Starting phenix.real_space_refine
on Tue Jan 14 02:52:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqq_39502/01_2025/8yqq_39502_trim.cif"
  }
  resolution = 3.95
  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=   0.002 sd=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    3217      2.51       5
     N     883      2.21       5
     O     994      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 5141
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 285, 2218
          Classifications: {'peptide': 285}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 267}
    Chain: "B"
      Number of atoms: 2833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 364, 2833
          Classifications: {'peptide': 364}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 346}
    Chain: "A"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 60
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
    Chain: "B"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 30
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.69, per 1000 atoms: 0.72
  Number of scatterers: 5141
  At special positions: 0
  Unit cell: (68.04, 80.19, 134.46, 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      47     16.00
     O     994      8.00
     N     883      7.00
     C    3217      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=18, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 327 " - pdb=" SG  CYS A 352 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 370 " - pdb=" SG  CYS A 423 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 382 " - pdb=" SG  CYS A 603 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 466 " - pdb=" SG  CYS A 546 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 495 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 476 " - pdb=" SG  CYS A 565 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 485 " - pdb=" SG  CYS A 516 " distance=1.98
    Simple disulfide: pdb=" SG  CYS A 504 " - pdb=" SG  CYS A 518 " distance=1.99
    Simple disulfide: pdb=" SG  CYS A 520 " - pdb=" SG  CYS A 533 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 556 " - pdb=" SG  CYS A 567 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 580 " - pdb=" SG  CYS A 586 " distance=2.01
    Simple disulfide: pdb=" SG  CYS B 133 " - pdb=" SG  CYS B 148 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 172 " - pdb=" SG  CYS B 231 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 185 " - pdb=" SG  CYS B 241 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 244 " - pdb=" SG  CYS B 365 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 281 " - pdb=" SG  CYS B 297 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 410 " - pdb=" SG  CYS B 426 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 437 " - pdb=" SG  CYS B 465 " 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 A 703 " - " ASN A 355 "
  Time building additional restraints: 1.26
  Conformation dependent library (CDL) restraints added in 598.7 milliseconds
  

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1204

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 12 sheets defined
      13.4% alpha, 23.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.59
  Creating SS restraints...
    Processing helix  chain 'A' and resid 328 through 334
      removed outlier: 3.681A  pdb=" N   TRP A 332 " --> pdb=" O   ASP A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 344
      removed outlier: 4.023A  pdb=" N   TRP A 344 " --> pdb=" O   PRO A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 362
    Processing helix  chain 'A' and resid 394 through 402
      removed outlier: 3.720A  pdb=" N   ARG A 398 " --> pdb=" O   ASN A 395 " (cutoff:3.500A)
      removed outlier: 4.959A  pdb=" N   ASP A 399 " --> pdb=" O   ARG A 396 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A 400 " --> pdb=" O   ARG A 397 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   LEU A 401 " --> pdb=" O   ARG A 398 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A 402 " --> pdb=" O   ASP A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 413
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 4.180A  pdb=" N   VAL A 434 " --> pdb=" O   LEU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
      removed outlier: 3.708A  pdb=" N   VAL A 482 " --> pdb=" O   ASP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 4.097A  pdb=" N   PHE A 572 " --> pdb=" O   PRO A 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 147
    Processing helix  chain 'B' and resid 177 through 187
      removed outlier: 3.951A  pdb=" N   GLY B 181 " --> pdb=" O   ASN B 177 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA B 183 " --> pdb=" O   ASN B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 480 through 491
