Starting phenix.real_space_refine
on Thu Mar  6 06:51:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yqq_39502/03_2025/8yqq_39502_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yqq_39502/03_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_39502/03_2025/8yqq_39502.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yqq_39502/03_2025/8yqq_39502.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yqq_39502/03_2025/8yqq_39502_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yqq_39502/03_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-5624/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: 3.83, per 1000 atoms: 0.74
  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: 1.19
  Conformation dependent library (CDL) restraints added in 635.9 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: 0.66
  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: 1.45 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:             2.650
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     16.320
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.100
-------------------------------------------------------------------------------
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  : 0.546 
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: 0.1640
  time to fit residues: 31.9330
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  : 0.528 
-------------------------------------------------------------------------------
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 = 0.066630 restraints weight = 8428.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.067519 restraints weight = 5501.671|
|-----------------------------------------------------------------------------|
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  : 0.756 
Fit side-chains
REVERT: A  502 ARG cc_start: 0.8308 (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: 0.8014 (OUTLIER) cc_final: 0.6993 (m170)
REVERT: A  578 ASP cc_start: 0.7954 (OUTLIER) cc_final: 0.7563 (m-30)
REVERT: B  188 MET cc_start: 0.6776 (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: 0.8293 (mmt) cc_final: 0.6621 (mmt)
  outliers start: 21
  outliers final: 14
  residues processed: 108
  average time/residue: 0.1989
  time to fit residues: 29.0074
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  : 0.622 
-------------------------------------------------------------------------------
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:    0.8980
   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:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0770
   chunk 7 optimal weight:    0.5980
   chunk 33 optimal weight:    0.1980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.2785 r_free = 0.2785 target = 0.075516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.064806 restraints weight = 12996.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.066311 restraints weight = 8560.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.067317 restraints weight = 6080.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.2545

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= 0.169
  Angle     :  0.657  15.703   7183  Z= 0.318
  Chirality :  0.053   0.646    782
  Planarity :  0.005   0.054    929
  Dihedral  :  8.044  59.537    864
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  6.05 %
    Favored  : 93.80 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 19.55 %
    Favored  : 77.31 %
  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: -2.08 (0.32), residues: 645
  helix: -1.84 (0.52), residues: 69
  sheet: -1.71 (0.39), residues: 162
  loop : -1.14 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 269 
 HIS   0.011   0.001   HIS A 562 
 PHE   0.016   0.002   PHE A 577 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.003   0.000   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
  110 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 1.161 
Fit side-chains
REVERT: A  413 ASN cc_start: 0.8467 (m-40) cc_final: 0.8214 (m-40)
REVERT: A  544 GLU cc_start: 0.8903 (mp0) cc_final: 0.8673 (mp0)
REVERT: B  384 TRP cc_start: 0.8863 (m-90) cc_final: 0.8659 (m-90)
REVERT: B  458 ASP cc_start: 0.8690 (t0) cc_final: 0.8310 (t0)
REVERT: B  463 SER cc_start: 0.8998 (t) cc_final: 0.8544 (p)
REVERT: B  488 MET cc_start: 0.8436 (mmt) cc_final: 0.7211 (mmt)
  outliers start: 18
  outliers final: 9
  residues processed: 104
  average time/residue: 0.2644
  time to fit residues: 36.9837
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 77
  time to evaluate  : 0.905 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 B residue  157 ILE
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:    0.9990
   chunk 37 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 35 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9990
