Starting phenix.real_space_refine
on Wed Apr 30 00:30:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8snm_40629/04_2025/8snm_40629.cif"
  }
  resolution = 3.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.059
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     Zn      1      6.06       5
     S      69      5.16       5
     C    5719      2.51       5
     N    1529      2.21       5
     O    1667      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 8986
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 3929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3929
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 467}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 14
    Chain: "A"
      Number of atoms: 1406
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1406
          Classifications: {'peptide': 175}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 41
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "B"
      Number of atoms: 3649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 468, 3649
          Classifications: {'peptide': 468}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 17, 'TRANS': 450}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 13
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' CA': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5195  SG  CYS A 184      44.254  25.694  36.116  1.00 74.22           S

  Time building chain proxies: 5.89, per 1000 atoms: 0.66
  Number of scatterers: 8986
  At special positions: 0
  Unit cell: (70.992, 110.432, 152.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Ca      1     19.99
     S      69     16.00
     O    1667      8.00
     N    1529      7.00
     C    5719      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=22, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 447 " - pdb=" SG  CYS C 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 470 " - pdb=" SG  CYS C 520 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 471 " - pdb=" SG  CYS C 487 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 479 " - pdb=" SG  CYS C 564 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 527 " - pdb=" SG  CYS C 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 571 " - pdb=" SG  CYS C 587 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 572 " - pdb=" SG  CYS C 606 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 579 " - pdb=" SG  CYS C 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 225 " - pdb=" SG  CYS B 333 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 365 " - pdb=" SG  CYS B 469 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 478 " - pdb=" SG  CYS B 506 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 489 " - pdb=" SG  CYS B 502 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 501 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 514 " - pdb=" SG  CYS B 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 521 " - pdb=" SG  CYS B 548 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 542 " - pdb=" SG  CYS B 573 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 567 " - pdb=" SG  CYS B 578 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 582 " - pdb=" SG  CYS B 604 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 591 " - pdb=" SG  CYS B 611 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 593 " - pdb=" SG  CYS B 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 600 " - pdb=" SG  CYS B 635 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 630 " - pdb=" SG  CYS B 641 " 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
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 901 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 415 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 409 "
        pdb="ZN    ZN B 901 " - pdb=" NE2 HIS B 405 "
        pdb="ZN    ZN B 901 " - pdb=" SG  CYS A 184 "
      Number of angles added : 3


