Starting phenix.real_space_refine
on Fri Jun  6 18:57:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.57
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fz5_50893/06_2025/9fz5_50893.cif"
  }
  resolution = 3.57
  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=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    5074      2.51       5
     N    1397      2.21       5
     O    1579      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8082
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6002
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 740, 6002
          Classifications: {'peptide': 740}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 710}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 1169
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1169
          Classifications: {'peptide': 149}
          Link IDs: {'PTRANS': 8, 'TRANS': 140}
    Chain: "C"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 911
          Classifications: {'peptide': 117}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 10, 'TRANS': 106}
  Time building chain proxies: 5.80, per 1000 atoms: 0.72
  Number of scatterers: 8082
  At special positions: 0
  Unit cell: (95.76, 85.12, 117.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1579      8.00
     N    1397      7.00
     C    5074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  31 " - pdb=" SG  CYS A 724 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 173 " - pdb=" SG  CYS A 725 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  67 " - pdb=" SG  CYS C 123 " 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: 2.01
  Conformation dependent library (CDL) restraints added in 923.5 milliseconds
  

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1882

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 13 sheets defined
      9.8% alpha, 27.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 26 through 33
      removed outlier: 3.969A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 302
    Processing helix  chain 'A' and resid 464 through 470
    Processing helix  chain 'A' and resid 537 through 541
      removed outlier: 3.855A  pdb=" N   PHE A 541 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.534A  pdb=" N   ILE A 664 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 673
      removed outlier: 3.547A  pdb=" N   SER A 673 " --> pdb=" O   LYS A 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 46 through 59
      removed outlier: 3.812A  pdb=" N   ARG B  52 " --> pdb=" O   SER B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 137 through 147
      removed outlier: 3.928A  pdb=" N   ASP B 141 " --> pdb=" O   ASP B 137 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   MET B 142 " --> pdb=" O   ASN B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 158
      removed outlier: 3.893A  pdb=" N   GLU B 153 " --> pdb=" O   ASP B 149 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   LEU B 155 " --> pdb=" O   ALA B 151 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ILE B 156 " --> pdb=" O   ALA B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 168
      removed outlier: 3.916A  pdb=" N   ILE B 162 " --> pdb=" O   LYS B 158 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ARG B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA B 168 " --> pdb=" O   ALA B 164 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 120 through 130
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55
      removed outlier: 6.567A  pdb=" N   ASP A  85 " --> pdb=" O   GLY A  71 " (cutoff:3.500A)
      removed outlier: 6.707A  pdb=" N   VAL A  73 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   GLN A  83 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ILE A  75 " --> pdb=" O   ARG A  81 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   ARG A  81 " --> pdb=" O   ILE A  75 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A  80 " --> pdb=" O   ASP A 113 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ASP A 113 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   LEU A  82 " --> pdb=" O   HIS A 111 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   HIS A 111 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
      removed outlier: 4.982A  pdb=" N   ALA A  84 " --> pdb=" O   ASN A 109 " (cutoff:3.500A)
      removed outlier: 7.537A  pdb=" N   ASN A 109 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ALA A 106 " --> pdb=" O   GLY A 124 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   VAL A 110 " --> pdb=" O   LYS A 120 " (cutoff:3.500A)
      removed outlier: 4.541A  pdb=" N   LYS A 120 " --> pdb=" O   VAL A 110 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   TYR A 112 " --> pdb=" O   ILE A 118 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   ILE A 118 " --> pdb=" O   TYR A 112 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 139 through 141
      removed outlier: 3.593A  pdb=" N   ARG A 148 " --> pdb=" O   THR A 171 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LYS A 150 " --> pdb=" O   SER A 169 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL A 183 " --> pdb=" O   ARG A 202 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 190
      removed outlier: 3.836A  pdb=" N   VAL A 195 " --> pdb=" O   ASP A 190 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 233 through 234
    current: chain 'A' and resid 412 through 419
      removed outlier: 3.682A  pdb=" N   GLN A 413 " --> pdb=" O   HIS A 431 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   ALA A 427 " --> pdb=" O   PHE A 417 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 427 through 432
    current: chain 'A' and resid 445 through 457
      removed outlier: 3.921A  pdb=" N   LYS A 486 " --> pdb=" O   GLU A 450 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   LYS A 452 " --> pdb=" O   GLN A 484 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN A 484 " --> pdb=" O   LYS A 452 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 482 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 479 through 486