   chunk 61 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   overall best weight:    0.8384

-------------------------------------------------------------------------------
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 = 0.2735 r_free = 0.2735 target = 0.073122 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2517 r_free = 0.2517 target = 0.062452 restraints weight = 13309.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.064091 restraints weight = 8903.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.064552 restraints weight = 6231.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.2990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5276  Z= 0.228
  Angle     :  0.650  14.876   7183  Z= 0.322
  Chirality :  0.054   0.644    782
  Planarity :  0.005   0.048    929
  Dihedral  :  7.986  58.951    853
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.75 %
    Favored  : 92.09 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.29 %
    Favored  : 75.39 %
  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: -1.80 (0.32), residues: 645
  helix: -1.11 (0.60), residues: 63
  sheet: -1.63 (0.40), residues: 160
  loop : -1.01 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B 176 
 HIS   0.004   0.001   HIS A 465 
 PHE   0.019   0.002   PHE B 311 
 TYR   0.018   0.002   TYR A 426 
 ARG   0.004   0.001   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
  98 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.712 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  413 ASN cc_start: 0.8505 (m-40) cc_final: 0.8232 (m-40)
REVERT: A  544 GLU cc_start: 0.8959 (mp0) cc_final: 0.8662 (mp0)
REVERT: B  157 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7679 (mt)
REVERT: B  293 THR cc_start: 0.8668 (t) cc_final: 0.8430 (t)
REVERT: B  458 ASP cc_start: 0.8660 (t0) cc_final: 0.8353 (t0)
REVERT: B  463 SER cc_start: 0.9053 (t) cc_final: 0.8551 (p)
  outliers start: 19
  outliers final: 13
  residues processed: 92
  average time/residue: 0.2659
  time to fit residues: 30.6216
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
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  256 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:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 45 optimal weight:    0.6980
   chunk 21 optimal weight:    4.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 42 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.071371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.060662 restraints weight = 13330.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2505 r_free = 0.2505 target = 0.062234 restraints weight = 8882.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.063131 restraints weight = 6245.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.2523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.3308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5276  Z= 0.325
  Angle     :  0.690  13.906   7183  Z= 0.343
  Chirality :  0.055   0.650    782
  Planarity :  0.005   0.061    929
  Dihedral  :  8.452  59.207    853
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.91 %
    Favored  : 91.94 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.77 %
    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: -1.83 (0.32), residues: 645
  helix: -1.08 (0.59), residues: 62
  sheet: -1.39 (0.40), residues: 158
  loop : -1.17 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 176 
 HIS   0.006   0.002   HIS B 169 
 PHE   0.018   0.002   PHE B 209 
 TYR   0.021   0.002   TYR A 426 
 ARG   0.006   0.001   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
  93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
REVERT: A  410 GLN cc_start: 0.7848 (mm110) cc_final: 0.7430 (mt0)
REVERT: A  413 ASN cc_start: 0.8461 (m-40) cc_final: 0.8221 (m-40)
REVERT: A  494 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7829 (pt)
REVERT: A  544 GLU cc_start: 0.9006 (mp0) cc_final: 0.8725 (mp0)
REVERT: B  157 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7669 (mt)
REVERT: B  268 PRO cc_start: 0.8523 (Cg_endo) cc_final: 0.8209 (Cg_exo)
REVERT: B  463 SER cc_start: 0.9040 (t) cc_final: 0.8736 (p)
  outliers start: 20
  outliers final: 14
  residues processed: 88
  average time/residue: 0.2343
  time to fit residues: 26.7801
Evaluate side-chains
  82 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  469 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 A residue  607 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  341 THR
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:    1.9990
   chunk 20 optimal weight:    0.0470
   chunk 21 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 48 optimal weight:    0.0170
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.3518

-------------------------------------------------------------------------------
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
