliers start: 5
  outliers final: 0
  residues processed: 151
  average time/residue: 0.2278
  time to fit residues: 43.5495
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  291 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
B 501 ASN
E 345 HIS
** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.080806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.063978 restraints weight = 17163.668|
|-----------------------------------------------------------------------------|
r_work (start): 0.2944 rms_B_bonded: 3.26
r_work: 0.2808 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8457
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   6735  Z= 0.376
  Angle     :  0.641   8.311   9152  Z= 0.331
  Chirality :  0.045   0.161    977
  Planarity :  0.005   0.038   1178
  Dihedral  :  5.875  52.452   1015
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  9.00 %
    Favored  : 89.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.11 (0.28), residues: 793
  helix:  1.39 (0.25), residues: 390
  sheet:  0.81 (0.72), residues: 42
  loop :  0.11 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP E 165 
 HIS   0.009   0.002   HIS E  34 
 PHE   0.018   0.002   PHE E 369 
 TYR   0.018   0.001   TYR E 385 
 ARG   0.004   0.001   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
  77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: B  470 THR cc_start: 0.9329 (p) cc_final: 0.8943 (t)
REVERT: B  506 GLN cc_start: 0.9264 (mt0) cc_final: 0.8746 (mt0)
REVERT: E  483 GLU cc_start: 0.8989 (tp30) cc_final: 0.8692 (tp30)
  outliers start: 10
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1893
  time to fit residues: 19.2990
Evaluate side-chains
  66 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 58
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  458 LYS
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  298 VAL
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 67 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.083116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.065927 restraints weight = 17165.431|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 3.36
r_work: 0.2837 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6735  Z= 0.199
  Angle     :  0.518   6.637   9152  Z= 0.267
  Chirality :  0.041   0.158    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  5.249  53.801   1013
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.14 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.68 (0.26), residues: 387
  sheet:  0.66 (0.73), residues: 42
  loop :  0.29 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP E 165 
 HIS   0.006   0.001   HIS E  34 
 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 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
  74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: B  470 THR cc_start: 0.9270 (p) cc_final: 0.8854 (t)
REVERT: B  506 GLN cc_start: 0.9293 (mt0) cc_final: 0.8782 (mt0)
REVERT: E  376 MET cc_start: 0.9078 (ttm) cc_final: 0.8812 (tpp)
REVERT: E  474 MET cc_start: 0.9099 (mmm) cc_final: 0.8671 (mmt)
REVERT: E  483 GLU cc_start: 0.8978 (tp30) cc_final: 0.8662 (tp30)
  outliers start: 5
  outliers final: 3
  residues processed: 73
  average time/residue: 0.1692
  time to fit residues: 17.2740
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 67
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.079220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.061969 restraints weight = 17658.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 3.35
r_work: 0.2755 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
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      :  0.007   0.055   6735  Z= 0.421
  Angle     :  0.622  10.862   9152  Z= 0.317
  Chirality :  0.045   0.161    977
  Planarity :  0.004   0.042   1178
  Dihedral  :  5.683  54.268   1013
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 11.29 %
    Favored  : 87.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.24 (0.30), residues: 793
  helix:  1.40 (0.26), residues: 395
  sheet:  0.59 (0.73), residues: 42
  loop :  0.33 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.008   0.002   HIS E  34 
 PHE   0.018   0.002   PHE E 369 
 TYR   0.020   0.002   TYR E 385 
 ARG   0.003   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
  77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.727 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.9057 (mt-10) cc_final: 0.8070 (tm-30)
REVERT: E  376 MET cc_start: 0.9084 (ttm) cc_final: 0.8735 (tpp)
REVERT: E  483 GLU cc_start: 0.8997 (tp30) cc_final: 0.8708 (tp30)
  outliers start: 12
  outliers final: 10
  residues processed: 75
  average time/residue: 0.1806
  time to fit residues: 18.5618
Evaluate side-chains
  69 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  458 LYS
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  524 VAL
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  436 ILE
Chi-restraints excluded: chain E residue  475 LYS
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.7380

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.081927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.065339 restraints weight = 17203.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 3.18
r_work: 0.2837 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8572
moved from start:          0.3060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6735  Z= 0.204
  Angle     :  0.516   8.805   9152  Z= 0.262
  Chirality :  0.041   0.157    977
  Planarity :  0.003   0.041   1178
  Dihedral  :  5.253  54.916   1013
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.00 %