  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2122

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 11 sheets defined
      37.8% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'C' and resid 343 through 349
    Processing helix  chain 'C' and resid 361 through 367
    Processing helix  chain 'C' and resid 373 through 395
      removed outlier: 3.710A  pdb=" N   TYR C 377 " --> pdb=" O   PRO C 373 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLY C 395 " --> pdb=" O   ILE C 391 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 433 through 441
    Processing helix  chain 'C' and resid 444 through 449
    Processing helix  chain 'C' and resid 451 through 467
      removed outlier: 4.049A  pdb=" N   ASP C 467 " --> pdb=" O   ASP C 463 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 533 through 537
      removed outlier: 3.816A  pdb=" N   ILE C 537 " --> pdb=" O   GLY C 534 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 541 through 545
    Processing helix  chain 'C' and resid 559 through 564
      removed outlier: 3.769A  pdb=" N   CYS C 564 " --> pdb=" O   LEU C 560 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 583 through 590
    Processing helix  chain 'C' and resid 600 through 604
    Processing helix  chain 'C' and resid 605 through 612
      removed outlier: 4.062A  pdb=" N   LYS C 609 " --> pdb=" O   HIS C 605 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 626 through 631
      removed outlier: 3.524A  pdb=" N   SER C 631 " --> pdb=" O   ARG C 627 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 637 through 660
      removed outlier: 4.455A  pdb=" N   ARG C 653 " --> pdb=" O   MET C 649 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP C 654 " --> pdb=" O   THR C 650 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 660 through 683
    Processing helix  chain 'C' and resid 691 through 709
    Processing helix  chain 'C' and resid 715 through 735
      removed outlier: 4.210A  pdb=" N   ALA C 719 " --> pdb=" O   ARG C 715 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 740 through 756
      removed outlier: 3.764A  pdb=" N   HIS C 744 " --> pdb=" O   ASP C 740 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 768 through 795
    Processing helix  chain 'C' and resid 801 through 803
      No H-bonds generated for 'chain 'C' and resid 801 through 803'
    Processing helix  chain 'C' and resid 804 through 809
      removed outlier: 3.879A  pdb=" N   THR C 808 " --> pdb=" O   ILE C 804 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 815 through 820
    Processing helix  chain 'A' and resid 32 through 39
      removed outlier: 4.071A  pdb=" N   SER A  37 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   LEU A  38 " --> pdb=" O   LYS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 86 through 90
      removed outlier: 3.827A  pdb=" N   ARG A  89 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 110 through 112
      No H-bonds generated for 'chain 'A' and resid 110 through 112'
    Processing helix  chain 'A' and resid 153 through 156
      removed outlier: 3.758A  pdb=" N   VAL A 156 " --> pdb=" O   TRP A 153 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 153 through 156'
    Processing helix  chain 'A' and resid 170 through 172
      No H-bonds generated for 'chain 'A' and resid 170 through 172'
    Processing helix  chain 'A' and resid 190 through 194
    Processing helix  chain 'B' and resid 232 through 239
    Processing helix  chain 'B' and resid 243 through 265
    Processing helix  chain 'B' and resid 313 through 325
    Processing helix  chain 'B' and resid 343 through 347
      removed outlier: 3.508A  pdb=" N   GLY B 346 " --> pdb=" O   PHE B 343 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR B 347 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 343 through 347'
    Processing helix  chain 'B' and resid 395 through 410
    Processing helix  chain 'B' and resid 451 through 465
      removed outlier: 3.816A  pdb=" N   SER B 457 " --> pdb=" O   CYS B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 580 through 585
    Processing helix  chain 'B' and resid 647 through 658
      removed outlier: 3.596A  pdb=" N   GLN B 658 " --> pdb=" O   ASP B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 660 through 671
    Processing helix  chain 'B' and resid 671 through 698
      removed outlier: 3.528A  pdb=" N   SER B 675 " --> pdb=" O   ASN B 671 " (cutoff:3.500A)
      Proline residue:  B 686  - end of helix
    Processing sheet with id=AA1, first strand: chain 'C' and resid 403 through 411
    Processing sheet with id=AA2, first strand: chain 'C' and resid 481 through 482
    Processing sheet with id=AA3, first strand: chain 'C' and resid 579 through 582
      removed outlier: 3.515A  pdb=" N   TYR C 593 " --> pdb=" O   CYS C 572 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 42 through 43
      removed outlier: 3.829A  pdb=" N   ARG A 126 " --> pdb=" O   ASN A 141 " (cutoff:3.500A)
      removed outlier: 6.003A  pdb=" N   SER A 125 " --> pdb=" O   VAL A 119 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   VAL A 119 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 104 through 107
      removed outlier: 4.355A  pdb=" N   VAL A  96 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   CYS B 225 " --> pdb=" O   ILE B 277 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   ILE B 279 " --> pdb=" O   CYS B 225 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   LEU B 227 " --> pdb=" O   ILE B 279 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   GLN B 281 " --> pdb=" O   LEU B 227 " (cutoff:3.500A)
      removed outlier: 8.289A  pdb=" N   LEU B 334 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LYS B 226 " --> pdb=" O   LEU B 334 " (cutoff:3.500A)
      removed outlier: 7.726A  pdb=" N   HIS B 336 " --> pdb=" O   LYS B 226 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   LEU B 228 " --> pdb=" O   HIS B 336 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   PHE B 338 " --> pdb=" O   LEU B 228 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL B 230 " --> pdb=" O   PHE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 368 through 371
    Processing sheet with id=AA7, first strand: chain 'B' and resid 388 through 389
    Processing sheet with id=AA8, first strand: chain 'B' and resid 522 through 523
    Processing sheet with id=AA9, first strand: chain 'B' and resid 533 through 535
    Processing sheet with id=AB1, first strand: chain 'B' and resid 589 through 590
      removed outlier: 4.111A  pdb=" N   GLU B 589 " --> pdb=" O   ARG B 605 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   VAL B 612 " --> pdb=" O   CYS B 604 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 633 through 635

    344 hydrogen bonds defined for protein.
    984 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: 2.38