** 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 = 0.2769 r_free = 0.2769 target = 0.074791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2556 r_free = 0.2556 target = 0.064156 restraints weight = 13065.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.065947 restraints weight = 8652.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.067106 restraints weight = 5497.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   5276  Z= 0.160
  Angle     :  0.593  11.437   7183  Z= 0.298
  Chirality :  0.051   0.617    782
  Planarity :  0.004   0.048    929
  Dihedral  :  7.309  57.521    853
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 6.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.24 %
    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: -1.67 (0.32), residues: 645
  helix: -0.87 (0.63), residues: 64
  sheet: -1.35 (0.45), residues: 139
  loop : -1.08 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 269 
 HIS   0.003   0.001   HIS A 465 
 PHE   0.011   0.001   PHE A 577 
 TYR   0.013   0.001   TYR A 426 
 ARG   0.004   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
  93 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 74
  time to evaluate  : 0.639 
Fit side-chains
REVERT: A  410 GLN cc_start: 0.7726 (mm110) cc_final: 0.7333 (mt0)
REVERT: A  413 ASN cc_start: 0.8437 (m-40) cc_final: 0.8208 (m-40)
REVERT: A  502 ARG cc_start: 0.8569 (ptp-170) cc_final: 0.7876 (ptp-170)
REVERT: A  536 LYS cc_start: 0.8915 (mmpt) cc_final: 0.8492 (mmpt)
REVERT: A  544 GLU cc_start: 0.8930 (mp0) cc_final: 0.8689 (mp0)
REVERT: B  157 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7593 (mt)
REVERT: B  268 PRO cc_start: 0.8529 (Cg_endo) cc_final: 0.8243 (Cg_exo)
REVERT: B  270 GLN cc_start: 0.9021 (tp40) cc_final: 0.8119 (tp40)
REVERT: B  458 ASP cc_start: 0.8671 (t0) cc_final: 0.8282 (t0)
REVERT: B  463 SER cc_start: 0.9055 (t) cc_final: 0.8713 (p)
  outliers start: 19
  outliers final: 14
  residues processed: 89
  average time/residue: 0.1620
  time to fit residues: 18.8949
Evaluate side-chains
  86 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 71
  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  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 A residue  607 LEU
Chi-restraints excluded: chain B residue  151 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  331 VAL
Chi-restraints excluded: chain B residue  361 VAL
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:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 59 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 6 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0270
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.6038

-------------------------------------------------------------------------------
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 = 0.2754 r_free = 0.2754 target = 0.073987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.063412 restraints weight = 12800.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.064802 restraints weight = 8675.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.065550 restraints weight = 5899.011|
|-----------------------------------------------------------------------------|
r_work (final): 0.2577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.3597

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= 0.194
  Angle     :  0.598  11.432   7183  Z= 0.300
  Chirality :  0.052   0.621    782
  Planarity :  0.004   0.046    929
  Dihedral  :  7.451  57.095    853
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.42 %
    Favored  : 76.27 %
  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: -1.51 (0.32), residues: 645
  helix: -0.76 (0.63), residues: 64
  sheet: -1.16 (0.42), residues: 149
  loop : -0.98 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 269 
 HIS   0.003   0.001   HIS B 169 
 PHE   0.011   0.001   PHE B 209 
 TYR   0.014   0.001   TYR A 426 
 ARG   0.005   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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8673 (mmm160) cc_final: 0.7757 (mmm160)
REVERT: A  413 ASN cc_start: 0.8436 (m-40) cc_final: 0.8171 (m-40)
REVERT: A  536 LYS cc_start: 0.8913 (mmpt) cc_final: 0.8484 (mmpt)
REVERT: A  544 GLU cc_start: 0.8949 (mp0) cc_final: 0.8666 (mp0)
REVERT: B  157 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7627 (mt)
REVERT: B  268 PRO cc_start: 0.8516 (Cg_endo) cc_final: 0.8225 (Cg_exo)
REVERT: B  270 GLN cc_start: 0.9009 (tp40) cc_final: 0.8127 (tp40)
REVERT: B  458 ASP cc_start: 0.8726 (t0) cc_final: 0.8312 (t0)
REVERT: B  463 SER cc_start: 0.8983 (t) cc_final: 0.8732 (p)
  outliers start: 19
  outliers final: 16
  residues processed: 86
  average time/residue: 0.1856
  time to fit residues: 20.6055
Evaluate side-chains
  87 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 70