      removed outlier: 3.519A  pdb=" N   TYR B 485 " --> pdb=" O   THR B 481 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA B 490 " --> pdb=" O   ARG B 486 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 337 through 338
    Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 349
    Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 371
      removed outlier: 6.282A  pdb=" N   VAL A 365 " --> pdb=" O   SER A 428 " (cutoff:3.500A)
      removed outlier: 6.600A  pdb=" N   SER A 428 " --> pdb=" O   VAL A 365 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 392
      removed outlier: 3.686A  pdb=" N   PHE A 391 " --> pdb=" O   PHE A 589 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 459 through 463
      removed outlier: 4.225A  pdb=" N   ASP A 578 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 576 " --> pdb=" O   TYR A 462 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 466 through 468
      removed outlier: 4.396A  pdb=" N   CYS A 466 " --> pdb=" O   VAL A 538 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 507 through 509
      removed outlier: 6.502A  pdb=" N   THR A 509 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
      removed outlier: 5.072A  pdb=" N   LYS A 513 " --> pdb=" O   THR A 509 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 150
      removed outlier: 3.504A  pdb=" N   ARG B 150 " --> pdb=" O   GLN B 159 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER B 167 " --> pdb=" O   SER B 162 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 196 through 200
    Processing sheet with id=AB1, first strand: chain 'B' and resid 209 through 211
    Processing sheet with id=AB2, first strand: chain 'B' and resid 270 through 275
      removed outlier: 3.744A  pdb=" N   CYS B 281 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
      removed outlier: 6.023A  pdb=" N   VAL B 275 " --> pdb=" O   HIS B 279 " (cutoff:3.500A)
      removed outlier: 5.337A  pdb=" N   HIS B 279 " --> pdb=" O   VAL B 275 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   LEU B 348 " --> pdb=" O   VAL B 331 " (cutoff:3.500A)
      removed outlier: 4.796A  pdb=" N   VAL B 331 " --> pdb=" O   LEU B 348 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LYS B 350 " --> pdb=" O   GLU B 329 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   VAL B 328 " --> pdb=" O   TRP B 308 " (cutoff:3.500A)
      removed outlier: 6.041A  pdb=" N   TRP B 308 " --> pdb=" O   VAL B 328 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 378 through 383
      removed outlier: 4.250A  pdb=" N   CYS B 426 " --> pdb=" O   ILE B 405 " (cutoff:3.500A)
      removed outlier: 7.640A  pdb=" N   VAL B 473 " --> pdb=" O   SER B 460 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   SER B 460 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   THR B 447 " --> pdb=" O   TRP B 454 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   LEU B 445 " --> pdb=" O   ILE B 456 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B 382 " --> pdb=" O   PRO B 444 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   SER B 448 " --> pdb=" O   LEU B 378 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   LEU B 378 " --> pdb=" O   SER B 448 " (cutoff:3.500A)

    109 hydrogen bonds defined for protein.
    270 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: 1.30

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 885
        1.32 -     1.45: 1510
        1.45 -     1.57: 2825
        1.57 -     1.70: 0
        1.70 -     1.83: 56
  Bond restraints: 5276
  Sorted by residual:
  bond pdb=" CA  SER A 563 "
       pdb=" CB  SER A 563 "
    ideal  model  delta    sigma   weight residual
    1.533  1.450  0.083 1.69e-02 3.50e+03 2.40e+01
  bond pdb=" C   PRO A 496 "
       pdb=" O   PRO A 496 "
    ideal  model  delta    sigma   weight residual
    1.233  1.194  0.039 9.90e-03 1.02e+04 1.56e+01
  bond pdb=" N   ILE A 588 "
       pdb=" CA  ILE A 588 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.11e-02 8.12e+03 1.45e+01
  bond pdb=" CA  SER A 488 "
       pdb=" CB  SER A 488 "
    ideal  model  delta    sigma   weight residual
    1.531  1.476  0.055 1.53e-02 4.27e+03 1.31e+01
  bond pdb=" C   PRO A 490 "
       pdb=" O   PRO A 490 "
    ideal  model  delta    sigma   weight residual
    1.240  1.200  0.040 1.12e-02 7.97e+03 1.30e+01
  ... (remaining 5271 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 6625
        2.37 -     4.74: 479
        4.74 -     7.11: 65
        7.11 -     9.48: 11
        9.48 -    11.85: 3
  Bond angle restraints: 7183
  Sorted by residual:
  angle pdb=" N   ARG A 447 "
        pdb=" CA  ARG A 447 "
        pdb=" C   ARG A 447 "
      ideal   model   delta    sigma   weight residual
     113.50  103.12   10.38 1.23e+00 6.61e-01 7.12e+01
  angle pdb=" N   PRO A 475 "
        pdb=" CA  PRO A 475 "
        pdb=" C   PRO A 475 "
