Starting phenix.real_space_refine
on Tue May  7 01:51:07 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wtd_37832/05_2024/8wtd_37832.pdb"
  }
  resolution = 3.06
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.072
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    4134      2.51       5
     N    1069      2.21       5
     O    1216      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  171": "OE1" <-> "OE2"
    Residue "A GLU  182": "OE1" <-> "OE2"
    Residue "B TYR  453": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib"
  Total number of atoms: 6456
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4845
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 4845
          Classifications: {'peptide': 594}
          Link IDs: {'PTRANS': 27, 'TRANS': 566}
    Chain: "B"
      Number of atoms: 1555
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1555
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 3.99, per 1000 atoms: 0.62
  Number of scatterers: 6456
  At special positions: 0
  Unit cell: (73.528, 91.304, 117.16, 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    1216      8.00
     N    1069      7.00
     C    4134      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " 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=1.99

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 901 " - " ASN A 546 "
      " NAG A 902 " - " ASN A  90 "
      " NAG A 903 " - " ASN A 322 "
      " NAG A 904 " - " ASN A  53 "
  Time building additional restraints: 2.53
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1490

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      53.8% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 29
    Processing helix  chain 'A' and resid 31 through 53
      removed outlier: 3.935A  pdb=" N   GLU A  35 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   GLU A  37 " --> pdb=" O   ASN A  33 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 79
      removed outlier: 3.545A  pdb=" N   VAL A  59 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
    Processing helix  chain 'A' and resid 91 through 101
    Processing helix  chain 'A' and resid 109 through 130
    Processing helix  chain 'A' and resid 146 through 154
    Processing helix  chain 'A' and resid 157 through 194
      removed outlier: 3.721A  pdb=" N   GLY A 173 " --> pdb=" O   ARG A 169 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
      removed outlier: 3.991A  pdb=" N   GLU A 182 " --> pdb=" O   PRO A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
      removed outlier: 3.630A  pdb=" N   ASN A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ALA A 251 " --> pdb=" O   LYS A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 293 through 300
    Processing helix  chain 'A' and resid 303 through 319
    Processing helix  chain 'A' and resid 324 through 331
      removed outlier: 4.156A  pdb=" N   TRP A 328 " --> pdb=" O   THR A 324 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLU A 329 " --> pdb=" O   GLN A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.578A  pdb=" N   TYR A 385 " --> pdb=" O   TYR A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.679A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA A 413 " --> pdb=" O   SER A 409 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 422
    Processing helix  chain 'A' and resid 431 through 446
    Processing helix  chain 'A' and resid 449 through 466
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.745A  pdb=" N   GLU A 483 " --> pdb=" O   GLU A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 502
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 512 through 533
      removed outlier: 4.115A  pdb=" N   TYR A 516 " --> pdb=" O   PHE A 512 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   THR A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 520 " --> pdb=" O   TYR A 516 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   PHE A 523 " --> pdb=" O   THR A 519 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 542
      removed outlier: 3.543A  pdb=" N   LYS A 541 " --> pdb=" O   PRO A 538 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   CYS A 542 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 538 through 542'
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 3.852A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 574
      removed outlier: 3.738A  pdb=" N   VAL A 573 " --> pdb=" O   ALA A 569 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'A' and resid 600 through 602
      No H-bonds generated for 'chain 'A' and resid 600 through 602'
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.692A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   PHE B 342 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 3.533A  pdb=" N   PHE B 371 " --> pdb=" O   ILE B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 389
      removed outlier: 3.601A  pdb=" N   ASP B 389 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 386 through 389'
    Processing helix  chain 'B' and resid 406 through 410
    Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.233A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.531A  pdb=" N   LYS B 356 " --> pdb=" O   ALA B 397 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ASN B 437 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 7.423A  pdb=" N   PHE B 374 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 361 through 362
      removed outlier: 6.356A  pdb=" N   CYS B 361 " --> pdb=" O   CYS B 525 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 448 through 454
      removed outlier: 8.324A  pdb=" N   ASN B 450 " --> pdb=" O   SER B 494 " (cutoff:3.500A)
      removed outlier: 8.309A  pdb=" N   SER B 494 " --> pdb=" O   ASN B 450 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   LEU B 452 " --> pdb=" O   LEU B 492 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   LEU B 492 " --> pdb=" O   LEU B 452 " (cutoff:3.500A)

    298 hydrogen bonds defined for protein.
    843 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: 1.87

