Starting phenix.real_space_refine
on Tue Feb 11 22:22:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sy4_25516/02_2025/7sy4_25516.cif"
  }
  resolution = 3.35
  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=   0.025
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    4192      2.51       5
     N    1078      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6554
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1594
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1594
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "E"
      Number of atoms: 4862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4862
          Classifications: {'peptide': 596}
          Link IDs: {'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: 5.33, per 1000 atoms: 0.81
  Number of scatterers: 6554
  At special positions: 0
  Unit cell: (82, 84, 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    1247      8.00
     N    1078      7.00
     C    4192      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=2.02
    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=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    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: 1.63
  Conformation dependent library (CDL) restraints added in 926.5 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:
      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: 0.66
  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 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.754A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 20 through 53
      removed outlier: 4.006A  pdb=" N   GLU E  35 " --> pdb=" O   LYS E  31 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   ASP E  38 " --> pdb=" O   HIS E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 55 through 81
      removed outlier: 3.516A  pdb=" N   GLN E  81 " --> pdb=" O   SER E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 84 through 88
      removed outlier: 3.775A  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: 4.056A  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: 3.944A  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: 3.726A  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: 3.658A  pdb=" N   LEU E 222 " --> pdb=" O   SER E 218 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ILE E 223 " --> pdb=" O   ARG E 219 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU E 224 " --> pdb=" O   GLY E 220 " (cutoff:3.500A)
      removed outlier: 3.775A  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: 3.768A  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: 3.610A  pdb=" N   TRP E 328 " --> pdb=" O   THR E 324 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 365 through 385
      removed outlier: 3.709A  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: 4.279A  pdb=" N   HIS E 401 " --> pdb=" O   ASN E 397 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU E 402 " --> pdb=" O   GLU E 398 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY E 405 " --> pdb=" O   HIS E 401 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   MET E 408 " --> pdb=" O   VAL E 404 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ALA E 413 " --> pdb=" O   SER E 409 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 414 through 421
    Processing helix  chain 'E' and resid 431 through 447
      removed outlier: 3.558A  pdb=" N   GLU E 435 " --> pdb=" O   ASP E 431 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 448 through 465
      removed outlier: 4.375A  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: 3.719A  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: 4.509A  pdb=" N   TYR E 516 " --> pdb=" O   PHE E 512 " (cutoff:3.500A)
      removed outlier: 3.596A  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: 3.917A  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: 3.945A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.834A  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: 3.753A  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: 6.050A  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: 6.333A  pdb=" N   ASP E 355 " --> pdb=" O   LEU E 351 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    906 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: 1.76