      ideal   model   delta    sigma   weight residual
     113.75  104.29    9.46 1.49e+00 4.50e-01 4.03e+01
  angle pdb=" C   THR A 602 "
        pdb=" CA  THR A 602 "
        pdb=" CB  THR A 602 "
      ideal   model   delta    sigma   weight residual
     111.74  103.25    8.49 1.37e+00 5.33e-01 3.84e+01
  angle pdb=" N   GLN A 559 "
        pdb=" CA  GLN A 559 "
        pdb=" C   GLN A 559 "
      ideal   model   delta    sigma   weight residual
     113.41  106.01    7.40 1.22e+00 6.72e-01 3.68e+01
  angle pdb=" CA  HIS A 562 "
        pdb=" CB  HIS A 562 "
        pdb=" CG  HIS A 562 "
      ideal   model   delta    sigma   weight residual
     113.80  119.33   -5.53 1.00e+00 1.00e+00 3.06e+01
  ... (remaining 7178 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.97: 2963
       23.97 -    47.94: 241
       47.94 -    71.91: 41
       71.91 -    95.87: 6
       95.87 -   119.84: 4
  Dihedral angle restraints: 3255
    sinusoidal: 1380
      harmonic: 1875
  Sorted by residual:
  dihedral pdb=" CD  ARG A 517 "
           pdb=" NE  ARG A 517 "
           pdb=" CZ  ARG A 517 "
           pdb=" NH1 ARG A 517 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   86.60  -86.60     1      1.00e+01 1.00e-02 9.03e+01
  dihedral pdb=" CB  CYS A 485 "
           pdb=" SG  CYS A 485 "
           pdb=" SG  CYS A 516 "
           pdb=" CB  CYS A 516 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  156.79  -63.79     1      1.00e+01 1.00e-02 5.36e+01
  dihedral pdb=" CD  ARG A 585 "
           pdb=" NE  ARG A 585 "
           pdb=" CZ  ARG A 585 "
           pdb=" NH1 ARG A 585 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   60.32  -60.32     1      1.00e+01 1.00e-02 4.85e+01
  ... (remaining 3252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 560
       0.069 -    0.139: 171
       0.139 -    0.208: 43
       0.208 -    0.278: 7
       0.278 -    0.347: 1
  Chirality restraints: 782
  Sorted by residual:
  chirality pdb=" C1  NAG A 703 "
            pdb=" ND2 ASN A 355 "
            pdb=" C2  NAG A 703 "
            pdb=" O5  NAG A 703 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.75    0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CA  ARG A 447 "
            pdb=" N   ARG A 447 "
            pdb=" C   ARG A 447 "
            pdb=" CB  ARG A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.71e+00
  chirality pdb=" CA  ASN A 598 "
            pdb=" N   ASN A 598 "
            pdb=" C   ASN A 598 "
            pdb=" CB  ASN A 598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 779 not shown)

  Planarity restraints: 930
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 355 "    0.115 2.00e-02 2.50e+03   4.11e-01 2.11e+03
        pdb=" CG  ASN A 355 "   -0.068 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 355 "    0.401 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 355 "   -0.756 2.00e-02 2.50e+03
        pdb=" C1  NAG A 703 "    0.308 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B 502 "    0.347 2.00e-02 2.50e+03   2.99e-01 1.12e+03
        pdb=" C7  NAG B 502 "   -0.084 2.00e-02 2.50e+03
        pdb=" C8  NAG B 502 "    0.129 2.00e-02 2.50e+03
        pdb=" N2  NAG B 502 "   -0.532 2.00e-02 2.50e+03
        pdb=" O7  NAG B 502 "    0.140 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 701 "   -0.346 2.00e-02 2.50e+03   2.98e-01 1.11e+03
        pdb=" C7  NAG A 701 "    0.083 2.00e-02 2.50e+03
        pdb=" C8  NAG A 701 "   -0.113 2.00e-02 2.50e+03
        pdb=" N2  NAG A 701 "    0.531 2.00e-02 2.50e+03
        pdb=" O7  NAG A 701 "   -0.156 2.00e-02 2.50e+03
  ... (remaining 927 not shown)

  Histogram of nonbonded interaction distances:
        1.45 -     2.14: 3
        2.14 -     2.83: 1695
        2.83 -     3.52: 6799
        3.52 -     4.21: 12060
        4.21 -     4.90: 19794
  Nonbonded interactions: 40351
  Sorted by model distance:
  nonbonded pdb=" O3  NAG B 501 "
            pdb=" O5  NAG B 502 "
     model   vdw
     1.447 3.040
  nonbonded pdb=" O   ASN A 605 "
            pdb=" N   LEU A 607 "
     model   vdw
     1.913 3.120
  nonbonded pdb=" O3  NAG B 501 "
            pdb=" C1  NAG B 502 "
     model   vdw
     2.079 3.470
  nonbonded pdb=" OE1 GLU B 178 "
            pdb=" OG  SER B 197 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OE2 GLU B 299 "
            pdb=" OH  TYR B 337 "
     model   vdw
     2.263 3.040
  ... (remaining 40346 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 group one per residue
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:             1.410
  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:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.600
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
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      :  0.008   0.083   5276  Z= 0.536
  Angle     :  1.283  11.846   7183  Z= 0.833