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 1069
        1.29 -     1.42: 1837
        1.42 -     1.55: 3676
        1.55 -     1.68: 0
        1.68 -     1.81: 58
  Bond restraints: 6640
  Sorted by residual:
  bond pdb=" C   PRO B 491 "
       pdb=" O   PRO B 491 "
    ideal  model  delta    sigma   weight residual
    1.235  1.156  0.079 1.30e-02 5.92e+03 3.70e+01
  bond pdb=" CA  ALA A  36 "
       pdb=" CB  ALA A  36 "
    ideal  model  delta    sigma   weight residual
    1.529  1.450  0.079 1.58e-02 4.01e+03 2.50e+01
  bond pdb=" CA  SER B 494 "
       pdb=" CB  SER B 494 "
    ideal  model  delta    sigma   weight residual
    1.532  1.454  0.077 1.59e-02 3.96e+03 2.38e+01
  bond pdb=" CA  SER B 490 "
       pdb=" CB  SER B 490 "
    ideal  model  delta    sigma   weight residual
    1.526  1.454  0.073 1.53e-02 4.27e+03 2.25e+01
  bond pdb=" C   PRO B 486 "
       pdb=" O   PRO B 486 "
    ideal  model  delta    sigma   weight residual
    1.233  1.190  0.043 9.60e-03 1.09e+04 2.03e+01
  ... (remaining 6635 not shown)

  Histogram of bond angle deviations from ideal:
       95.40 -   103.12: 62
      103.12 -   110.85: 2196
      110.85 -   118.57: 2959
      118.57 -   126.29: 3665
      126.29 -   134.01: 144
  Bond angle restraints: 9026
  Sorted by residual:
  angle pdb=" N   LYS A  31 "
        pdb=" CA  LYS A  31 "
        pdb=" C   LYS A  31 "
      ideal   model   delta    sigma   weight residual
     113.72  102.68   11.04 1.30e+00 5.92e-01 7.21e+01
  angle pdb=" C   PRO B 486 "
        pdb=" CA  PRO B 486 "
        pdb=" CB  PRO B 486 "
      ideal   model   delta    sigma   weight residual
     111.40  103.78    7.62 9.10e-01 1.21e+00 7.02e+01
  angle pdb=" CA  ASP A  30 "
        pdb=" CB  ASP A  30 "
        pdb=" CG  ASP A  30 "
      ideal   model   delta    sigma   weight residual
     112.60  120.71   -8.11 1.00e+00 1.00e+00 6.58e+01
  angle pdb=" N   PRO B 491 "
        pdb=" CA  PRO B 491 "
        pdb=" CB  PRO B 491 "
      ideal   model   delta    sigma   weight residual
     103.25   95.40    7.85 1.05e+00 9.07e-01 5.58e+01
  angle pdb=" N   TYR B 489 "
        pdb=" CA  TYR B 489 "
        pdb=" CB  TYR B 489 "
      ideal   model   delta    sigma   weight residual
     110.49  123.07  -12.58 1.69e+00 3.50e-01 5.54e+01
  ... (remaining 9021 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.48: 3455
       20.48 -    40.96: 393
       40.96 -    61.43: 110
       61.43 -    81.91: 10
       81.91 -   102.39: 10
  Dihedral angle restraints: 3978
    sinusoidal: 1658
      harmonic: 2320
  Sorted by residual:
  dihedral pdb=" CB  CYS A 344 "
           pdb=" SG  CYS A 344 "
           pdb=" SG  CYS A 361 "
           pdb=" CB  CYS A 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.78   54.22     1      1.00e+01 1.00e-02 3.99e+01
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.16  -54.16     1      1.00e+01 1.00e-02 3.98e+01
  dihedral pdb=" C   PHE A  28 "
           pdb=" N   PHE A  28 "
           pdb=" CA  PHE A  28 "
           pdb=" CB  PHE A  28 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.45  -14.15     0      2.50e+00 1.60e-01 3.20e+01
  ... (remaining 3975 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 822
       0.068 -    0.135: 111
       0.135 -    0.203: 12
       0.203 -    0.271: 8
       0.271 -    0.338: 2
  Chirality restraints: 955
  Sorted by residual:
  chirality pdb=" CA  PHE A  28 "
            pdb=" N   PHE A  28 "
            pdb=" C   PHE A  28 "
            pdb=" CB  PHE A  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.86e+00
  chirality pdb=" CA  CYS B 488 "
            pdb=" N   CYS B 488 "
            pdb=" C   CYS B 488 "
            pdb=" CB  CYS B 488 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.79   -0.28 2.00e-01 2.50e+01 2.01e+00
  chirality pdb=" CA  ASN B 487 "
            pdb=" N   ASN B 487 "
            pdb=" C   ASN B 487 "
            pdb=" CB  ASN B 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  ... (remaining 952 not shown)