  Time building geometry restraints manager: 1.89 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: 1776
        1.47 -     1.59: 2824
        1.59 -     1.72: 0
        1.72 -     1.84: 58
  Bond restraints: 6737
  Sorted by residual:
  bond pdb=" C1  NAG E 702 "
       pdb=" O5  NAG E 702 "
    ideal  model  delta    sigma   weight residual
    1.406  1.456 -0.050 2.00e-02 2.50e+03 6.27e+00
  bond pdb=" C1  NAG E 704 "
       pdb=" O5  NAG E 704 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 5.09e+00
  bond pdb=" C1  NAG E 703 "
       pdb=" O5  NAG E 703 "
    ideal  model  delta    sigma   weight residual
    1.406  1.451 -0.045 2.00e-02 2.50e+03 4.98e+00
  bond pdb=" C1  NAG E 705 "
       pdb=" O5  NAG E 705 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 3.97e+00
  bond pdb=" C1  NAG E 706 "
       pdb=" O5  NAG E 706 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.68e+00
  ... (remaining 6732 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 8787
        1.96 -     3.93: 314
        3.93 -     5.89: 42
        5.89 -     7.85: 8
        7.85 -     9.82: 4
  Bond angle restraints: 9155
  Sorted by residual:
  angle pdb=" N   PHE E  32 "
        pdb=" CA  PHE E  32 "
        pdb=" C   PHE E  32 "
      ideal   model   delta    sigma   weight residual
     111.04  103.72    7.32 1.55e+00 4.16e-01 2.23e+01
  angle pdb=" C   SER B 359 "
        pdb=" N   ASN B 360 "
        pdb=" CA  ASN B 360 "
      ideal   model   delta    sigma   weight residual
     122.82  128.97   -6.15 1.42e+00 4.96e-01 1.88e+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  123.24   -8.84 2.30e+00 1.89e-01 1.48e+01
  angle pdb=" CA  TYR B 495 "
        pdb=" CB  TYR B 495 "
        pdb=" CG  TYR B 495 "
      ideal   model   delta    sigma   weight residual
     113.90  120.23   -6.33 1.80e+00 3.09e-01 1.24e+01
  angle pdb=" N   LYS E 234 "
        pdb=" CA  LYS E 234 "
        pdb=" C   LYS E 234 "
      ideal   model   delta    sigma   weight residual
     113.16  118.06   -4.90 1.42e+00 4.96e-01 1.19e+01
  ... (remaining 9150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.13: 3689
       17.13 -    34.26: 312
       34.26 -    51.39: 45
       51.39 -    68.52: 9
       68.52 -    85.65: 12
  Dihedral angle restraints: 4067
    sinusoidal: 1728
      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  -43.96  -42.04     1      1.00e+01 1.00e-02 2.47e+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   14.88   64.12     1      2.00e+01 2.50e-03 1.35e+01
  dihedral pdb=" CA  ALA E 396 "
           pdb=" C   ALA E 396 "
           pdb=" N   ASN E 397 "
           pdb=" CA  ASN E 397 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.62   16.38     0      5.00e+00 4.00e-02 1.07e+01
  ... (remaining 4064 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 714
       0.052 -    0.105: 197
       0.105 -    0.157: 55
       0.157 -    0.210: 10
       0.210 -    0.262: 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 1.72e+00
  chirality pdb=" C1  NAG E 703 "
            pdb=" ND2 ASN E 103 "
            pdb=" C2  NAG E 703 "
            pdb=" O5  NAG E 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  PRO B 491 "
            pdb=" N   PRO B 491 "
            pdb=" C   PRO B 491 "
            pdb=" CB  PRO B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.52    0.20 2.00e-01 2.50e+01 1.03e+00
  ... (remaining 975 not shown)