  Chirality :  0.073   0.347    782
  Planarity :  0.036   0.495    929
  Dihedral  : 17.141 119.842   1997
  Min Nonbonded Distance : 1.447

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  2.79 %
    Allowed  :  9.92 %
    Favored  : 87.29 %
  Rotamer:
    Outliers :  8.03 %
    Allowed  : 12.39 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -3.12 (0.30), residues: 645
  helix: -3.36 (0.40), residues: 69
  sheet: -0.95 (0.47), residues: 132
  loop : -2.37 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP B 269 
 HIS   0.006   0.001   HIS A 562 
 PHE   0.026   0.002   PHE A 383 
 TYR   0.031   0.002   TYR A 501 
 ARG   0.012   0.001   ARG B 409 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 120
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  337 SER cc_start: 0.9441 (m) cc_final: 0.9094 (t)
REVERT: A  410 GLN cc_start: 0.7969 (mm110) cc_final: 0.7715 (mt0)
REVERT: A  517 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7787 (mtm-85)
REVERT: A  538 VAL cc_start: 0.9538 (OUTLIER) cc_final: 0.9338 (t)
REVERT: A  544 GLU cc_start: 0.8893 (mp0) cc_final: 0.8644 (mp0)
REVERT: A  552 ASN cc_start: 0.9140 (t0) cc_final: 0.8784 (t0)
REVERT: A  581 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8177 (mt)
REVERT: A  602 THR cc_start: 0.9054 (OUTLIER) cc_final: 0.8770 (t)
REVERT: A  604 SER cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (m)
REVERT: A  606 ASP cc_start: 0.8625 (m-30) cc_final: 0.8352 (m-30)
REVERT: B  268 PRO cc_start: 0.8464 (Cg_endo) cc_final: 0.8187 (Cg_exo)
REVERT: B  463 SER cc_start: 0.8674 (t) cc_final: 0.8389 (p)
  outliers start: 46
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1702
  time to fit residues: 32.8440
Evaluate side-chains
  115 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 86
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  444 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  457 SER
Chi-restraints excluded: chain A residue  465 HIS
Chi-restraints excluded: chain A residue  469 VAL
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  488 SER
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  510 LEU
Chi-restraints excluded: chain A residue  513 LYS
Chi-restraints excluded: chain A residue  516 CYS
Chi-restraints excluded: chain A residue  517 ARG
Chi-restraints excluded: chain A residue  519 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  531 ASN
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  538 VAL
Chi-restraints excluded: chain A residue  556 CYS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  568 SER
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  604 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0970
   chunk 58 optimal weight:    0.0020
   overall best weight:    0.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 433 ASN
A 562 HIS
A 587 ASN
A 598 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.075691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.065117 restraints weight = 12971.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2615 r_free = 0.2615 target = 0.066631 restraints weight = 8428.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.067518 restraints weight = 5501.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8251
moved from start:          0.2004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   5276  Z= 0.192
  Angle     :  0.710  16.054   7183  Z= 0.346
  Chirality :  0.053   0.627    782
  Planarity :  0.005   0.059    929
  Dihedral  :  9.442  57.173    893
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.31 %
    Allowed  :  6.51 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 17.80 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -2.58 (0.31), residues: 645
  helix: -2.49 (0.44), residues: 70
  sheet: -1.68 (0.41), residues: 155
  loop : -1.62 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 269 
 HIS   0.003   0.001   HIS B 227 
 PHE   0.021   0.002   PHE A 577 
 TYR   0.020   0.002   TYR A 458 
 ARG   0.005   0.001   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.572 
Fit side-chains
REVERT: A  502 ARG cc_start: 0.8309 (ptp-170) cc_final: 0.7959 (ptp-170)
REVERT: A  544 GLU cc_start: 0.8876 (mp0) cc_final: 0.8589 (mp0)
REVERT: A  562 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.6994 (m170)
REVERT: A  578 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: B  188 MET cc_start: 0.6775 (ttm) cc_final: 0.6509 (ttp)
REVERT: B  268 PRO cc_start: 0.8595 (Cg_endo) cc_final: 0.8349 (Cg_exo)
REVERT: B  384 TRP cc_start: 0.8814 (m-90) cc_final: 0.8603 (m-90)
REVERT: B  458 ASP cc_start: 0.8712 (t0) cc_final: 0.8370 (t0)
REVERT: B  463 SER cc_start: 0.8988 (t) cc_final: 0.8661 (p)
REVERT: B  488 MET cc_start: 0.8294 (mmt) cc_final: 0.6621 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1632
  time to fit residues: 23.9014