    current: chain 'A' and resid 505 through 512
      removed outlier: 3.689A  pdb=" N   THR A 505 " --> pdb=" O   TYR A 567 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY A 561 " --> pdb=" O   ARG A 511 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 558 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 5.070A  pdb=" N   ILE A 582 " --> pdb=" O   VAL A 558 " (cutoff:3.500A)
      removed outlier: 6.819A  pdb=" N   THR A 560 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   GLY A 580 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   VAL A 562 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   SER A 578 " --> pdb=" O   VAL A 562 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   SER A 564 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   ASN A 576 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   ILE A 566 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ARG A 574 " --> pdb=" O   TRP A 614 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   TRP A 614 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ASN A 576 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   THR A 612 " --> pdb=" O   ASN A 576 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   SER A 578 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.340A  pdb=" N   GLY A 610 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   GLY A 580 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   TRP A 608 " --> pdb=" O   GLY A 580 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   ILE A 582 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   TYR A 584 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TRP A 608 " --> pdb=" O   TYR A 628 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   TYR A 628 " --> pdb=" O   TRP A 608 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   ILE A 626 " --> pdb=" O   GLY A 610 " (cutoff:3.500A)
      removed outlier: 4.474A  pdb=" N   THR A 612 " --> pdb=" O   GLY A 624 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLY A 624 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ARG A 623 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   SER A 641 " --> pdb=" O   ARG A 623 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   GLY A 625 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   THR A 637 " --> pdb=" O   GLN A 627 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER A 638 " --> pdb=" O   TYR A 658 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 640 " --> pdb=" O   TYR A 656 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   TYR A 656 " --> pdb=" O   SER A 640 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ASN A 655 " --> pdb=" O   GLY A 686 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLN A 684 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   ALA A 689 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ILE A 699 " --> pdb=" O   TRP A 691 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASP A 706 " --> pdb=" O   LYS A 711 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LYS A 711 " --> pdb=" O   ASP A 706 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 711 through 712
    current: chain 'A' and resid 726 through 730
      removed outlier: 3.624A  pdb=" N   ALA A 727 " --> pdb=" O   GLU A 757 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   GLU A 757 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ARG A 729 " --> pdb=" O   ASN A 755 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 243 through 244
      removed outlier: 3.782A  pdb=" N   PHE A 243 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 255 through 256
      removed outlier: 3.540A  pdb=" N   ASP A 256 " --> pdb=" O   ARG A 277 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ARG A 277 " --> pdb=" O   ASP A 256 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 273 through 275
      removed outlier: 4.122A  pdb=" N   LEU A 289 " --> pdb=" O   ASN A 274 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 312 through 319
      removed outlier: 3.700A  pdb=" N   GLY A 319 " --> pdb=" O   PHE A 327 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   TYR A 363 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 359
      removed outlier: 4.152A  pdb=" N   THR A 374 " --> pdb=" O   PHE A 359 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 736 through 739
      removed outlier: 3.695A  pdb=" N   VAL A 747 " --> pdb=" O   ASN A 737 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 35 through 39
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 61 through 62
    current: chain 'B' and resid 97 through 108
      removed outlier: 3.512A  pdb=" N   MET B 102 " --> pdb=" O   VAL B 122 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   VAL B 122 " --> pdb=" O   MET B 102 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 96 through 98
      removed outlier: 3.768A  pdb=" N   ILE C  74 " --> pdb=" O   ARG C  68 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ARG C  68 " --> pdb=" O   ILE C  74 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL C  76 " --> pdb=" O   ASP C  66 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ILE C  53 " --> pdb=" O   GLN C  69 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   VAL C  58 " --> pdb=" O   GLY C  36 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLY C  36 " --> pdb=" O   VAL C  58 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLN C  39 " --> pdb=" O   GLU C 114 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLU C 114 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 100 through 101
      removed outlier: 3.804A  pdb=" N   TYR C 108 " --> pdb=" O   MET C 111 " (cutoff:3.500A)

    163 hydrogen bonds defined for protein.
    438 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: 2.69