  Planarity restraints: 1183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 169 "   -0.016 2.00e-02 2.50e+03   3.25e-02 1.06e+01
        pdb=" C   ARG E 169 "    0.056 2.00e-02 2.50e+03
        pdb=" O   ARG E 169 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   SER E 170 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU E  29 "    0.015 2.00e-02 2.50e+03   3.07e-02 9.46e+00
        pdb=" C   LEU E  29 "   -0.053 2.00e-02 2.50e+03
        pdb=" O   LEU E  29 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ASP E  30 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA E  36 "   -0.015 2.00e-02 2.50e+03   2.95e-02 8.68e+00
        pdb=" C   ALA E  36 "    0.051 2.00e-02 2.50e+03
        pdb=" O   ALA E  36 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU E  37 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1180 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.86: 2205
        2.86 -     3.37: 5969
        3.37 -     3.88: 11213
        3.88 -     4.39: 12524
        4.39 -     4.90: 21658
  Nonbonded interactions: 53569
  Sorted by model distance:
  nonbonded pdb=" OH  TYR E 183 "
            pdb=" OD1 ASP E 509 "
     model   vdw
     2.345 3.040
  nonbonded pdb=" O   ASN E 117 "
            pdb=" ND2 ASN E 121 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OD1 ASN B 487 "
            pdb=" OH  TYR E  83 "
     model   vdw
     2.369 3.040
  nonbonded pdb=" O   MET E 152 "
            pdb=" NH1 ARG E 161 "
     model   vdw
     2.369 3.120
  ... (remaining 53564 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:             3.430
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.260
  Find NCS groups from input model:        0.070
  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:2.940
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
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   0.055   6737  Z= 0.319
  Angle     :  0.846   9.819   9155  Z= 0.461
  Chirality :  0.055   0.262    978
  Planarity :  0.007   0.063   1176
  Dihedral  : 13.360  85.655   2549
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 2.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  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: -0.68 (0.26), residues: 793
  helix: -0.29 (0.23), residues: 387
  sheet:  0.99 (0.73), residues: 43
  loop : -0.68 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP E 165 
 HIS   0.005   0.001   HIS E 378 
 PHE   0.030   0.002   PHE E 369 
 TYR   0.028   0.002   TYR B 495 
 ARG   0.009   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
  108 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.746 
Fit side-chains
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8365 (mt-10)
REVERT: B  414 GLN cc_start: 0.9364 (mm-40) cc_final: 0.9059 (mm-40)
REVERT: B  420 ASP cc_start: 0.9060 (m-30) cc_final: 0.8777 (m-30)
REVERT: E   37 GLU cc_start: 0.8226 (tt0) cc_final: 0.7840 (tp30)
REVERT: E   82 MET cc_start: 0.8690 (mtp) cc_final: 0.8253 (ttm)
REVERT: E  323 MET cc_start: 0.9194 (mmp) cc_final: 0.8739 (mmm)
REVERT: E  367 ASP cc_start: 0.9374 (m-30) cc_final: 0.9118 (p0)
REVERT: E  368 ASP cc_start: 0.8701 (m-30) cc_final: 0.8012 (m-30)
REVERT: E  409 SER cc_start: 0.9539 (t) cc_final: 0.9192 (p)
REVERT: E  429 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8156 (tm-30)
REVERT: E  435 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8766 (mm-30)
REVERT: E  462 MET cc_start: 0.9332 (mtp) cc_final: 0.9099 (mtt)
REVERT: E  471 ASP cc_start: 0.8880 (p0) cc_final: 0.8604 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.2625
  time to fit residues: 35.4922
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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:    0.9980
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3174 r_free = 0.3174 target = 0.062383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.046516 restraints weight = 22247.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.2736 rms_B_bonded: 3.88
r_work: 0.2579 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6737  Z= 0.269
  Angle     :  0.576   6.645   9155  Z= 0.301
  Chirality :  0.043   0.179    978
  Planarity :  0.005   0.037   1176
  Dihedral  :  5.311  50.798   1013
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.29 %
    Favored  : 91.00 %
  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:  0.74 (0.28), residues: 793
  helix:  1.13 (0.25), residues: 388
  sheet:  0.79 (0.74), residues: 43
  loop : -0.15 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 378 
 PHE   0.015   0.001   PHE E 523 
 TYR   0.025   0.001   TYR E  50 
 ARG   0.006   0.001   ARG B 466 

*********************** 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
  61 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8603 (mt-10)
REVERT: B  498 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8792 (mm-40)
REVERT: E  270 MET cc_start: 0.9210 (tpp) cc_final: 0.8802 (tpp)
REVERT: E  323 MET cc_start: 0.9409 (mmp) cc_final: 0.9082 (mmm)
REVERT: E  332 MET cc_start: 0.8916 (ptm) cc_final: 0.8664 (ttp)
REVERT: E  360 MET cc_start: 0.8445 (tpt) cc_final: 0.8136 (tmm)
REVERT: E  368 ASP cc_start: 0.8999 (m-30) cc_final: 0.8527 (t0)
REVERT: E  429 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8043 (tm-30)
REVERT: E  471 ASP cc_start: 0.9043 (p0) cc_final: 0.8776 (t0)
  outliers start: 5
  outliers final: 1
  residues processed: 60
  average time/residue: 0.1481
  time to fit residues: 13.3788
Evaluate side-chains
  48 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain E residue  447 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 27 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 46 optimal weight:    0.1980
   chunk 66 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 44 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.062462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.046612 restraints weight = 22529.732|
|-----------------------------------------------------------------------------|
r_work (start): 0.2763 rms_B_bonded: 3.93
r_work: 0.2607 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.2348