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  444 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  509 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  531 ASN
Chi-restraints excluded: chain A residue  532 THR
Chi-restraints excluded: chain A residue  562 HIS
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  607 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 372 ASN
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 ASN
A 595 ASN
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 368 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.073523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.062800 restraints weight = 13055.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.064285 restraints weight = 8654.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2578 r_free = 0.2578 target = 0.065337 restraints weight = 6145.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.2573
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   5276  Z= 0.231
  Angle     :  0.689  16.180   7183  Z= 0.337
  Chirality :  0.054   0.662    782
  Planarity :  0.005   0.053    929
  Dihedral  :  8.650  59.792    864
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.44 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.90 %
    Favored  : 76.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -2.15 (0.31), residues: 645
  helix: -1.90 (0.51), residues: 69
  sheet: -1.83 (0.40), residues: 154
  loop : -1.18 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B 269 
 HIS   0.016   0.002   HIS A 562 
 PHE   0.018   0.002   PHE A 577 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.004   0.001   ARG B 409 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.582 
Fit side-chains
REVERT: A  413 ASN cc_start: 0.8457 (m-40) cc_final: 0.8208 (m-40)
REVERT: A  544 GLU cc_start: 0.8923 (mp0) cc_final: 0.8669 (mp0)
REVERT: B  157 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7656 (mt)
REVERT: B  231 CYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8242 (m)
REVERT: B  434 VAL cc_start: 0.9113 (t) cc_final: 0.8912 (t)
REVERT: B  458 ASP cc_start: 0.8706 (t0) cc_final: 0.8343 (t0)
REVERT: B  463 SER cc_start: 0.9010 (t) cc_final: 0.8744 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 98
  average time/residue: 0.1976
  time to fit residues: 25.1759
Evaluate side-chains
  84 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 2.029 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  231 CYS
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 61 optimal weight:    0.4980
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.073343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.062620 restraints weight = 13264.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.064227 restraints weight = 8711.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.065114 restraints weight = 6094.872|
|-----------------------------------------------------------------------------|
r_work (final): 0.2568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5276  Z= 0.215
  Angle     :  0.644  15.318   7183  Z= 0.315
  Chirality :  0.053   0.645    782
  Planarity :  0.004   0.050    929
  Dihedral  :  7.799  58.971    853
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.82 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.59 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.84 (0.32), residues: 645
  helix: -1.23 (0.59), residues: 63
  sheet: -1.49 (0.40), residues: 160
  loop : -1.10 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 176 
 HIS   0.004   0.001   HIS A 465 
 PHE   0.019   0.002   PHE A 577 
 TYR   0.017   0.002   TYR A 426 
 ARG   0.003   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 79
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7670 (mm110) cc_final: 0.7257 (mt0)
REVERT: A  413 ASN cc_start: 0.8485 (m-40) cc_final: 0.8226 (m-40)
REVERT: A  544 GLU cc_start: 0.8959 (mp0) cc_final: 0.8693 (mp0)
REVERT: B  157 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7637 (mt)
REVERT: B  268 PRO cc_start: 0.8531 (Cg_endo) cc_final: 0.8224 (Cg_exo)
REVERT: B  434 VAL cc_start: 0.9132 (t) cc_final: 0.8892 (t)
REVERT: B  458 ASP cc_start: 0.8684 (t0) cc_final: 0.8371 (t0)
REVERT: B  463 SER cc_start: 0.9031 (t) cc_final: 0.8764 (p)
  outliers start: 21
  outliers final: 12
  residues processed: 93
  average time/residue: 0.1789
  time to fit residues: 21.7433
Evaluate side-chains
  85 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  566 PHE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 14 optimal weight:    0.3980
   chunk 45 optimal weight:    0.0370
   chunk 21 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.074177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.063597 restraints weight = 13161.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.064990 restraints weight = 8745.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.065755 restraints weight = 5864.963|