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2049
        1.33 -     1.46: 2684
        1.46 -     1.59: 4383
        1.59 -     1.72: 0
        1.72 -     1.85: 83
  Bond restraints: 9199
  Sorted by residual:
  bond pdb=" C   TRP B 684 "
       pdb=" O   TRP B 684 "
    ideal  model  delta    sigma   weight residual
    1.236  1.199  0.037 1.15e-02 7.56e+03 1.02e+01
  bond pdb=" CA  GLY C 517 "
       pdb=" C   GLY C 517 "
    ideal  model  delta    sigma   weight residual
    1.509  1.481  0.028 1.04e-02 9.25e+03 7.50e+00
  bond pdb=" CA  SER C 516 "
       pdb=" CB  SER C 516 "
    ideal  model  delta    sigma   weight residual
    1.530  1.490  0.040 1.57e-02 4.06e+03 6.54e+00
  bond pdb=" CA  SER C 516 "
       pdb=" C   SER C 516 "
    ideal  model  delta    sigma   weight residual
    1.524  1.494  0.030 1.24e-02 6.50e+03 5.94e+00
  bond pdb=" CA  THR C 515 "
       pdb=" C   THR C 515 "
    ideal  model  delta    sigma   weight residual
    1.521  1.493  0.029 1.31e-02 5.83e+03 4.77e+00
  ... (remaining 9194 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 12096
        1.99 -     3.98: 316
        3.98 -     5.97: 39
        5.97 -     7.95: 7
        7.95 -     9.94: 5
  Bond angle restraints: 12463
  Sorted by residual:
  angle pdb=" N   GLY C 517 "
        pdb=" CA  GLY C 517 "
        pdb=" C   GLY C 517 "
      ideal   model   delta    sigma   weight residual
     111.09  102.51    8.58 1.33e+00 5.65e-01 4.16e+01
  angle pdb=" N   ASN A 174 "
        pdb=" CA  ASN A 174 "
        pdb=" C   ASN A 174 "
      ideal   model   delta    sigma   weight residual
     108.08  117.42   -9.34 1.69e+00 3.50e-01 3.05e+01
  angle pdb=" CA  ASN A 174 "
        pdb=" C   ASN A 174 "
        pdb=" N   VAL A 175 "
      ideal   model   delta    sigma   weight residual
     119.63  115.16    4.47 8.10e-01 1.52e+00 3.04e+01
  angle pdb=" C   ASN A 174 "
        pdb=" CA  ASN A 174 "
        pdb=" CB  ASN A 174 "
      ideal   model   delta    sigma   weight residual
     116.63  110.23    6.40 1.16e+00 7.43e-01 3.04e+01
  angle pdb=" C   ALA B 270 "
        pdb=" CA  ALA B 270 "
        pdb=" CB  ALA B 270 "
      ideal   model   delta    sigma   weight residual
     116.54  110.56    5.98 1.15e+00 7.56e-01 2.71e+01
  ... (remaining 12458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 5039
       17.72 -    35.44: 401
       35.44 -    53.16: 63
       53.16 -    70.88: 21
       70.88 -    88.60: 8
  Dihedral angle restraints: 5532
    sinusoidal: 2239
      harmonic: 3293
  Sorted by residual:
  dihedral pdb=" CB  CYS B 582 "
           pdb=" SG  CYS B 582 "
           pdb=" SG  CYS B 604 "
           pdb=" CB  CYS B 604 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -174.60   88.60     1      1.00e+01 1.00e-02 9.37e+01
  dihedral pdb=" CB  CYS B 591 "
           pdb=" SG  CYS B 591 "
           pdb=" SG  CYS B 611 "
           pdb=" CB  CYS B 611 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.88   64.88     1      1.00e+01 1.00e-02 5.52e+01
  dihedral pdb=" CB  CYS B 514 "
           pdb=" SG  CYS B 514 "
           pdb=" SG  CYS B 522 "
           pdb=" CB  CYS B 522 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -142.84   56.84     1      1.00e+01 1.00e-02 4.35e+01
  ... (remaining 5529 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 1068
       0.052 -    0.104: 254
       0.104 -    0.156: 39
       0.156 -    0.207: 3
       0.207 -    0.259: 2
  Chirality restraints: 1366
  Sorted by residual:
  chirality pdb=" CA  ASN A 174 "
            pdb=" N   ASN A 174 "
            pdb=" C   ASN A 174 "
            pdb=" CB  ASN A 174 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.68e+00
  chirality pdb=" CA  VAL C 430 "
            pdb=" N   VAL C 430 "
            pdb=" C   VAL C 430 "
            pdb=" CB  VAL C 430 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.22    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  SER B 608 "
            pdb=" N   SER B 608 "
            pdb=" C   SER B 608 "
            pdb=" CB  SER B 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.70   -0.19 2.00e-01 2.50e+01 9.36e-01
  ... (remaining 1363 not shown)

  Planarity restraints: 1602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 612 "   -0.089 5.00e-02 4.00e+02   1.33e-01 2.82e+01
        pdb=" N   PRO B 613 "    0.229 5.00e-02 4.00e+02
        pdb=" CA  PRO B 613 "   -0.071 5.00e-02 4.00e+02
        pdb=" CD  PRO B 613 "   -0.070 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 312 "   -0.014 2.00e-02 2.50e+03   1.95e-02 9.55e+00
        pdb=" CG  TRP B 312 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 312 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 312 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 312 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 312 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 312 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 312 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 312 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 312 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 685 "    0.049 5.00e-02 4.00e+02   7.34e-02 8.62e+00
        pdb=" N   PRO B 686 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO B 686 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 686 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1599 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 511
        2.73 -     3.27: 9305
        3.27 -     3.81: 14987
        3.81 -     4.36: 18810
        4.36 -     4.90: 31509
  Nonbonded interactions: 75122
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN C 624 "
            pdb=" OH  TYR C 626 "
     model   vdw
     2.183 3.040
  nonbonded pdb=" OD2 ASP C 475 "
            pdb=" OG1 THR A  62 "
     model   vdw
     2.187 3.040
  nonbonded pdb=" OH  TYR B 340 "
            pdb=" OG1 THR B 393 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" NH1 ARG A  89 "
            pdb=" OG1 THR A 116 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" OG1 THR C 376 "
            pdb=" OE1 GLU C 656 "
     model   vdw
     2.209 3.040
  ... (remaining 75117 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:             2.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     25.290
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
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      :  0.004   0.150   9225  Z= 0.239
  Angle     :  0.763  15.422  12510  Z= 0.447
  Chirality :  0.046   0.259   1366
  Planarity :  0.006   0.133   1602
  Dihedral  : 13.051  83.445   3344
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.60 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.24), residues: 1126
  helix:  0.98 (0.27), residues: 358
  sheet: -0.21 (0.48), residues: 111
  loop : -1.36 (0.22), residues: 657