  Planarity restraints: 1169
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A  81 "   -0.025 2.00e-02 2.50e+03   5.01e-02 2.51e+01
        pdb=" C   GLN A  81 "    0.087 2.00e-02 2.50e+03
        pdb=" O   GLN A  81 "   -0.032 2.00e-02 2.50e+03
        pdb=" N   MET A  82 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR B 470 "   -0.017 2.00e-02 2.50e+03   3.14e-02 9.84e+00
        pdb=" C   THR B 470 "    0.054 2.00e-02 2.50e+03
        pdb=" O   THR B 470 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 471 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 478 "   -0.043 5.00e-02 4.00e+02   6.54e-02 6.83e+00
        pdb=" N   PRO B 479 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO B 479 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 479 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1166 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1201
        2.77 -     3.30: 6090
        3.30 -     3.83: 11023
        3.83 -     4.37: 12761
        4.37 -     4.90: 22451
  Nonbonded interactions: 53526
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.232 2.440
  nonbonded pdb=" OG  SER B 438 "
            pdb=" OD2 ASP B 442 "
     model   vdw
     2.249 2.440
  nonbonded pdb=" OH  TYR A 215 "
            pdb=" OE1 GLU A 571 "
     model   vdw
     2.261 2.440
  nonbonded pdb=" OH  TYR A 237 "
            pdb=" O   VAL A 485 "
     model   vdw
     2.267 2.440
  nonbonded pdb=" O   ASP A 499 "
            pdb=" OG  SER A 502 "
     model   vdw
     2.268 2.440
  ... (remaining 53521 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.050
  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:             0.000
  Extract box with map and model:          7.000
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     21.810
  Find NCS groups from input model:        0.130
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
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   0.079   6640  Z= 0.322
  Angle     :  0.901  12.584   9026  Z= 0.563
  Chirality :  0.053   0.338    955
  Planarity :  0.004   0.065   1165
  Dihedral  : 18.482 102.391   2470
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.76 %
    Allowed  :  5.34 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 23.34 %
    Favored  : 75.94 %
  Cbeta Deviations :  0.94 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.02 (0.31), residues: 786
  helix:  0.90 (0.27), residues: 403
  sheet:  1.39 (0.86), residues: 44
  loop : -1.35 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 168 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.027   0.001   TYR B 453 
 ARG   0.002   0.000   ARG B 457 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 0.651 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.6860 (tt0) cc_final: 0.6326 (mt-10)
REVERT: A  102 GLN cc_start: 0.7864 (mm110) cc_final: 0.7586 (mm-40)
REVERT: A  168 TRP cc_start: 0.7271 (t-100) cc_final: 0.6659 (t-100)
REVERT: A  224 GLU cc_start: 0.5770 (mt-10) cc_final: 0.5432 (mm-30)
REVERT: A  227 GLU cc_start: 0.6494 (tt0) cc_final: 0.5957 (mt-10)
REVERT: A  325 GLN cc_start: 0.7254 (tm130) cc_final: 0.7025 (tp-100)
REVERT: A  402 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7198 (mt-10)
REVERT: A  480 MET cc_start: 0.7646 (mtp) cc_final: 0.7376 (mtp)