  Time building geometry restraints manager: 2.39 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1385
        1.30 -     1.43: 2242
        1.43 -     1.56: 4586
        1.56 -     1.69: 0
        1.69 -     1.82: 58
  Bond restraints: 8271
  Sorted by residual:
  bond pdb=" C   ASP A 422 "
       pdb=" N   ASP A 423 "
    ideal  model  delta    sigma   weight residual
    1.334  1.420 -0.087 1.30e-02 5.92e+03 4.45e+01
  bond pdb=" C   ARG A 421 "
       pdb=" N   ASP A 422 "
    ideal  model  delta    sigma   weight residual
    1.335  1.250  0.085 1.35e-02 5.49e+03 3.99e+01
  bond pdb=" C   THR A 420 "
       pdb=" N   ARG A 421 "
    ideal  model  delta    sigma   weight residual
    1.331  1.243  0.088 1.43e-02 4.89e+03 3.78e+01
  bond pdb=" C   LYS A 346 "
       pdb=" N   TYR A 347 "
    ideal  model  delta    sigma   weight residual
    1.333  1.399 -0.065 1.34e-02 5.57e+03 2.37e+01
  bond pdb=" CA  ARG A 421 "
       pdb=" C   ARG A 421 "
    ideal  model  delta    sigma   weight residual
    1.520  1.464  0.057 1.22e-02 6.72e+03 2.16e+01
  ... (remaining 8266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.43: 11087
        2.43 -     4.86: 128
        4.86 -     7.29: 20
        7.29 -     9.72: 11
        9.72 -    12.15: 4
  Bond angle restraints: 11250
  Sorted by residual:
  angle pdb=" CA  ASP A 422 "
        pdb=" C   ASP A 422 "
        pdb=" N   ASP A 423 "
      ideal   model   delta    sigma   weight residual
     118.08  130.23  -12.15 1.30e+00 5.92e-01 8.74e+01
  angle pdb=" N   THR A 420 "
        pdb=" CA  THR A 420 "
        pdb=" C   THR A 420 "
      ideal   model   delta    sigma   weight residual
     112.93  122.71   -9.78 1.12e+00 7.97e-01 7.63e+01
  angle pdb=" CA  ASP A 422 "
        pdb=" CB  ASP A 422 "
        pdb=" CG  ASP A 422 "
      ideal   model   delta    sigma   weight residual
     112.60  120.51   -7.91 1.00e+00 1.00e+00 6.25e+01
  angle pdb=" CA  ASP A 423 "
        pdb=" C   ASP A 423 "
        pdb=" O   ASP A 423 "
      ideal   model   delta    sigma   weight residual
     119.95  111.02    8.93 1.18e+00 7.18e-01 5.73e+01
  angle pdb=" CA  ASP A 423 "
        pdb=" CB  ASP A 423 "
        pdb=" CG  ASP A 423 "
      ideal   model   delta    sigma   weight residual
     112.60  119.82   -7.22 1.00e+00 1.00e+00 5.22e+01
  ... (remaining 11245 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4115
       17.84 -    35.69: 593
       35.69 -    53.53: 179
       53.53 -    71.37: 35
       71.37 -    89.22: 13
  Dihedral angle restraints: 4935
    sinusoidal: 1989
      harmonic: 2946
  Sorted by residual:
  dihedral pdb=" CB  CYS A  31 "
           pdb=" SG  CYS A  31 "
           pdb=" SG  CYS A 724 "
           pdb=" CB  CYS A 724 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.10  -88.90     1      1.00e+01 1.00e-02 9.42e+01
  dihedral pdb=" CB  CYS A 173 "
           pdb=" SG  CYS A 173 "
           pdb=" SG  CYS A 725 "
           pdb=" CB  CYS A 725 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  171.03  -78.03     1      1.00e+01 1.00e-02 7.61e+01
  dihedral pdb=" C   ARG A 421 "
           pdb=" N   ARG A 421 "
           pdb=" CA  ARG A 421 "
           pdb=" CB  ARG A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -104.17  -18.43     0      2.50e+00 1.60e-01 5.43e+01
  ... (remaining 4932 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.089: 1100
       0.089 -    0.179: 92
       0.179 -    0.268: 4
       0.268 -    0.358: 0
       0.358 -    0.447: 3
  Chirality restraints: 1199
  Sorted by residual:
  chirality pdb=" CA  ASP A 422 "
            pdb=" N   ASP A 422 "
            pdb=" C   ASP A 422 "
            pdb=" CB  ASP A 422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.06    0.45 2.00e-01 2.50e+01 5.00e+00
  chirality pdb=" CA  THR A 420 "
            pdb=" N   THR A 420 "
            pdb=" C   THR A 420 "
            pdb=" CB  THR A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.13    0.40 2.00e-01 2.50e+01 3.92e+00
  chirality pdb=" CB  THR A 420 "
            pdb=" CA  THR A 420 "
            pdb=" OG1 THR A 420 "
            pdb=" CG2 THR A 420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.18    0.37 2.00e-01 2.50e+01 3.37e+00
  ... (remaining 1196 not shown)