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6737  Z= 0.169
  Angle     :  0.494   5.693   9155  Z= 0.257
  Chirality :  0.040   0.150    978
  Planarity :  0.004   0.037   1176
  Dihedral  :  4.893  53.383   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  9.43 %
    Favored  : 90.00 %
  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:  1.23 (0.29), residues: 793
  helix:  1.67 (0.26), residues: 381
  sheet:  0.53 (0.72), residues: 43
  loop :  0.02 (0.31), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E  34 
 PHE   0.015   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 466 

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

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

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

  1586 Ramachandran restraints generated.
    793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.718 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8715 (mt-10)
REVERT: B  498 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8715 (mm-40)
REVERT: E  123 MET cc_start: 0.8894 (mmm) cc_final: 0.8673 (mmt)
REVERT: E  142 LEU cc_start: 0.9435 (mm) cc_final: 0.9134 (tp)
REVERT: E  270 MET cc_start: 0.9063 (tpp) cc_final: 0.8537 (tpp)
REVERT: E  323 MET cc_start: 0.9514 (mmp) cc_final: 0.9059 (mmm)
REVERT: E  332 MET cc_start: 0.8969 (ptm) cc_final: 0.8710 (ttp)
REVERT: E  360 MET cc_start: 0.8279 (tpt) cc_final: 0.8034 (tmm)
REVERT: E  368 ASP cc_start: 0.8819 (m-30) cc_final: 0.8567 (t0)
  outliers start: 4
  outliers final: 0
  residues processed: 57
  average time/residue: 0.1252
  time to fit residues: 11.1309
Evaluate side-chains
  45 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0970
   chunk 41 optimal weight:    0.2980
   chunk 15 optimal weight:    0.0060
   chunk 19 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0040
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    0.2980
   chunk 22 optimal weight:    4.9990
   overall best weight:    0.1406

-------------------------------------------------------------------------------
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 = 0.3232 r_free = 0.3232 target = 0.064619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.048889 restraints weight = 22541.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.99
r_work: 0.2693 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6737  Z= 0.124
  Angle     :  0.456   5.233   9155  Z= 0.238
  Chirality :  0.039   0.132    978
  Planarity :  0.003   0.035   1176
  Dihedral  :  4.582  55.319   1013
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  9.86 %
    Favored  : 89.86 %
  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:  1.49 (0.29), residues: 793
  helix:  1.85 (0.26), residues: 386
  sheet:  0.52 (0.72), residues: 43
  loop :  0.18 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.002   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E  50 
 ARG   0.006   0.000   ARG B 403 

*********************** 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
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  405 ASP cc_start: 0.8987 (p0) cc_final: 0.8738 (p0)
REVERT: E  270 MET cc_start: 0.8950 (tpp) cc_final: 0.8414 (tpp)
REVERT: E  462 MET cc_start: 0.9625 (mtm) cc_final: 0.9379 (mtm)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.1308
  time to fit residues: 10.4423
Evaluate side-chains
  44 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue  447 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3172 r_free = 0.3172 target = 0.062226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.046371 restraints weight = 22415.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2755 rms_B_bonded: 3.90
r_work: 0.2602 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6737  Z= 0.191
  Angle     :  0.476   5.608   9155  Z= 0.247
  Chirality :  0.040   0.142    978
  Planarity :  0.003   0.036   1176
  Dihedral  :  4.535  54.669   1013
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 10.14 %
    Favored  : 89.14 %
  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:  1.78 (0.30), residues: 793
  helix:  2.04 (0.26), residues: 385
  sheet:  0.65 (0.74), residues: 43
  loop :  0.41 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP E 165 
 HIS   0.002   0.001   HIS E 374 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.012   0.001   TYR B 495 
 ARG   0.003   0.000   ARG B 466 