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.050   0.002   TRP B 312 
 HIS   0.009   0.001   HIS B 405 
 PHE   0.015   0.001   PHE B 323 
 TYR   0.012   0.001   TYR C 797 
 ARG   0.008   0.001   ARG C 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14106 (  344)
  hydrogen bonds       : angle       6.41998 (  984)
  metal coordination   : bond        0.08411 (    4)
  metal coordination   : angle       9.45740 (    3)
  SS BOND              : bond        0.00318 (   22)
  SS BOND              : angle       1.72893 (   44)
  covalent geometry    : bond        0.00414 ( 9199)
  covalent geometry    : angle       0.74325 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  434 SER cc_start: 0.8184 (m) cc_final: 0.7874 (p)
REVERT: C  515 THR cc_start: 0.8782 (p) cc_final: 0.8226 (t)
REVERT: C  529 GLU cc_start: 0.7222 (tt0) cc_final: 0.6675 (tt0)
REVERT: C  694 SER cc_start: 0.8856 (m) cc_final: 0.8547 (p)
REVERT: C  728 LEU cc_start: 0.7914 (tp) cc_final: 0.7714 (mm)
REVERT: B  224 THR cc_start: 0.9035 (m) cc_final: 0.8532 (p)
REVERT: B  564 ASP cc_start: 0.6807 (m-30) cc_final: 0.5906 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2696
  time to fit residues: 92.6113
Evaluate side-chains
  110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.0010
   chunk 84 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0470
   chunk 28 optimal weight:    0.0570
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 87 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.4980
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.2802

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

Flipped N/Q/H residues before XYZ refinement:
** C 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 555 ASN
C 695 GLN
A  52 GLN
A  92 GLN
B 320 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.118029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.096080 restraints weight = 18025.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.099290 restraints weight = 10187.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.101448 restraints weight = 7094.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7685
moved from start:          0.2994

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9225  Z= 0.128
  Angle     :  0.633   8.899  12510  Z= 0.326
  Chirality :  0.043   0.161   1366
  Planarity :  0.005   0.084   1602
  Dihedral  :  4.635  24.038   1221
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 10.00 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.24), residues: 1126
  helix:  1.56 (0.27), residues: 362
  sheet: -0.18 (0.47), residues: 120
  loop : -1.27 (0.22), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 312 
 HIS   0.006   0.001   HIS B 692 
 PHE   0.018   0.001   PHE B 655 
 TYR   0.023   0.001   TYR C 685 
 ARG   0.005   0.001   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03814 (  344)
  hydrogen bonds       : angle       5.16811 (  984)
  metal coordination   : bond        0.02423 (    4)
  metal coordination   : angle       5.35981 (    3)
  SS BOND              : bond        0.00396 (   22)
  SS BOND              : angle       1.86950 (   44)
  covalent geometry    : bond        0.00292 ( 9199)
  covalent geometry    : angle       0.61923 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  412 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.7971 (mmm-85)
REVERT: C  515 THR cc_start: 0.8323 (p) cc_final: 0.7958 (t)
REVERT: C  529 GLU cc_start: 0.7604 (tt0) cc_final: 0.7156 (tt0)
REVERT: C  555 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.7955 (t0)
REVERT: C  618 ASN cc_start: 0.8721 (t0) cc_final: 0.8310 (t0)
REVERT: C  694 SER cc_start: 0.8832 (m) cc_final: 0.8425 (p)
REVERT: C  740 ASP cc_start: 0.6143 (p0) cc_final: 0.5621 (p0)
REVERT: C  816 PHE cc_start: 0.7770 (t80) cc_final: 0.7567 (t80)
REVERT: A   61 GLN cc_start: 0.8322 (tt0) cc_final: 0.7987 (tm-30)
REVERT: B  267 TRP cc_start: 0.7625 (m100) cc_final: 0.7251 (m100)
REVERT: B  345 MET cc_start: 0.7870 (mmp) cc_final: 0.7595 (mmm)
REVERT: B  564 ASP cc_start: 0.6411 (m-30) cc_final: 0.5389 (t0)
REVERT: B  693 CYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7743 (t)
  outliers start: 19
  outliers final: 8
  residues processed: 143
  average time/residue: 0.2226
  time to fit residues: 43.7723
Evaluate side-chains
  100 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  463 ASP
Chi-restraints excluded: chain C residue  555 ASN
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   87 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  693 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 107 optimal weight:    0.7980
   chunk 86 optimal weight:    0.0170
   chunk 10 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.7620