    Favored  : 86.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.37 (0.30), residues: 793
  helix:  1.53 (0.26), residues: 394
  sheet:  0.43 (0.72), residues: 42
  loop :  0.41 (0.33), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP E 610 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   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
  77 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E  323 MET cc_start: 0.9081 (mmt) cc_final: 0.8727 (mmt)
REVERT: E  376 MET cc_start: 0.9083 (ttm) cc_final: 0.8814 (mmm)
REVERT: E  474 MET cc_start: 0.9156 (mmp) cc_final: 0.8790 (mmp)
REVERT: E  483 GLU cc_start: 0.8962 (tp30) cc_final: 0.8666 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1810
  time to fit residues: 19.0309
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  156 LEU
Chi-restraints excluded: chain E residue  475 LYS
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 28 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   overall best weight:    1.1982

-------------------------------------------------------------------------------
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 = 0.3267 r_free = 0.3267 target = 0.080250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.063743 restraints weight = 17156.823|
|-----------------------------------------------------------------------------|
r_work (start): 0.2933 rms_B_bonded: 3.14
r_work: 0.2805 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8598
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   6735  Z= 0.292
  Angle     :  0.545   8.699   9152  Z= 0.278
  Chirality :  0.042   0.152    977
  Planarity :  0.004   0.041   1178
  Dihedral  :  5.349  55.308   1013
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 12.14 %
    Favored  : 86.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.36 (0.30), residues: 793
  helix:  1.50 (0.26), residues: 395
  sheet:  0.35 (0.72), residues: 42
  loop :  0.43 (0.34), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP E 610 
 HIS   0.006   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.016   0.001   TYR E 385 
 ARG   0.003   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
  78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8039 (tm-30)
REVERT: B  506 GLN cc_start: 0.9264 (mt0) cc_final: 0.8748 (mt0)
REVERT: E  323 MET cc_start: 0.9056 (mmt) cc_final: 0.8674 (mmt)
REVERT: E  376 MET cc_start: 0.9126 (ttm) cc_final: 0.8774 (mmm)
REVERT: E  483 GLU cc_start: 0.8972 (tp30) cc_final: 0.8692 (tp30)
  outliers start: 12
  outliers final: 10
  residues processed: 78
  average time/residue: 0.1862
  time to fit residues: 19.8854
Evaluate side-chains
  72 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  359 SER
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  423 LEU
Chi-restraints excluded: chain E residue  475 LYS
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9980
   chunk 62 optimal weight:    0.0070
   chunk 67 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   overall best weight:    1.1402

-------------------------------------------------------------------------------
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 = 0.3268 r_free = 0.3268 target = 0.080277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.063622 restraints weight = 17289.508|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 3.18
r_work: 0.2805 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8603
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   6735  Z= 0.281
  Angle     :  0.546   8.142   9152  Z= 0.279
  Chirality :  0.042   0.148    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  5.329  55.552   1013
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.86 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.38 (0.30), residues: 793
  helix:  1.39 (0.26), residues: 402
  sheet:  0.25 (0.70), residues: 47
  loop :  0.62 (0.34), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP E 610 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E 385 
 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
  75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8046 (tm-30)
REVERT: B  506 GLN cc_start: 0.9268 (mt0) cc_final: 0.8754 (mt0)
REVERT: E  376 MET cc_start: 0.9116 (ttm) cc_final: 0.8809 (tpp)
  outliers start: 13
  outliers final: 8
  residues processed: 75
  average time/residue: 0.1866
  time to fit residues: 19.4354
Evaluate side-chains
  68 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  423 LEU
Chi-restraints excluded: chain E residue  475 LYS
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   chunk 71 optimal weight:    2.9990
   chunk 31 optimal weight:    6.9990
   chunk 40 optimal weight:    0.5980
   chunk 70 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3289 r_free = 0.3289 target = 0.081442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.064671 restraints weight = 17256.908|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.19
r_work: 0.2827 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6735  Z= 0.220
  Angle     :  0.524   7.812   9152  Z= 0.267
  Chirality :  0.041   0.149    977
  Planarity :  0.004   0.038   1178
  Dihedral  :  5.169  55.685   1013
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.43 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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 (0.30), residues: 793
  helix:  1.51 (0.26), residues: 400
  sheet:  0.18 (0.70), residues: 47
  loop :  0.63 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP E 610 
 HIS   0.005   0.001   HIS E  34 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.003   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