*********************** 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
  53 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 48
  time to evaluate  : 0.736 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  498 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8812 (mm-40)
REVERT: E   23 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9110 (pt0)
REVERT: E  267 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9229 (mm)
REVERT: E  270 MET cc_start: 0.8872 (tpp) cc_final: 0.8271 (tpp)
REVERT: E  332 MET cc_start: 0.9052 (ttp) cc_final: 0.8628 (ppp)
REVERT: E  368 ASP cc_start: 0.9103 (m-30) cc_final: 0.8507 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1312
  time to fit residues: 10.7202
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  447 VAL
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 43 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3167 r_free = 0.3167 target = 0.061775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.046085 restraints weight = 22517.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 3.86
r_work: 0.2616 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8590
moved from start:          0.2974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6737  Z= 0.213
  Angle     :  0.487   5.954   9155  Z= 0.252
  Chirality :  0.040   0.146    978
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.564  55.347   1013
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  9.86 %
    Favored  : 89.14 %
  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:  1.83 (0.30), residues: 793
  helix:  2.04 (0.26), residues: 385
  sheet:  0.51 (0.74), residues: 43
  loop :  0.52 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 403 

*********************** 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
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8871 (mp0) cc_final: 0.8104 (mp0)
REVERT: B  498 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8820 (mm-40)
REVERT: E   82 MET cc_start: 0.9137 (mtp) cc_final: 0.8788 (ttp)
REVERT: E   86 GLN cc_start: 0.9097 (pm20) cc_final: 0.8778 (pm20)
REVERT: E  267 LEU cc_start: 0.9629 (OUTLIER) cc_final: 0.9293 (mm)
REVERT: E  270 MET cc_start: 0.8860 (tpp) cc_final: 0.8244 (tpp)
REVERT: E  323 MET cc_start: 0.9163 (mmm) cc_final: 0.8741 (mmm)
REVERT: E  332 MET cc_start: 0.9096 (ttp) cc_final: 0.8721 (ppp)
REVERT: E  360 MET cc_start: 0.8093 (tmm) cc_final: 0.7444 (tmm)
REVERT: E  368 ASP cc_start: 0.9070 (m-30) cc_final: 0.8495 (t0)
REVERT: E  462 MET cc_start: 0.9635 (mtm) cc_final: 0.9174 (mtt)
  outliers start: 7
  outliers final: 3
  residues processed: 54
  average time/residue: 0.1395
  time to fit residues: 11.6795
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  318 VAL
Chi-restraints excluded: chain E residue  447 VAL
Chi-restraints excluded: chain E residue  506 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 51 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 73 optimal weight:    0.7980
   chunk 52 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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 = 0.3127 r_free = 0.3127 target = 0.060187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.044654 restraints weight = 22787.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.2718 rms_B_bonded: 3.81
r_work: 0.2570 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.2570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8563
moved from start:          0.3166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6737  Z= 0.279
  Angle     :  0.528   6.340   9155  Z= 0.272
  Chirality :  0.041   0.158    978
  Planarity :  0.004   0.035   1176
  Dihedral  :  4.681  55.009   1013
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.43 %
    Favored  : 88.29 %
  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:  1.79 (0.30), residues: 793
  helix:  1.94 (0.26), residues: 392
  sheet:  0.38 (0.72), residues: 43
  loop :  0.57 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.014   0.001   PHE E 369 
 TYR   0.014   0.001   TYR B 453 
 ARG   0.004   0.000   ARG B 403 