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

Flipped N/Q/H residues before XYZ refinement:
C 403 GLN
C 425 GLN
** C 474 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 556 HIS
C 800 ASN
A  92 GLN
** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.115006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.092550 restraints weight = 18728.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.095660 restraints weight = 10667.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.097764 restraints weight = 7466.024|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9225  Z= 0.146
  Angle     :  0.591  10.173  12510  Z= 0.305
  Chirality :  0.043   0.142   1366
  Planarity :  0.005   0.066   1602
  Dihedral  :  4.480  23.909   1221
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 13.03 %
    Favored  : 85.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.24), residues: 1126
  helix:  1.86 (0.27), residues: 356
  sheet: -0.06 (0.48), residues: 120
  loop : -1.26 (0.22), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 153 
 HIS   0.006   0.001   HIS C 556 
 PHE   0.012   0.001   PHE B 652 
 TYR   0.015   0.001   TYR C 685 
 ARG   0.006   0.001   ARG B 610 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03633 (  344)
  hydrogen bonds       : angle       4.83091 (  984)
  metal coordination   : bond        0.02596 (    4)
  metal coordination   : angle       3.94253 (    3)
  SS BOND              : bond        0.00439 (   22)
  SS BOND              : angle       1.57733 (   44)
  covalent geometry    : bond        0.00333 ( 9199)
  covalent geometry    : angle       0.58110 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.114 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.7965 (t0) cc_final: 0.6865 (p0)
REVERT: C  515 THR cc_start: 0.8245 (p) cc_final: 0.7907 (t)
REVERT: C  618 ASN cc_start: 0.8640 (t0) cc_final: 0.8357 (t0)
REVERT: C  694 SER cc_start: 0.8927 (m) cc_final: 0.8510 (p)
REVERT: B  435 MET cc_start: 0.8986 (mmm) cc_final: 0.8210 (mmm)
REVERT: B  693 CYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7797 (t)
  outliers start: 18
  outliers final: 9
  residues processed: 117
  average time/residue: 0.2018
  time to fit residues: 33.7033
Evaluate side-chains
  92 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  762 ILE
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  693 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 4 optimal weight:    0.5980
   chunk 27 optimal weight:    0.0670
   chunk 94 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 53 optimal weight:    0.2980
   chunk 31 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.3316

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

Flipped N/Q/H residues before XYZ refinement:
C 800 ASN
A  92 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.115266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.093398 restraints weight = 18432.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.096521 restraints weight = 10301.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.098615 restraints weight = 7114.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.4151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9225  Z= 0.104
  Angle     :  0.538   8.671  12510  Z= 0.277
  Chirality :  0.041   0.156   1366
  Planarity :  0.004   0.062   1602
  Dihedral  :  4.287  23.413   1221
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 14.14 %
    Favored  : 84.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.01 (0.24), residues: 1126
  helix:  1.94 (0.27), residues: 365
  sheet: -0.01 (0.48), residues: 118
  loop : -1.23 (0.22), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 738 
 HIS   0.004   0.001   HIS C 556 
 PHE   0.024   0.001   PHE B 655 
 TYR   0.010   0.001   TYR C 685 
 ARG   0.006   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  344)
  hydrogen bonds       : angle       4.57898 (  984)
  metal coordination   : bond        0.01244 (    4)
  metal coordination   : angle       2.09273 (    3)
  SS BOND              : bond        0.00326 (   22)
  SS BOND              : angle       1.36902 (   44)
  covalent geometry    : bond        0.00236 ( 9199)
  covalent geometry    : angle       0.53227 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.7858 (t0) cc_final: 0.7147 (p0)
REVERT: C  515 THR cc_start: 0.8047 (p) cc_final: 0.7697 (t)
REVERT: C  618 ASN cc_start: 0.8581 (t0) cc_final: 0.8280 (t0)
REVERT: A   61 GLN cc_start: 0.8296 (tt0) cc_final: 0.7872 (tm-30)
REVERT: A   64 THR cc_start: 0.7483 (OUTLIER) cc_final: 0.7192 (m)
REVERT: A   67 GLU cc_start: 0.7705 (tt0) cc_final: 0.7503 (tt0)
REVERT: B  528 GLU cc_start: 0.7539 (tp30) cc_final: 0.7240 (tm-30)
  outliers start: 18
  outliers final: 8
  residues processed: 110
  average time/residue: 0.2215
  time to fit residues: 36.0424
Evaluate side-chains
  95 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  463 ASP
Chi-restraints excluded: chain C residue  566 ILE
Chi-restraints excluded: chain C residue  762 ILE
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   78 HIS
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  602 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0470
   chunk 3 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 89 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 104 optimal weight:    0.0770
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.4836