|-----------------------------------------------------------------------------|
r_work (final): 0.2582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8363
moved from start:          0.3245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5276  Z= 0.182
  Angle     :  0.611  12.943   7183  Z= 0.301
  Chirality :  0.052   0.628    782
  Planarity :  0.004   0.048    929
  Dihedral  :  7.750  58.522    853
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.05 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.42 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.32), residues: 645
  helix: -0.98 (0.61), residues: 63
  sheet: -1.32 (0.41), residues: 160
  loop : -1.07 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 384 
 HIS   0.003   0.001   HIS A 465 
 PHE   0.020   0.002   PHE B 311 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.003   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.632 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7651 (mm110) cc_final: 0.7228 (mt0)
REVERT: A  413 ASN cc_start: 0.8463 (m-40) cc_final: 0.8198 (m-40)
REVERT: A  544 GLU cc_start: 0.8946 (mp0) cc_final: 0.8712 (mp0)
REVERT: B  157 ILE cc_start: 0.8061 (OUTLIER) cc_final: 0.7569 (mt)
REVERT: B  268 PRO cc_start: 0.8537 (Cg_endo) cc_final: 0.8261 (Cg_exo)
REVERT: B  434 VAL cc_start: 0.9124 (t) cc_final: 0.8887 (t)
REVERT: B  458 ASP cc_start: 0.8649 (t0) cc_final: 0.8366 (t0)
REVERT: B  463 SER cc_start: 0.9065 (t) cc_final: 0.8616 (p)
  outliers start: 16
  outliers final: 10
  residues processed: 91
  average time/residue: 0.1764
  time to fit residues: 21.1294
Evaluate side-chains
  84 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  487 LYS
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  503 HIS
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 37 optimal weight:    0.0270
   chunk 20 optimal weight:    0.0770
   chunk 21 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0980
   chunk 40 optimal weight:    0.9990
   chunk 58 optimal weight:    0.0170
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.0634

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 227 HIS
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 411 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.077989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.067562 restraints weight = 13022.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.069209 restraints weight = 8557.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.070103 restraints weight = 5496.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5276  Z= 0.133
  Angle     :  0.565  11.113   7183  Z= 0.283
  Chirality :  0.050   0.579    782
  Planarity :  0.004   0.045    929
  Dihedral  :  6.813  56.225    853
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.59 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.50 (0.33), residues: 645
  helix: -0.82 (0.63), residues: 63
  sheet: -1.37 (0.46), residues: 131
  loop : -0.91 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 384 
 HIS   0.002   0.000   HIS A 465 
 PHE   0.016   0.001   PHE B 311 
 TYR   0.012   0.001   TYR A 426 
 ARG   0.002   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8425 (m-40) cc_final: 0.8192 (m-40)
REVERT: A  536 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8463 (mmpt)
REVERT: A  544 GLU cc_start: 0.8834 (mp0) cc_final: 0.8631 (mp0)
REVERT: B  157 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7566 (mt)
REVERT: B  268 PRO cc_start: 0.8509 (Cg_endo) cc_final: 0.8249 (Cg_exo)
REVERT: B  293 THR cc_start: 0.8659 (t) cc_final: 0.8433 (t)
REVERT: B  434 VAL cc_start: 0.9080 (t) cc_final: 0.8819 (t)
REVERT: B  458 ASP cc_start: 0.8594 (t0) cc_final: 0.8372 (t0)
REVERT: B  463 SER cc_start: 0.9101 (t) cc_final: 0.8729 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 96
  average time/residue: 0.1516
  time to fit residues: 19.4270
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0870
   chunk 22 optimal weight:    0.3980
   chunk 59 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    0.5980
   overall best weight:    0.5560

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.075346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.064801 restraints weight = 12790.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.066209 restraints weight = 8639.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.066993 restraints weight = 5818.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.2608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.3562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5276  Z= 0.183
  Angle     :  0.595  11.232   7183  Z= 0.295
  Chirality :  0.051   0.604    782
  Planarity :  0.004   0.042    929
  Dihedral  :  6.910  59.031    847