  time to evaluate  : 0.621 
-------------------------------------------------------------------------------
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  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  542 ILE
Chi-restraints excluded: chain A residue  602 THR
Chi-restraints excluded: chain A residue  607 LEU
Chi-restraints excluded: chain B residue  151 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 44 optimal weight:    0.1980
   chunk 6 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0060
   chunk 24 optimal weight:    0.8980
   chunk 1 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0970
   chunk 56 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.2782 r_free = 0.2782 target = 0.075102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.064409 restraints weight = 13091.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.065791 restraints weight = 8913.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.066578 restraints weight = 6011.654|
|-----------------------------------------------------------------------------|
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   5276  Z= 0.157
  Angle     :  0.592  11.233   7183  Z= 0.297
  Chirality :  0.050   0.601    782
  Planarity :  0.004   0.046    929
  Dihedral  :  6.944  59.219    853
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.97 %
    Allowed  : 20.77 %
    Favored  : 76.27 %
  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: -1.51 (0.33), residues: 645
  helix: -0.71 (0.64), residues: 64
  sheet: -1.30 (0.45), residues: 139
  loop : -0.95 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 269 
 HIS   0.002   0.001   HIS A 465 
 PHE   0.010   0.001   PHE A 383 
 TYR   0.015   0.001   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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8640 (mmm160) cc_final: 0.8409 (mmp80)
REVERT: A  413 ASN cc_start: 0.8424 (m-40) cc_final: 0.8189 (m-40)
REVERT: A  447 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8391 (ptt180)
REVERT: A  536 LYS cc_start: 0.8896 (mmpt) cc_final: 0.8497 (mmpt)
REVERT: A  544 GLU cc_start: 0.8910 (mp0) cc_final: 0.8638 (mp0)
REVERT: A  553 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.8219 (mt-10)
REVERT: B  157 ILE cc_start: 0.8003 (pt) cc_final: 0.7558 (mt)
REVERT: B  268 PRO cc_start: 0.8546 (Cg_endo) cc_final: 0.8275 (Cg_exo)
REVERT: B  458 ASP cc_start: 0.8740 (t0) cc_final: 0.8338 (t0)
  outliers start: 17
  outliers final: 14
  residues processed: 87
  average time/residue: 0.1736
  time to fit residues: 19.7531
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  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  411 SER
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  526 SER
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  151 LEU
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:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9980
   chunk 12 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 39 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.072813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2517 r_free = 0.2517 target = 0.062144 restraints weight = 13255.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2542 r_free = 0.2542 target = 0.063485 restraints weight = 8955.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.064200 restraints weight = 6129.796|
|-----------------------------------------------------------------------------|
r_work (final): 0.2556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8387
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   5276  Z= 0.229
  Angle     :  0.644  11.513   7183  Z= 0.319
  Chirality :  0.052   0.615    782
  Planarity :  0.004   0.043    929
  Dihedral  :  7.048  56.116    847
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.75 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.47 %
    Favored  : 75.39 %
  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: -1.51 (0.32), residues: 645
  helix: -0.65 (0.64), residues: 63
  sheet: -1.20 (0.41), residues: 153
  loop : -0.97 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 380 
 HIS   0.004   0.001   HIS B 169 
 PHE   0.015   0.002   PHE B 311 
 TYR   0.016   0.002   TYR A 426 
 ARG   0.006   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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8664 (mmm160) cc_final: 0.8430 (mmp80)
REVERT: A  413 ASN cc_start: 0.8451 (m-40) cc_final: 0.8192 (m-40)
REVERT: A  447 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8332 (ptt180)
REVERT: A  536 LYS cc_start: 0.8910 (mmpt) cc_final: 0.8488 (mmpt)
REVERT: A  544 GLU cc_start: 0.8933 (mp0) cc_final: 0.8628 (mp0)
REVERT: A  553 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8215 (mt-10)
REVERT: B  157 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7634 (mt)