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
C 635 HIS
C 800 ASN
A  92 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.114762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.092463 restraints weight = 18425.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.095480 restraints weight = 10569.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.097463 restraints weight = 7437.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.4481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9225  Z= 0.115
  Angle     :  0.566  13.802  12510  Z= 0.282
  Chirality :  0.042   0.223   1366
  Planarity :  0.004   0.057   1602
  Dihedral  :  4.205  23.247   1221
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.97 %
    Favored  : 95.03 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 14.44 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.24), residues: 1126
  helix:  2.06 (0.28), residues: 359
  sheet:  0.04 (0.48), residues: 116
  loop : -1.18 (0.22), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 267 
 HIS   0.004   0.001   HIS C 556 
 PHE   0.020   0.001   PHE B 652 
 TYR   0.009   0.001   TYR C 685 
 ARG   0.006   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03204 (  344)
  hydrogen bonds       : angle       4.53635 (  984)
  metal coordination   : bond        0.01548 (    4)
  metal coordination   : angle       1.97826 (    3)
  SS BOND              : bond        0.00203 (   22)
  SS BOND              : angle       1.28046 (   44)
  covalent geometry    : bond        0.00266 ( 9199)
  covalent geometry    : angle       0.56160 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.7943 (t0) cc_final: 0.7373 (p0)
REVERT: C  515 THR cc_start: 0.8107 (p) cc_final: 0.7758 (t)
REVERT: C  618 ASN cc_start: 0.8540 (t0) cc_final: 0.8243 (t0)
REVERT: A   64 THR cc_start: 0.7584 (OUTLIER) cc_final: 0.7315 (m)
REVERT: B  435 MET cc_start: 0.8762 (mmm) cc_final: 0.8095 (mmm)
REVERT: B  693 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7697 (p)
  outliers start: 27
  outliers final: 13
  residues processed: 109
  average time/residue: 0.2675
  time to fit residues: 43.3756
Evaluate side-chains
  102 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.998 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  646 VAL
Chi-restraints excluded: chain C residue  717 TRP
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain A residue   64 THR
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  693 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0270
   chunk 31 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   overall best weight:    1.0040

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 800 ASN
A  65 HIS
A  92 GLN
B 497 ASN
B 535 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.110532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.088214 restraints weight = 18504.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.091101 restraints weight = 10627.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.093102 restraints weight = 7568.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.4808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9225  Z= 0.159
  Angle     :  0.593  10.429  12510  Z= 0.298
  Chirality :  0.043   0.182   1366
  Planarity :  0.004   0.052   1602
  Dihedral  :  4.248  23.369   1221
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 15.35 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1126
  helix:  1.88 (0.28), residues: 363
  sheet: -0.10 (0.47), residues: 118
  loop : -1.20 (0.22), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 267 
 HIS   0.004   0.001   HIS C 635 
 PHE   0.017   0.001   PHE C 812 
 TYR   0.010   0.001   TYR B 298 
 ARG   0.005   0.000   ARG A  31 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03477 (  344)
  hydrogen bonds       : angle       4.60461 (  984)
  metal coordination   : bond        0.02321 (    4)
  metal coordination   : angle       2.35236 (    3)
  SS BOND              : bond        0.00252 (   22)
  SS BOND              : angle       1.44692 (   44)
  covalent geometry    : bond        0.00377 ( 9199)
  covalent geometry    : angle       0.58696 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 99
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.8142 (t0) cc_final: 0.7517 (p0)
REVERT: C  515 THR cc_start: 0.8161 (p) cc_final: 0.7839 (t)
REVERT: C  529 GLU cc_start: 0.8076 (tt0) cc_final: 0.7736 (tt0)
REVERT: C  694 SER cc_start: 0.8966 (m) cc_final: 0.8526 (p)
REVERT: B  435 MET cc_start: 0.8867 (mmm) cc_final: 0.8188 (mmm)
REVERT: B  693 CYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7688 (t)
  outliers start: 28
  outliers final: 18
  residues processed: 118
  average time/residue: 0.2072
  time to fit residues: 35.1906
Evaluate side-chains
  107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  463 ASP
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain C residue  664 ILE
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  762 ILE
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain C residue  790 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain B residue  265 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  400 ASP
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Chi-restraints excluded: chain B residue  693 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    0.0270
   chunk 80 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 4 optimal weight:    0.8980
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 104 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 8 optimal weight:    0.0670
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.4776

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 800 ASN
A  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.113034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.090155 restraints weight = 18799.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.093123 restraints weight = 10977.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.095117 restraints weight = 7842.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.4939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9225  Z= 0.110
  Angle     :  0.559  11.334  12510  Z= 0.281
  Chirality :  0.042   0.165   1366
  Planarity :  0.004   0.051   1602
  Dihedral  :  4.193  23.548   1221
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.36 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1126
  helix:  1.99 (0.28), residues: 363
  sheet:  0.18 (0.49), residues: 108
  loop : -1.19 (0.22), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 267 
 HIS   0.009   0.001   HIS C 556 
 PHE   0.022   0.001   PHE B 652 
 TYR   0.007   0.001   TYR C 626 
 ARG   0.007   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03156 (  344)
  hydrogen bonds       : angle       4.52544 (  984)
  metal coordination   : bond        0.01328 (    4)
  metal coordination   : angle       1.77004 (    3)
  SS BOND              : bond        0.00180 (   22)
  SS BOND              : angle       1.22353 (   44)
  covalent geometry    : bond        0.00257 ( 9199)
  covalent geometry    : angle       0.55431 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.8062 (t0) cc_final: 0.7554 (p0)
REVERT: C  515 THR cc_start: 0.8138 (p) cc_final: 0.7821 (t)
REVERT: C  618 ASN cc_start: 0.8481 (t0) cc_final: 0.8084 (t0)
REVERT: C  650 THR cc_start: 0.8728 (m) cc_final: 0.8506 (m)
REVERT: C  694 SER cc_start: 0.8883 (m) cc_final: 0.8437 (p)
REVERT: B  435 MET cc_start: 0.8816 (mmm) cc_final: 0.8139 (mmm)
  outliers start: 26
  outliers final: 16
  residues processed: 118
  average time/residue: 0.2060
  time to fit residues: 34.0400
Evaluate side-chains
  110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain C residue  646 VAL
Chi-restraints excluded: chain C residue  664 ILE
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  762 ILE
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain C residue  800 ASN
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 108 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 69 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0370
   chunk 100 optimal weight:    6.9990
   overall best weight:    0.6458