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.99 %
    Favored  : 75.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.41 (0.33), residues: 645
  helix: -0.79 (0.63), residues: 63
  sheet: -1.09 (0.44), residues: 139
  loop : -0.91 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 384 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.011   0.001   PHE B 209 
 TYR   0.017   0.001   TYR A 528 
 ARG   0.004   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8487 (m-40) cc_final: 0.8209 (m-40)
REVERT: A  536 LYS cc_start: 0.8873 (mmpt) cc_final: 0.8471 (mmpt)
REVERT: A  540 VAL cc_start: 0.9453 (t) cc_final: 0.9186 (p)
REVERT: A  544 GLU cc_start: 0.8887 (mp0) cc_final: 0.8673 (mp0)
REVERT: B  157 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7555 (mt)
REVERT: B  268 PRO cc_start: 0.8529 (Cg_endo) cc_final: 0.8249 (Cg_exo)
REVERT: B  293 THR cc_start: 0.8688 (t) cc_final: 0.8453 (t)
REVERT: B  434 VAL cc_start: 0.9100 (t) cc_final: 0.8879 (t)
REVERT: B  458 ASP cc_start: 0.8646 (t0) cc_final: 0.8420 (t0)
REVERT: B  463 SER cc_start: 0.9031 (t) cc_final: 0.8735 (p)
  outliers start: 13
  outliers final: 10
  residues processed: 88
  average time/residue: 0.1624
  time to fit residues: 18.9120
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 77
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    0.0370
   chunk 44 optimal weight:    0.9980
   chunk 6 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9980
   chunk 24 optimal weight:    0.3980
   chunk 1 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.075122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.064720 restraints weight = 12946.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.066058 restraints weight = 9065.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.066751 restraints weight = 6216.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5276  Z= 0.184
  Angle     :  0.602  11.346   7183  Z= 0.299
  Chirality :  0.051   0.598    782
  Planarity :  0.004   0.041    929
  Dihedral  :  6.897  56.399    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 20.07 %
    Favored  : 76.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.37 (0.33), residues: 645
  helix: -0.73 (0.64), residues: 63
  sheet: -1.08 (0.44), residues: 139
  loop : -0.88 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 384 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.011   0.001   PHE B 311 
 TYR   0.018   0.002   TYR A 528 
 ARG   0.005   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.561 
Fit side-chains
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8483 (m-40) cc_final: 0.8169 (m-40)
REVERT: A  447 ARG cc_start: 0.8846 (ptm160) cc_final: 0.8592 (ptt180)
REVERT: A  536 LYS cc_start: 0.8874 (mmpt) cc_final: 0.8474 (mmpt)
REVERT: A  540 VAL cc_start: 0.9442 (t) cc_final: 0.9208 (p)
REVERT: A  544 GLU cc_start: 0.8915 (mp0) cc_final: 0.8683 (mp0)
REVERT: A  553 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8203 (mt-10)
REVERT: B  157 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7606 (mt)
REVERT: B  268 PRO cc_start: 0.8555 (Cg_endo) cc_final: 0.8271 (Cg_exo)
REVERT: B  293 THR cc_start: 0.8668 (t) cc_final: 0.8444 (t)
REVERT: B  458 ASP cc_start: 0.8590 (t0) cc_final: 0.8382 (t0)
REVERT: B  463 SER cc_start: 0.8979 (t) cc_final: 0.8726 (p)
  outliers start: 18
  outliers final: 14
  residues processed: 90
  average time/residue: 0.1699
  time to fit residues: 20.0089
Evaluate side-chains
  90 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 44 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 12 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0570
   chunk 39 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.074995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.064303 restraints weight = 13187.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.065736 restraints weight = 8766.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.066438 restraints weight = 5894.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   5276  Z= 0.175
  Angle     :  0.604  11.343   7183  Z= 0.300
  Chirality :  0.051   0.592    782
  Planarity :  0.004   0.041    929
  Dihedral  :  6.850  56.460    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.59 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.40 (0.33), residues: 645
  helix: -0.68 (0.65), residues: 64
  sheet: -1.21 (0.46), residues: 129
  loop : -0.88 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 384 
 HIS   0.002   0.001   HIS B 138 
 PHE   0.011   0.001   PHE B 311 
 TYR   0.016   0.001   TYR A 528 
 ARG   0.005   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8614 (mmm160) cc_final: 0.7890 (mmm160)
REVERT: A  413 ASN cc_start: 0.8511 (m-40) cc_final: 0.8181 (m-40)
REVERT: A  447 ARG cc_start: 0.8823 (ptm160) cc_final: 0.8603 (ptt180)