  75 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
REVERT: B  506 GLN cc_start: 0.9279 (mt0) cc_final: 0.8711 (mt0)
REVERT: E  376 MET cc_start: 0.9094 (ttm) cc_final: 0.8888 (tpp)
REVERT: E  483 GLU cc_start: 0.8985 (tp30) cc_final: 0.8708 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1848
  time to fit residues: 19.2986
Evaluate side-chains
  71 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  423 LEU
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 36 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 4 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 41 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   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 442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.082384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.065621 restraints weight = 17314.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 3.22
r_work: 0.2840 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8570
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6735  Z= 0.186
  Angle     :  0.515   7.331   9152  Z= 0.262
  Chirality :  0.041   0.161    977
  Planarity :  0.003   0.037   1178
  Dihedral  :  4.955  55.815   1013
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 12.29 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.58 (0.30), residues: 793
  helix:  1.59 (0.26), residues: 400
  sheet:  0.18 (0.72), residues: 47
  loop :  0.71 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP E 610 
 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 B 452 

*********************** 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
  78 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.842 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8023 (tm-30)
REVERT: B  470 THR cc_start: 0.8989 (p) cc_final: 0.8618 (t)
REVERT: B  506 GLN cc_start: 0.9282 (mt0) cc_final: 0.8684 (mt0)
REVERT: E  560 LEU cc_start: 0.9129 (mt) cc_final: 0.8843 (tp)
REVERT: E  564 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8754 (mp0)
  outliers start: 9
  outliers final: 7
  residues processed: 76
  average time/residue: 0.1860
  time to fit residues: 19.5349
Evaluate side-chains
  74 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 67
  time to evaluate  : 0.663 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  423 LEU
Chi-restraints excluded: chain E residue  436 ILE
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.1980
   chunk 16 optimal weight:    0.2980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3302 r_free = 0.3302 target = 0.082328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2974 r_free = 0.2974 target = 0.065449 restraints weight = 17326.441|
|-----------------------------------------------------------------------------|
r_work (start): 0.2967 rms_B_bonded: 3.23
r_work: 0.2839 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6735  Z= 0.200
  Angle     :  0.523   7.366   9152  Z= 0.267
  Chirality :  0.041   0.148    977
  Planarity :  0.004   0.040   1178
  Dihedral  :  4.933  55.953   1013
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.57 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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 (0.30), residues: 793
  helix:  1.58 (0.26), residues: 400
  sheet:  0.19 (0.72), residues: 47
  loop :  0.74 (0.35), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.001   TRP E 610 
 HIS   0.004   0.001   HIS E 239 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   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
  79 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.818 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8023 (tm-30)
REVERT: B  470 THR cc_start: 0.8952 (p) cc_final: 0.8576 (t)
REVERT: B  506 GLN cc_start: 0.9282 (mt0) cc_final: 0.8679 (mt0)
REVERT: E  483 GLU cc_start: 0.8951 (tp30) cc_final: 0.8704 (tp30)
  outliers start: 8
  outliers final: 5
  residues processed: 78
  average time/residue: 0.1966
  time to fit residues: 21.3459
Evaluate side-chains
  70 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   55 THR
Chi-restraints excluded: chain E residue  148 LEU
Chi-restraints excluded: chain E residue  488 VAL
Chi-restraints excluded: chain E residue  506 VAL
Chi-restraints excluded: chain E residue  581 VAL
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 63 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
E 154 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.081985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.064998 restraints weight = 17500.806|
|-----------------------------------------------------------------------------|
r_work (start): 0.2957 rms_B_bonded: 3.25
r_work: 0.2828 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8586
moved from start:          0.3416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6735  Z= 0.230
  Angle     :  0.542   7.563   9152  Z= 0.276
  Chirality :  0.042   0.156    977
  Planarity :  0.004   0.039   1178
  Dihedral  :  5.010  56.034   1013
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  : 13.14 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.68 (0.30), residues: 793
  helix:  1.68 (0.26), residues: 392
  sheet:  0.14 (0.72), residues: 47
  loop :  0.77 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.001   TRP E 610 
 HIS   0.004   0.001   HIS E 239 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.013   0.001   TYR E 385 
 ARG   0.001   0.000   ARG E 245 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2911.25 seconds
wall clock time: 50 minutes 56.23 seconds (3056.23 seconds total)