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 800 ASN
A  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.112439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.089650 restraints weight = 18907.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.092595 restraints weight = 11003.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.094569 restraints weight = 7877.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.5098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9225  Z= 0.124
  Angle     :  0.572  11.715  12510  Z= 0.287
  Chirality :  0.042   0.258   1366
  Planarity :  0.004   0.050   1602
  Dihedral  :  4.165  23.374   1221
  Min Nonbonded Distance : 2.273

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.77 %
    Favored  : 80.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.10 (0.25), residues: 1126
  helix:  1.98 (0.28), residues: 366
  sheet:  0.20 (0.49), residues: 108
  loop : -1.15 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP B 267 
 HIS   0.013   0.001   HIS C 556 
 PHE   0.011   0.001   PHE C 668 
 TYR   0.007   0.001   TYR B 298 
 ARG   0.007   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03164 (  344)
  hydrogen bonds       : angle       4.54242 (  984)
  metal coordination   : bond        0.01589 (    4)
  metal coordination   : angle       1.74202 (    3)
  SS BOND              : bond        0.00199 (   22)
  SS BOND              : angle       1.13086 (   44)
  covalent geometry    : bond        0.00293 ( 9199)
  covalent geometry    : angle       0.56815 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.8121 (t0) cc_final: 0.7657 (p0)
REVERT: C  515 THR cc_start: 0.8123 (p) cc_final: 0.7805 (t)
REVERT: C  618 ASN cc_start: 0.8518 (t0) cc_final: 0.8109 (t0)
REVERT: C  650 THR cc_start: 0.8726 (m) cc_final: 0.8497 (m)
REVERT: C  694 SER cc_start: 0.8902 (m) cc_final: 0.8444 (p)
REVERT: A   61 GLN cc_start: 0.8143 (tt0) cc_final: 0.7833 (tm-30)
REVERT: A  153 TRP cc_start: 0.8555 (p-90) cc_final: 0.7679 (p-90)
REVERT: B  435 MET cc_start: 0.8827 (mmm) cc_final: 0.8134 (mmm)
  outliers start: 25
  outliers final: 18
  residues processed: 114
  average time/residue: 0.2717
  time to fit residues: 44.7672
Evaluate side-chains
  112 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 3.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain C residue  646 VAL
Chi-restraints excluded: chain C residue  664 ILE
Chi-restraints excluded: chain C residue  709 SER
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain C residue  790 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0270
   chunk 105 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.6638