REVERT: A  547 SER cc_start: 0.8332 (t) cc_final: 0.7914 (p)
REVERT: A  552 GLN cc_start: 0.7398 (tp40) cc_final: 0.7114 (tp40)
REVERT: A  562 LYS cc_start: 0.8300 (ttpp) cc_final: 0.7512 (mttp)
REVERT: A  577 LYS cc_start: 0.7994 (mtmt) cc_final: 0.7628 (mtpp)
REVERT: A  589 GLU cc_start: 0.6757 (tp30) cc_final: 0.6483 (tp30)
REVERT: B  356 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8294 (tttm)
REVERT: B  471 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7121 (mt-10)
REVERT: B  493 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7035 (tm130)
  outliers start: 5
  outliers final: 1
  residues processed: 118
  average time/residue: 0.1968
  time to fit residues: 30.2427
Evaluate side-chains
  93 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain B residue  471 GLU
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 59 optimal weight:    0.0370
   chunk 32 optimal weight:    0.0170
   chunk 20 optimal weight:    3.9990
   chunk 39 optimal weight:    5.9990
   chunk 31 optimal weight:    0.4980
   chunk 61 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
A 531 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7650
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6640  Z= 0.157
  Angle     :  0.533   7.358   9026  Z= 0.267
  Chirality :  0.042   0.190    955
  Planarity :  0.004   0.044   1165
  Dihedral  :  7.529  56.755    948
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.11 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 22.91 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.31), residues: 786
  helix:  1.18 (0.27), residues: 399
  sheet:  1.07 (0.80), residues: 44
  loop : -1.11 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.007   0.001   TYR A 497 
 ARG   0.002   0.000   ARG A 559 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.628 
Fit side-chains
REVERT: A   75 GLU cc_start: 0.6714 (tt0) cc_final: 0.6089 (mt-10)
REVERT: A  102 GLN cc_start: 0.7841 (mm110) cc_final: 0.7576 (mm-40)
REVERT: A  168 TRP cc_start: 0.7072 (t-100) cc_final: 0.6710 (t-100)
REVERT: A  224 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5501 (mm-30)
REVERT: A  227 GLU cc_start: 0.6490 (tt0) cc_final: 0.5926 (mt-10)
REVERT: A  325 GLN cc_start: 0.7333 (tm130) cc_final: 0.6992 (tp-100)
REVERT: A  402 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7255 (mt-10)
REVERT: A  480 MET cc_start: 0.7460 (mtp) cc_final: 0.7235 (mtp)
REVERT: A  547 SER cc_start: 0.8383 (t) cc_final: 0.8146 (t)
REVERT: A  552 GLN cc_start: 0.7529 (tp40) cc_final: 0.7237 (tp40)
REVERT: A  562 LYS cc_start: 0.8445 (ttpp) cc_final: 0.7812 (tttp)
REVERT: A  577 LYS cc_start: 0.8032 (mtmt) cc_final: 0.7663 (mtpp)
REVERT: A  589 GLU cc_start: 0.6903 (tp30) cc_final: 0.6562 (tp30)
REVERT: B  356 LYS cc_start: 0.8515 (ttmm) cc_final: 0.8287 (tttm)
  outliers start: 14
  outliers final: 6
  residues processed: 97
  average time/residue: 0.1639
  time to fit residues: 21.7452
Evaluate side-chains
  87 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 81
  time to evaluate  : 0.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  493 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 58 optimal weight:    0.0570
   chunk 48 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.0302