*********************** 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
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8681 (mt-10)
REVERT: B  442 ASP cc_start: 0.9053 (m-30) cc_final: 0.8806 (m-30)
REVERT: B  498 GLN cc_start: 0.9424 (OUTLIER) cc_final: 0.9213 (mt0)
REVERT: B  518 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7228 (tt)
REVERT: E   86 GLN cc_start: 0.9149 (pm20) cc_final: 0.8810 (pm20)
REVERT: E  267 LEU cc_start: 0.9614 (OUTLIER) cc_final: 0.9290 (mm)
REVERT: E  270 MET cc_start: 0.8747 (tpp) cc_final: 0.8062 (tpp)
REVERT: E  332 MET cc_start: 0.9203 (ttp) cc_final: 0.8785 (ppp)
REVERT: E  360 MET cc_start: 0.8209 (tmm) cc_final: 0.7418 (tmm)
REVERT: E  368 ASP cc_start: 0.9179 (m-30) cc_final: 0.8645 (t0)
REVERT: E  462 MET cc_start: 0.9618 (mtm) cc_final: 0.9350 (mtm)
  outliers start: 9
  outliers final: 1
  residues processed: 55
  average time/residue: 0.1507
  time to fit residues: 12.6401
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 45
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    0.1980
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3181 r_free = 0.3181 target = 0.062436 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.046689 restraints weight = 22598.219|
|-----------------------------------------------------------------------------|
r_work (start): 0.2772 rms_B_bonded: 3.90
r_work: 0.2619 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6737  Z= 0.157
  Angle     :  0.469   5.287   9155  Z= 0.242
  Chirality :  0.040   0.137    978
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.524  56.503   1013
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.43 %
    Favored  : 88.57 %
  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:  1.77 (0.30), residues: 793
  helix:  1.97 (0.26), residues: 391
  sheet:  0.27 (0.72), residues: 43
  loop :  0.52 (0.35), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.015   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 403 

*********************** 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
  56 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.814 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8101 (mp0)
REVERT: B  498 GLN cc_start: 0.9354 (OUTLIER) cc_final: 0.8837 (mm-40)
REVERT: B  518 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7202 (tt)
REVERT: E   82 MET cc_start: 0.9184 (mtp) cc_final: 0.8795 (ttp)
REVERT: E   86 GLN cc_start: 0.9116 (pm20) cc_final: 0.8774 (pm20)
REVERT: E  267 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9259 (mm)
REVERT: E  270 MET cc_start: 0.8656 (tpp) cc_final: 0.7990 (tpp)
REVERT: E  323 MET cc_start: 0.9276 (mmm) cc_final: 0.8860 (mmm)
REVERT: E  332 MET cc_start: 0.9111 (ttp) cc_final: 0.8754 (ppp)
REVERT: E  360 MET cc_start: 0.8016 (tmm) cc_final: 0.7378 (tmm)
REVERT: E  368 ASP cc_start: 0.9121 (m-30) cc_final: 0.8570 (t0)
  outliers start: 7
  outliers final: 2
  residues processed: 55
  average time/residue: 0.1362
  time to fit residues: 11.6892
Evaluate side-chains
  50 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  406 GLU
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 11 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0570
   chunk 51 optimal weight:    7.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3176 r_free = 0.3176 target = 0.062280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.046699 restraints weight = 22598.702|
|-----------------------------------------------------------------------------|
r_work (start): 0.2740 rms_B_bonded: 3.89
r_work: 0.2583 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8497
moved from start:          0.3305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6737  Z= 0.175
  Angle     :  0.484   7.230   9155  Z= 0.250
  Chirality :  0.040   0.167    978
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.483  56.251   1013
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 11.43 %
    Favored  : 87.86 %
  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:  1.77 (0.30), residues: 793
  helix:  1.98 (0.26), residues: 391
  sheet:  0.06 (0.70), residues: 45
  loop :  0.54 (0.35), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.012   0.001   PHE E 369 
 TYR   0.017   0.001   TYR E  50 
 ARG   0.002   0.000   ARG B 466 

*********************** 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
  52 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 47
  time to evaluate  : 0.758 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8901 (mp0) cc_final: 0.8685 (mt-10)
REVERT: B  498 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8822 (mm-40)
REVERT: B  518 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7195 (tt)
REVERT: E   86 GLN cc_start: 0.9152 (pm20) cc_final: 0.8802 (pm20)
REVERT: E  267 LEU cc_start: 0.9568 (OUTLIER) cc_final: 0.9257 (mm)
REVERT: E  270 MET cc_start: 0.8628 (tpp) cc_final: 0.7959 (tpp)
REVERT: E  323 MET cc_start: 0.9234 (mmm) cc_final: 0.8883 (mmm)
REVERT: E  332 MET cc_start: 0.9140 (ttp) cc_final: 0.8758 (ppp)
REVERT: E  360 MET cc_start: 0.8010 (tmm) cc_final: 0.7339 (tmm)
REVERT: E  368 ASP cc_start: 0.9119 (m-30) cc_final: 0.8562 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 52
  average time/residue: 0.1333
  time to fit residues: 10.7964
Evaluate side-chains
  49 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 44
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 19 optimal weight:    0.0770
   chunk 16 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 78 optimal weight:    6.9990
   chunk 9 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 54 optimal weight:    6.9990
   overall best weight:    0.6138