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
** C 595 HIS ** 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 = 0.3584 r_free = 0.3584 target = 0.112283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.089504 restraints weight = 18738.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.092449 restraints weight = 10998.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.094400 restraints weight = 7867.182|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.5203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9225  Z= 0.125
  Angle     :  0.574  11.675  12510  Z= 0.287
  Chirality :  0.042   0.241   1366
  Planarity :  0.004   0.050   1602
  Dihedral  :  4.154  23.362   1221
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.17 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.25), residues: 1126
  helix:  1.99 (0.28), residues: 366
  sheet:  0.26 (0.50), residues: 106
  loop : -1.11 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 267 
 HIS   0.008   0.001   HIS C 556 
 PHE   0.025   0.001   PHE B 652 
 TYR   0.028   0.001   TYR B 340 
 ARG   0.007   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03177 (  344)
  hydrogen bonds       : angle       4.55591 (  984)
  metal coordination   : bond        0.01617 (    4)
  metal coordination   : angle       1.77887 (    3)
  SS BOND              : bond        0.00215 (   22)
  SS BOND              : angle       1.03644 (   44)
  covalent geometry    : bond        0.00294 ( 9199)
  covalent geometry    : angle       0.57071 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 96
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.8132 (t0) cc_final: 0.7717 (p0)
REVERT: C  515 THR cc_start: 0.8094 (p) cc_final: 0.7782 (t)
REVERT: C  618 ASN cc_start: 0.8497 (t0) cc_final: 0.8082 (t0)
REVERT: C  650 THR cc_start: 0.8470 (m) cc_final: 0.8259 (m)
REVERT: C  694 SER cc_start: 0.8900 (m) cc_final: 0.8441 (p)
REVERT: B  435 MET cc_start: 0.8811 (mmm) cc_final: 0.8084 (mmm)
  outliers start: 20
  outliers final: 17
  residues processed: 109
  average time/residue: 0.2228
  time to fit residues: 34.3801
Evaluate side-chains
  110 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  556 HIS
Chi-restraints excluded: chain C residue  646 VAL
Chi-restraints excluded: chain C residue  664 ILE
Chi-restraints excluded: chain C residue  709 SER
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  736 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 100 optimal weight:    8.9990
   chunk 59 optimal weight:    0.4980
   chunk 111 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 103 optimal weight:    0.8980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 556 HIS
** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  61 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 = 0.3575 r_free = 0.3575 target = 0.111620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.088982 restraints weight = 18860.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.091824 restraints weight = 11055.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.093734 restraints weight = 7943.147|
|-----------------------------------------------------------------------------|
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7923
moved from start:          0.5306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9225  Z= 0.133
  Angle     :  0.581  11.878  12510  Z= 0.291
  Chirality :  0.042   0.240   1366
  Planarity :  0.004   0.049   1602
  Dihedral  :  4.151  23.402   1221
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 17.37 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.25), residues: 1126
  helix:  2.01 (0.28), residues: 366
  sheet:  0.23 (0.50), residues: 108
  loop : -1.13 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 267 
 HIS   0.009   0.001   HIS C 556 
 PHE   0.012   0.001   PHE C 668 
 TYR   0.024   0.001   TYR B 340 
 ARG   0.008   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  344)
  hydrogen bonds       : angle       4.55624 (  984)
  metal coordination   : bond        0.01793 (    4)
  metal coordination   : angle       1.86267 (    3)
  SS BOND              : bond        0.00222 (   22)
  SS BOND              : angle       1.02324 (   44)
  covalent geometry    : bond        0.00313 ( 9199)
  covalent geometry    : angle       0.57843 (12463)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 1.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  427 ASN cc_start: 0.8168 (t0) cc_final: 0.7768 (p0)
REVERT: C  515 THR cc_start: 0.8093 (p) cc_final: 0.7785 (t)
REVERT: C  650 THR cc_start: 0.8300 (m) cc_final: 0.8028 (m)
REVERT: C  694 SER cc_start: 0.8912 (m) cc_final: 0.8452 (p)
REVERT: A  153 TRP cc_start: 0.8586 (p-90) cc_final: 0.7709 (p-90)
REVERT: B  435 MET cc_start: 0.8822 (mmm) cc_final: 0.8060 (mmm)
  outliers start: 21
  outliers final: 17
  residues processed: 106
  average time/residue: 0.2219
  time to fit residues: 33.1230
Evaluate side-chains
  107 residues out of total 1010 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  646 VAL
Chi-restraints excluded: chain C residue  664 ILE
Chi-restraints excluded: chain C residue  709 SER
Chi-restraints excluded: chain C residue  721 LEU
Chi-restraints excluded: chain C residue  728 LEU
Chi-restraints excluded: chain C residue  749 LEU
Chi-restraints excluded: chain C residue  781 LEU
Chi-restraints excluded: chain A residue   69 LEU
Chi-restraints excluded: chain A residue   81 LEU
Chi-restraints excluded: chain A residue   88 GLU
Chi-restraints excluded: chain A residue  166 VAL
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  365 CYS
Chi-restraints excluded: chain B residue  382 SER
Chi-restraints excluded: chain B residue  570 LEU
Chi-restraints excluded: chain B residue  602 VAL
Chi-restraints excluded: chain B residue  668 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   chunk 49 optimal weight:    0.0980
   chunk 66 optimal weight:    0.9980
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 111 optimal weight:    0.7980
   chunk 106 optimal weight:    3.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** C 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  61 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.112008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.089244 restraints weight = 18822.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.092059 restraints weight = 11050.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.094051 restraints weight = 7994.456|
|-----------------------------------------------------------------------------|
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9225  Z= 0.123
  Angle     :  0.580  11.669  12510  Z= 0.289
  Chirality :  0.042   0.229   1366
  Planarity :  0.004   0.049   1602
  Dihedral  :  4.133  23.530   1221
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 17.68 %
    Favored  : 80.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.27 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.25), residues: 1126
  helix:  1.98 (0.28), residues: 366
  sheet:  0.24 (0.50), residues: 108
  loop : -1.12 (0.23), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP B 267 
 HIS   0.004   0.001   HIS C 635 
 PHE   0.032   0.001   PHE C 812 
 TYR   0.030   0.001   TYR B 340 
 ARG   0.007   0.000   ARG C 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03195 (  344)
  hydrogen bonds       : angle       4.55555 (  984)
  metal coordination   : bond        0.01573 (    4)
  metal coordination   : angle       1.79190 (    3)
  SS BOND              : bond        0.00158 (   22)
  SS BOND              : angle       0.92880 (   44)
  covalent geometry    : bond        0.00290 ( 9199)
  covalent geometry    : angle       0.57813 (12463)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3067.40 seconds
wall clock time: 55 minutes 17.54 seconds (3317.54 seconds total)