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

Flipped N/Q/H residues before XYZ refinement:
B 493 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6640  Z= 0.258
  Angle     :  0.584   7.870   9026  Z= 0.290
  Chirality :  0.043   0.141    955
  Planarity :  0.004   0.038   1165
  Dihedral  :  5.734  50.408    945
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 21.76 %
    Favored  : 75.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.30), residues: 786
  helix:  1.12 (0.27), residues: 405
  sheet:  0.80 (0.76), residues: 44
  loop : -1.07 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 477 
 HIS   0.006   0.001   HIS A  34 
 PHE   0.024   0.002   PHE A 369 
 TYR   0.013   0.001   TYR A 237 
 ARG   0.002   0.000   ARG B 355 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.782 
Fit side-chains
REVERT: A   30 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7778 (p0)
REVERT: A   68 LYS cc_start: 0.7082 (mmpt) cc_final: 0.6363 (mptt)
REVERT: A   75 GLU cc_start: 0.6687 (tt0) cc_final: 0.6080 (mt-10)
REVERT: A  102 GLN cc_start: 0.7900 (mm110) cc_final: 0.7461 (mm-40)
REVERT: A  168 TRP cc_start: 0.7520 (t-100) cc_final: 0.6989 (t-100)
REVERT: A  215 TYR cc_start: 0.7862 (m-80) cc_final: 0.7272 (m-80)
REVERT: A  224 GLU cc_start: 0.5849 (mt-10) cc_final: 0.5541 (mm-30)
REVERT: A  227 GLU cc_start: 0.6548 (tt0) cc_final: 0.6065 (mt-10)
REVERT: A  325 GLN cc_start: 0.7550 (tm130) cc_final: 0.7080 (tp-100)
REVERT: A  402 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7249 (mt-10)
REVERT: A  483 GLU cc_start: 0.7508 (pt0) cc_final: 0.7131 (mt-10)
REVERT: A  547 SER cc_start: 0.8499 (t) cc_final: 0.8214 (t)
REVERT: A  552 GLN cc_start: 0.7602 (tp40) cc_final: 0.7375 (tp40)
REVERT: A  558 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8034 (mp)
REVERT: A  562 LYS cc_start: 0.8693 (ttpp) cc_final: 0.7939 (tttp)
REVERT: A  577 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7714 (mtpp)
REVERT: A  589 GLU cc_start: 0.7069 (tp30) cc_final: 0.6653 (tp30)
REVERT: B  356 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8152 (tttm)
  outliers start: 22
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1700
  time to fit residues: 25.4057
Evaluate side-chains
  100 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue  229 THR
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  558 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0040
   chunk 71 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
A 137 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6640  Z= 0.181
  Angle     :  0.516   6.810   9026  Z= 0.258
  Chirality :  0.041   0.132    955
  Planarity :  0.004   0.037   1165
  Dihedral  :  4.761  34.713    942
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 24.50 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.30), residues: 786
  helix:  1.26 (0.27), residues: 405
  sheet:  0.79 (0.75), residues: 44
  loop : -1.02 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.005   0.001   HIS A  34 
 PHE   0.017   0.001   PHE A 369 
 TYR   0.008   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7102 (mmpt) cc_final: 0.6385 (mptt)
REVERT: A   75 GLU cc_start: 0.6603 (tt0) cc_final: 0.5979 (mt-10)
REVERT: A  102 GLN cc_start: 0.7871 (mm110) cc_final: 0.7596 (mm-40)
REVERT: A  166 GLU cc_start: 0.6706 (tp30) cc_final: 0.6403 (tp30)
REVERT: A  168 TRP cc_start: 0.7527 (t-100) cc_final: 0.7139 (t-100)
REVERT: A  224 GLU cc_start: 0.5854 (mt-10) cc_final: 0.5553 (mm-30)
REVERT: A  227 GLU cc_start: 0.6463 (tt0) cc_final: 0.5966 (mt-10)
REVERT: A  325 GLN cc_start: 0.7574 (tm130) cc_final: 0.7139 (tp-100)
REVERT: A  366 MET cc_start: 0.7254 (tpp) cc_final: 0.6414 (tpp)
REVERT: A  402 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7191 (mt-10)
REVERT: A  480 MET cc_start: 0.7456 (mtp) cc_final: 0.7159 (mtp)
REVERT: A  483 GLU cc_start: 0.7419 (pt0) cc_final: 0.7026 (mt-10)
REVERT: A  547 SER cc_start: 0.8508 (t) cc_final: 0.8231 (t)
REVERT: A  552 GLN cc_start: 0.7603 (tp40) cc_final: 0.7378 (tp40)
REVERT: A  562 LYS cc_start: 0.8636 (ttpp) cc_final: 0.7952 (tttp)
REVERT: A  577 LYS cc_start: 0.8000 (mtmt) cc_final: 0.7641 (mtpp)
REVERT: A  589 GLU cc_start: 0.6959 (tp30) cc_final: 0.6610 (tp30)
REVERT: B  356 LYS cc_start: 0.8449 (ttmm) cc_final: 0.8247 (tttm)
REVERT: B  365 TYR cc_start: 0.8010 (m-80) cc_final: 0.7797 (m-80)
  outliers start: 13
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1559
  time to fit residues: 20.3520
Evaluate side-chains
  95 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.723 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 1 optimal weight:    0.2980
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9980
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 14 optimal weight:    8.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6640  Z= 0.218
  Angle     :  0.541   7.340   9026  Z= 0.272
  Chirality :  0.042   0.133    955
  Planarity :  0.004   0.038   1165
  Dihedral  :  4.511  27.074    940
  Min Nonbonded Distance : 2.225