REVERT: A  536 LYS cc_start: 0.8881 (mmpt) cc_final: 0.8489 (mmpt)
REVERT: A  540 VAL cc_start: 0.9449 (t) cc_final: 0.9201 (p)
REVERT: A  544 GLU cc_start: 0.8929 (mp0) cc_final: 0.8689 (mp0)
REVERT: A  553 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8161 (mt-10)
REVERT: B  157 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7639 (mt)
REVERT: B  268 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8267 (Cg_exo)
REVERT: B  293 THR cc_start: 0.8640 (t) cc_final: 0.8429 (t)
REVERT: B  434 VAL cc_start: 0.9097 (t) cc_final: 0.8861 (t)
  outliers start: 16
  outliers final: 13
  residues processed: 83
  average time/residue: 0.1729
  time to fit residues: 18.9804
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.565 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0980
   chunk 26 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.074396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2547 r_free = 0.2547 target = 0.063697 restraints weight = 13144.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.065133 restraints weight = 8833.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.065766 restraints weight = 5891.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5276  Z= 0.192
  Angle     :  0.624  11.418   7183  Z= 0.309
  Chirality :  0.052   0.595    782
  Planarity :  0.004   0.045    929
  Dihedral  :  7.013  56.440    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.36 %
    Favored  : 93.64 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 20.94 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    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: -1.39 (0.32), residues: 645
  helix: -0.68 (0.64), residues: 64
  sheet: -1.08 (0.43), residues: 139
  loop : -0.91 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 384 
 HIS   0.002   0.001   HIS B 138 
 PHE   0.011   0.001   PHE B 209 
 TYR   0.016   0.002   TYR A 528 
 ARG   0.005   0.000   ARG B 470 

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

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

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1290 Ramachandran restraints generated.
    645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8613 (mmm160) cc_final: 0.7891 (mmm160)
REVERT: A  413 ASN cc_start: 0.8505 (m-40) cc_final: 0.8177 (m-40)
REVERT: A  447 ARG cc_start: 0.8834 (ptm160) cc_final: 0.8629 (ptt180)
REVERT: A  536 LYS cc_start: 0.8880 (mmpt) cc_final: 0.8477 (mmpt)
REVERT: A  540 VAL cc_start: 0.9446 (t) cc_final: 0.9201 (p)
REVERT: A  544 GLU cc_start: 0.8917 (mp0) cc_final: 0.8661 (mp0)
REVERT: A  553 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8198 (mt-10)
REVERT: B  157 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7696 (mt)
REVERT: B  268 PRO cc_start: 0.8554 (Cg_endo) cc_final: 0.8269 (Cg_exo)
  outliers start: 15
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1711
  time to fit residues: 19.1298
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  470 ASN
Chi-restraints excluded: chain A residue  482 VAL
Chi-restraints excluded: chain A residue  494 ILE
Chi-restraints excluded: chain A residue  504 CYS
Chi-restraints excluded: chain A residue  523 ASP
Chi-restraints excluded: chain A residue  535 GLN
Chi-restraints excluded: chain A residue  553 GLU
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  407 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 59 optimal weight:    0.7980
   chunk 38 optimal weight:    0.0970
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 62 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.6378

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

Flipped N/Q/H residues before XYZ refinement:
** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.074336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2546 r_free = 0.2546 target = 0.063577 restraints weight = 13217.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.065410 restraints weight = 8844.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.065773 restraints weight = 5913.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.3838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   5276  Z= 0.196
  Angle     :  0.623  11.464   7183  Z= 0.309
  Chirality :  0.051   0.597    782
  Planarity :  0.004   0.040    929
  Dihedral  :  7.126  56.444    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 20.77 %
    Favored  : 76.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.32), residues: 645
  helix: -0.71 (0.64), residues: 64
  sheet: -1.19 (0.41), residues: 151
  loop : -0.88 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 380 
 HIS   0.003   0.001   HIS B 138 
 PHE   0.011   0.001   PHE B 209 
 TYR   0.016   0.002   TYR A 528 
 ARG   0.003   0.000   ARG B 409 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1860.73 seconds
wall clock time: 35 minutes 1.35 seconds (2101.35 seconds total)