-------------------------------------------------------------------------------
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 = 0.3186 r_free = 0.3186 target = 0.062774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.047092 restraints weight = 22770.733|
|-----------------------------------------------------------------------------|
r_work (start): 0.2750 rms_B_bonded: 3.90
r_work: 0.2597 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6737  Z= 0.176
  Angle     :  0.518   8.173   9155  Z= 0.264
  Chirality :  0.041   0.166    978
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.480  56.444   1013
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.14 %
    Favored  : 87.14 %
  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:  1.76 (0.30), residues: 793
  helix:  1.91 (0.26), residues: 388
  sheet:  0.22 (0.71), residues: 43
  loop :  0.61 (0.35), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.013   0.001   PHE E 369 
 TYR   0.019   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 403 

********************** 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
  54 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 49
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  406 GLU cc_start: 0.8922 (mp0) cc_final: 0.8022 (mp0)
REVERT: B  498 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8836 (mm-40)
REVERT: B  518 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7180 (tt)
REVERT: E   82 MET cc_start: 0.9201 (mtp) cc_final: 0.8869 (ttm)
REVERT: E   86 GLN cc_start: 0.9156 (pm20) cc_final: 0.8803 (pm20)
REVERT: E  267 LEU cc_start: 0.9563 (OUTLIER) cc_final: 0.9237 (mm)
REVERT: E  270 MET cc_start: 0.8639 (tpp) cc_final: 0.7968 (tpp)
REVERT: E  323 MET cc_start: 0.9218 (mmm) cc_final: 0.8862 (mmm)
REVERT: E  332 MET cc_start: 0.9142 (ttp) cc_final: 0.8771 (ppp)
REVERT: E  360 MET cc_start: 0.7864 (tmm) cc_final: 0.7049 (tmm)
REVERT: E  368 ASP cc_start: 0.8978 (m-30) cc_final: 0.8634 (t0)
REVERT: E  480 MET cc_start: 0.9154 (mtp) cc_final: 0.8906 (mtt)
  outliers start: 5
  outliers final: 2
  residues processed: 54
  average time/residue: 0.1409
  time to fit residues: 11.7829
Evaluate side-chains
  51 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.747 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  498 GLN
Chi-restraints excluded: chain B residue  518 LEU
Chi-restraints excluded: chain E residue  233 ILE
Chi-restraints excluded: chain E residue  267 LEU
Chi-restraints excluded: chain E residue  318 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3174 r_free = 0.3174 target = 0.062181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.046473 restraints weight = 22895.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.2764 rms_B_bonded: 3.91
r_work: 0.2608 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.3452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6737  Z= 0.204
  Angle     :  0.542  16.198   9155  Z= 0.272
  Chirality :  0.041   0.142    978
  Planarity :  0.003   0.034   1176
  Dihedral  :  4.509  56.083   1013
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.57 %
    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:  1.78 (0.31), residues: 793
  helix:  1.89 (0.26), residues: 389
  sheet:  0.25 (0.71), residues: 43
  loop :  0.65 (0.36), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 165 
 HIS   0.003   0.001   HIS E 374 
 PHE   0.011   0.001   PHE E 369 
 TYR   0.019   0.001   TYR E  50 
 ARG   0.003   0.000   ARG B 403 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3068.96 seconds
wall clock time: 55 minutes 17.15 seconds (3317.15 seconds total)