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.73 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.06 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.30), residues: 786
  helix:  1.19 (0.27), residues: 404
  sheet:  0.67 (0.74), residues: 44
  loop : -0.99 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.019   0.001   PHE A 369 
 TYR   0.011   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.803 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7152 (mmpt) cc_final: 0.6428 (mptt)
REVERT: A   75 GLU cc_start: 0.6603 (tt0) cc_final: 0.5948 (mt-10)
REVERT: A  102 GLN cc_start: 0.7908 (mm110) cc_final: 0.7177 (mt0)
REVERT: A  166 GLU cc_start: 0.6739 (tp30) cc_final: 0.6390 (tp30)
REVERT: A  168 TRP cc_start: 0.7610 (t-100) cc_final: 0.7218 (t-100)
REVERT: A  215 TYR cc_start: 0.7888 (m-80) cc_final: 0.7365 (m-80)
REVERT: A  224 GLU cc_start: 0.5847 (mt-10) cc_final: 0.5540 (mm-30)
REVERT: A  227 GLU cc_start: 0.6475 (tt0) cc_final: 0.5982 (mt-10)
REVERT: A  325 GLN cc_start: 0.7620 (tm130) cc_final: 0.7221 (tp-100)
REVERT: A  366 MET cc_start: 0.7350 (tpp) cc_final: 0.6493 (tpp)
REVERT: A  402 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7202 (mt-10)
REVERT: A  480 MET cc_start: 0.7657 (mtp) cc_final: 0.7351 (mtp)
REVERT: A  547 SER cc_start: 0.8525 (t) cc_final: 0.8233 (t)
REVERT: A  552 GLN cc_start: 0.7645 (tp40) cc_final: 0.7399 (tp40)
REVERT: A  562 LYS cc_start: 0.8671 (ttpp) cc_final: 0.7923 (tttp)
REVERT: A  577 LYS cc_start: 0.8011 (mtmt) cc_final: 0.7670 (mtmt)
REVERT: A  589 GLU cc_start: 0.6957 (tp30) cc_final: 0.6578 (tp30)
REVERT: B  356 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8208 (tttm)
  outliers start: 16
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1583
  time to fit residues: 22.8916
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 44 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0970
   chunk 34 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 72 optimal weight:    2.9990
   chunk 8 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A  49 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6640  Z= 0.192
  Angle     :  0.519   6.991   9026  Z= 0.262
  Chirality :  0.042   0.133    955
  Planarity :  0.004   0.038   1165
  Dihedral  :  4.332  26.810    940
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 25.07 %
    Favored  : 73.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.30), residues: 786
  helix:  1.21 (0.27), residues: 404
  sheet:  0.75 (0.73), residues: 44
  loop : -1.00 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.012   0.001   TYR B 365 
 ARG   0.002   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7101 (mmpt) cc_final: 0.6402 (mptt)
REVERT: A  102 GLN cc_start: 0.7894 (mm110) cc_final: 0.7151 (mt0)
REVERT: A  166 GLU cc_start: 0.6773 (tp30) cc_final: 0.6426 (tp30)
REVERT: A  168 TRP cc_start: 0.7850 (t-100) cc_final: 0.7542 (t-100)
REVERT: A  215 TYR cc_start: 0.7846 (m-80) cc_final: 0.7387 (m-80)
REVERT: A  224 GLU cc_start: 0.5842 (mt-10) cc_final: 0.5532 (mm-30)
REVERT: A  227 GLU cc_start: 0.6464 (tt0) cc_final: 0.5957 (mt-10)
REVERT: A  366 MET cc_start: 0.7327 (tpp) cc_final: 0.6493 (tpp)
REVERT: A  476 LYS cc_start: 0.6263 (OUTLIER) cc_final: 0.5567 (tptp)
REVERT: A  480 MET cc_start: 0.7613 (mtp) cc_final: 0.7392 (mtp)
REVERT: A  547 SER cc_start: 0.8512 (t) cc_final: 0.8213 (t)
REVERT: A  552 GLN cc_start: 0.7624 (tp40) cc_final: 0.7382 (tp40)
REVERT: A  562 LYS cc_start: 0.8659 (ttpp) cc_final: 0.7906 (tttp)
REVERT: A  577 LYS cc_start: 0.8008 (mtmt) cc_final: 0.7667 (mtmt)
REVERT: B  493 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6893 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1759
  time to fit residues: 23.5841
Evaluate side-chains
  94 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0020
   chunk 47 optimal weight:    1.9990
   chunk 45 optimal weight:    0.2980
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 44 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 325 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6640  Z= 0.166
  Angle     :  0.500   7.064   9026  Z= 0.252
  Chirality :  0.041   0.131    955
  Planarity :  0.004   0.040   1165
  Dihedral  :  4.142  25.939    940
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.58 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 24.21 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.30), residues: 786
  helix:  1.38 (0.27), residues: 398
  sheet:  0.86 (0.74), residues: 44
  loop : -1.02 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.009   0.001   TYR A 385 
 ARG   0.001   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 83
  time to evaluate  : 0.759 
Fit side-chains
REVERT: A   68 LYS cc_start: 0.7083 (mmpt) cc_final: 0.6379 (mptt)
REVERT: A  102 GLN cc_start: 0.7855 (mm110) cc_final: 0.7101 (mt0)
REVERT: A  168 TRP cc_start: 0.7829 (t-100) cc_final: 0.7548 (t-100)
REVERT: A  215 TYR cc_start: 0.7854 (m-80) cc_final: 0.7373 (m-80)
REVERT: A  224 GLU cc_start: 0.5821 (mt-10) cc_final: 0.5509 (mm-30)
REVERT: A  227 GLU cc_start: 0.6423 (tt0) cc_final: 0.6030 (mt-10)
REVERT: A  353 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8541 (mtpt)
REVERT: A  366 MET cc_start: 0.7330 (tpp) cc_final: 0.6540 (tpp)
REVERT: A  476 LYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5587 (tptp)
REVERT: A  547 SER cc_start: 0.8508 (t) cc_final: 0.8205 (t)
REVERT: A  552 GLN cc_start: 0.7602 (tp40) cc_final: 0.7362 (tp40)
REVERT: A  577 LYS cc_start: 0.7955 (mtmt) cc_final: 0.7632 (mtmt)
REVERT: B  493 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.6882 (tm-30)
  outliers start: 16
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1547
  time to fit residues: 21.0616
Evaluate side-chains
  96 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 51 optimal weight:    0.6980
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0370
   chunk 68 optimal weight:    0.4980
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    0.6458