REVERT: B  268 PRO cc_start: 0.8535 (Cg_endo) cc_final: 0.8234 (Cg_exo)
REVERT: B  270 GLN cc_start: 0.8982 (tp40) cc_final: 0.8133 (tp40)
REVERT: B  458 ASP cc_start: 0.8783 (t0) cc_final: 0.8360 (t0)
  outliers start: 18
  outliers final: 15
  residues processed: 86
  average time/residue: 0.1850
  time to fit residues: 20.4869
Evaluate side-chains
  89 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  424 GLN
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  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  151 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain B residue  361 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 64
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 50 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   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 424 GLN
** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.072601 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2513 r_free = 0.2513 target = 0.061967 restraints weight = 13204.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2538 r_free = 0.2538 target = 0.063317 restraints weight = 8960.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.064055 restraints weight = 6092.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   5276  Z= 0.236
  Angle     :  0.654  11.578   7183  Z= 0.321
  Chirality :  0.053   0.617    782
  Planarity :  0.004   0.055    929
  Dihedral  :  7.077  56.057    847
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.29 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 21.29 %
    Favored  : 75.39 %
  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: -1.55 (0.32), residues: 645
  helix: -0.64 (0.64), residues: 62
  sheet: -1.21 (0.41), residues: 154
  loop : -1.01 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 380 
 HIS   0.004   0.001   HIS B 169 
 PHE   0.013   0.001   PHE B 209 
 TYR   0.020   0.002   TYR A 426 
 ARG   0.006   0.001   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
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  397 ARG cc_start: 0.8672 (mmm160) cc_final: 0.7756 (mmm160)
REVERT: A  413 ASN cc_start: 0.8453 (m-40) cc_final: 0.8199 (m-40)
REVERT: A  447 ARG cc_start: 0.8767 (ptm160) cc_final: 0.8325 (ptt180)
REVERT: A  536 LYS cc_start: 0.8918 (mmpt) cc_final: 0.8494 (mmpt)
REVERT: A  544 GLU cc_start: 0.8937 (mp0) cc_final: 0.8631 (mp0)
REVERT: A  553 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8269 (mt-10)
REVERT: B  157 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7639 (mt)
REVERT: B  268 PRO cc_start: 0.8542 (Cg_endo) cc_final: 0.8237 (Cg_exo)
REVERT: B  270 GLN cc_start: 0.8991 (tp40) cc_final: 0.8080 (tp40)
REVERT: B  293 THR cc_start: 0.8750 (t) cc_final: 0.8520 (t)
REVERT: B  458 ASP cc_start: 0.8801 (t0) cc_final: 0.8370 (t0)
  outliers start: 19
  outliers final: 17
  residues processed: 85
  average time/residue: 0.1862
  time to fit residues: 20.3448
Evaluate side-chains
  91 residues out of total 573 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 LEU
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  424 GLN
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  151 LEU
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  239 LEU
Chi-restraints excluded: chain B residue  256 ILE
Chi-restraints excluded: chain B residue  361 VAL
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:    0.9980
   chunk 61 optimal weight:    0.0370
   chunk 9 optimal weight:    2.9990
   chunk 59 optimal weight:    0.0030
   chunk 38 optimal weight:    0.0980
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3068

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.2780 r_free = 0.2780 target = 0.075004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.064445 restraints weight = 13230.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2597 r_free = 0.2597 target = 0.065919 restraints weight = 8835.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.066688 restraints weight = 5827.052|
|-----------------------------------------------------------------------------|
r_work (final): 0.2610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   5276  Z= 0.154
  Angle     :  0.613  11.339   7183  Z= 0.302
  Chirality :  0.051   0.592    782
  Planarity :  0.004   0.042    929
  Dihedral  :  6.553  56.288    847
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 21.82 %
    Favored  : 75.39 %
  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 (0.32), residues: 645
  helix: -0.56 (0.65), residues: 62
  sheet: -1.17 (0.44), residues: 142
  loop : -0.91 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 380 
 HIS   0.001   0.000   HIS A 465 
 PHE   0.011   0.001   PHE B 311 
 TYR   0.016   0.001   TYR A 426 
 ARG   0.005   0.000   ARG B 470 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1972.93 seconds
wall clock time: 35 minutes 58.20 seconds (2158.20 seconds total)