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6640  Z= 0.184
  Angle     :  0.508   7.144   9026  Z= 0.257
  Chirality :  0.041   0.130    955
  Planarity :  0.004   0.039   1165
  Dihedral  :  4.138  26.062    940
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 23.92 %
    Favored  : 73.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.30), residues: 786
  helix:  1.39 (0.27), residues: 398
  sheet:  0.88 (0.75), residues: 44
  loop : -1.06 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.014   0.001   TYR B 365 
 ARG   0.002   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7082 (mmpt) cc_final: 0.6371 (mptt)
REVERT: A  102 GLN cc_start: 0.7855 (mm110) cc_final: 0.7111 (mt0)
REVERT: A  168 TRP cc_start: 0.7860 (t-100) cc_final: 0.7605 (t-100)
REVERT: A  215 TYR cc_start: 0.7899 (m-80) cc_final: 0.7425 (m-80)
REVERT: A  224 GLU cc_start: 0.5805 (mt-10) cc_final: 0.5511 (mm-30)
REVERT: A  227 GLU cc_start: 0.6448 (tt0) cc_final: 0.6051 (mt-10)
REVERT: A  353 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8582 (mtpt)
REVERT: A  366 MET cc_start: 0.7257 (tpp) cc_final: 0.6456 (tpp)
REVERT: A  402 GLU cc_start: 0.7593 (mm-30) cc_final: 0.7198 (mt-10)
REVERT: A  476 LYS cc_start: 0.6127 (OUTLIER) cc_final: 0.5639 (tptp)
REVERT: A  547 SER cc_start: 0.8512 (t) cc_final: 0.8204 (t)
REVERT: A  552 GLN cc_start: 0.7596 (tp40) cc_final: 0.7357 (tp40)
REVERT: A  577 LYS cc_start: 0.7956 (mtmt) cc_final: 0.7631 (mtmt)
REVERT: A  582 ARG cc_start: 0.6733 (OUTLIER) cc_final: 0.6460 (mmm160)
REVERT: B  493 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6913 (tm-30)
  outliers start: 18
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1761
  time to fit residues: 22.8583
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain A residue  582 ARG
Chi-restraints excluded: chain B residue  360 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 66 optimal weight:    0.2980
   chunk 69 optimal weight:    0.7980
   chunk 46 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0980
   chunk 35 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2898

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6640  Z= 0.171
  Angle     :  0.500   7.009   9026  Z= 0.253
  Chirality :  0.041   0.130    955
  Planarity :  0.004   0.039   1165
  Dihedral  :  4.018  25.429    940
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.45 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 24.06 %
    Favored  : 73.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.30), residues: 786
  helix:  1.33 (0.27), residues: 403
  sheet:  0.92 (0.75), residues: 44
  loop : -1.01 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.015   0.001   PHE A 369 
 TYR   0.010   0.001   TYR A 385 
 ARG   0.001   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 82
  time to evaluate  : 0.932 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7070 (mmpt) cc_final: 0.6360 (mptt)
REVERT: A  102 GLN cc_start: 0.7850 (mm110) cc_final: 0.7106 (mt0)
REVERT: A  168 TRP cc_start: 0.7901 (t-100) cc_final: 0.7644 (t-100)
REVERT: A  215 TYR cc_start: 0.7882 (m-80) cc_final: 0.7446 (m-80)
REVERT: A  227 GLU cc_start: 0.6415 (tt0) cc_final: 0.6035 (mt-10)
REVERT: A  353 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8571 (mtpt)
REVERT: A  366 MET cc_start: 0.7233 (tpp) cc_final: 0.6445 (tpp)
REVERT: A  376 MET cc_start: 0.7945 (ttm) cc_final: 0.7665 (mmm)
REVERT: A  476 LYS cc_start: 0.6070 (OUTLIER) cc_final: 0.5649 (tptp)
REVERT: A  547 SER cc_start: 0.8503 (t) cc_final: 0.8203 (t)
REVERT: A  552 GLN cc_start: 0.7584 (tp40) cc_final: 0.7333 (tp40)
REVERT: A  577 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7583 (mtmt)
REVERT: B  493 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.6927 (tm-30)
  outliers start: 18
  outliers final: 11
  residues processed: 95
  average time/residue: 0.1801
  time to fit residues: 24.1391
Evaluate side-chains
  94 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0970
   chunk 6 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 18 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   overall best weight:    0.5978

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6640  Z= 0.179
  Angle     :  0.510   7.262   9026  Z= 0.256
  Chirality :  0.041   0.131    955
  Planarity :  0.004   0.039   1165
  Dihedral  :  4.007  25.005    940
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  4.71 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 24.06 %
    Favored  : 73.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.49 (0.30), residues: 786
  helix:  1.32 (0.27), residues: 403
  sheet:  0.91 (0.75), residues: 44
  loop : -0.98 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 168 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.015   0.001   TYR B 365 
 ARG   0.002   0.000   ARG A 460 

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

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

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1572 Ramachandran restraints generated.
    786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: A   68 LYS cc_start: 0.7087 (mmpt) cc_final: 0.6377 (mptt)
REVERT: A  102 GLN cc_start: 0.7845 (mm110) cc_final: 0.7090 (mt0)
REVERT: A  215 TYR cc_start: 0.7910 (m-80) cc_final: 0.7463 (m-80)
REVERT: A  227 GLU cc_start: 0.6436 (tt0) cc_final: 0.6050 (mt-10)
REVERT: A  353 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8589 (mtpt)
REVERT: A  366 MET cc_start: 0.7243 (tpp) cc_final: 0.6442 (tpp)
REVERT: A  397 ASN cc_start: 0.8360 (p0) cc_final: 0.8146 (p0)
REVERT: A  476 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5620 (tptp)
REVERT: A  547 SER cc_start: 0.8506 (t) cc_final: 0.8207 (t)
REVERT: A  552 GLN cc_start: 0.7588 (tp40) cc_final: 0.7331 (tp40)
REVERT: A  577 LYS cc_start: 0.7846 (mtmt) cc_final: 0.7549 (mtmt)
REVERT: B  493 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.6955 (tm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 94
  average time/residue: 0.2901
  time to fit residues: 37.5996
Evaluate side-chains
  99 residues out of total 694 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  324 THR
Chi-restraints excluded: chain A residue  343 VAL
Chi-restraints excluded: chain A residue  347 THR
Chi-restraints excluded: chain A residue  353 LYS
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  476 LYS
Chi-restraints excluded: chain A residue  494 ASP
Chi-restraints excluded: chain A residue  544 ILE
Chi-restraints excluded: chain A residue  578 ASN
Chi-restraints excluded: chain B residue  379 CYS
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  428 ASP
Chi-restraints excluded: chain B residue  493 GLN
Chi-restraints excluded: chain B residue  495 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 63 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4003 r_free = 0.4003 target = 0.178281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.143077 restraints weight = 6790.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3648 rms_B_bonded: 2.08
r_work: 0.3437 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.3285 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6640  Z= 0.221
  Angle     :  0.532   7.552   9026  Z= 0.268
  Chirality :  0.042   0.138    955
  Planarity :  0.004   0.039   1165
  Dihedral  :  4.156  25.490    940
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 23.92 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.30), residues: 786
  helix:  1.23 (0.27), residues: 403
  sheet:  0.89 (0.75), residues: 44
  loop : -0.96 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 477 
 HIS   0.004   0.001   HIS A  34 
 PHE   0.016   0.001   PHE A 369 
 TYR   0.012   0.001   TYR A 385 
 ARG   0.002   0.000   ARG A 460 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1930.29 seconds
wall clock time: 35 minutes 52.19 seconds (2152.19 seconds total)