  Planarity restraints: 1484
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 423 "   -0.012 2.00e-02 2.50e+03   2.40e-02 5.74e+00
        pdb=" C   ASP A 423 "    0.041 2.00e-02 2.50e+03
        pdb=" O   ASP A 423 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   MET A 424 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 341 "   -0.011 2.00e-02 2.50e+03   2.13e-02 4.52e+00
        pdb=" C   ASN A 341 "    0.037 2.00e-02 2.50e+03
        pdb=" O   ASN A 341 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP A 342 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 419 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.46e+00
        pdb=" C   ASN A 419 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 419 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   THR A 420 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1481 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.62: 104
        2.62 -     3.19: 6518
        3.19 -     3.76: 10777
        3.76 -     4.33: 14445
        4.33 -     4.90: 25264
  Nonbonded interactions: 57108
  Sorted by model distance:
  nonbonded pdb=" O   LYS B  70 "
            pdb=" OD1 ASP B  71 "
     model   vdw
     2.055 3.040
  nonbonded pdb=" O   HIS A  90 "
            pdb=" OG1 THR A 103 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ASN A 401 "
            pdb=" OD1 ASP A 402 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" N   GLU B  66 "
            pdb=" OE1 GLU B  66 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" OG  SER A  80 "
            pdb=" OD1 ASP A 114 "
     model   vdw
     2.279 3.040
  ... (remaining 57103 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:             51.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.440
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.040
  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:2.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   78.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
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   0.088   8274  Z= 0.261
  Angle     :  0.737  12.154  11256  Z= 0.438
  Chirality :  0.051   0.447   1199
  Planarity :  0.005   0.045   1484
  Dihedral  : 18.546  89.217   3044
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.50 %
    Allowed  :  9.84 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 30.94 %
    Favored  : 62.90 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.53 (0.24), residues: 996
  helix: -1.44 (0.50), residues: 101
  sheet: -3.26 (0.23), residues: 407
  loop : -3.04 (0.24), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  33 
 HIS   0.002   0.001   HIS A 416 
 PHE   0.006   0.001   PHE B 126 
 TYR   0.016   0.001   TYR C 108 
 ARG   0.002   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30522 (  163)
  hydrogen bonds       : angle      10.70075 (  438)
  SS BOND              : bond        0.00256 (    3)
  SS BOND              : angle       0.70146 (    6)
  covalent geometry    : bond        0.00437 ( 8271)
  covalent geometry    : angle       0.73665 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 107
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6787 (t60) cc_final: 0.6266 (t60)
REVERT: A  343 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.7986 (p90)
REVERT: A  421 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8671 (mtp180)
REVERT: A  448 ASN cc_start: 0.7672 (t0) cc_final: 0.7386 (t0)
REVERT: A  499 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6693 (tmm)
REVERT: A  581 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7948 (pp30)
REVERT: A  595 ILE cc_start: 0.8558 (mm) cc_final: 0.8237 (mt)
REVERT: A  754 PHE cc_start: 0.6620 (OUTLIER) cc_final: 0.6248 (t80)
REVERT: C   27 LYS cc_start: 0.7480 (OUTLIER) cc_final: 0.7148 (ttmm)
REVERT: C   96 LEU cc_start: 0.8196 (mp) cc_final: 0.7958 (mm)
  outliers start: 54
  outliers final: 42
  residues processed: 153
  average time/residue: 0.1939
  time to fit residues: 40.6481
Evaluate side-chains
  150 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 102
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  236 THR
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  251 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  395 ASP
Chi-restraints excluded: chain A residue  421 ARG
Chi-restraints excluded: chain A residue  423 ASP
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  581 GLN
Chi-restraints excluded: chain A residue  590 THR
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  710 ASN
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  783 THR
Chi-restraints excluded: chain B residue   26 THR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue   68 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain C residue   27 LYS
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   74 ILE
Chi-restraints excluded: chain C residue  106 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 89 optimal weight:    8.9990
   overall best weight:    1.3786

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

Flipped N/Q/H residues before XYZ refinement:
A 111 HIS
A 160 ASN
A 634 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.152105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.109852 restraints weight = 10697.034|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112927 restraints weight = 5647.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.114838 restraints weight = 3853.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8274  Z= 0.152
  Angle     :  0.614   9.423  11256  Z= 0.324
  Chirality :  0.046   0.174   1199
  Planarity :  0.005   0.045   1484
  Dihedral  :  9.192  58.444   1220
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.94 %
    Favored  : 88.86 %
  Rotamer:
    Outliers :  6.16 %
    Allowed  : 29.68 %
    Favored  : 64.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.36 (0.24), residues: 996
  helix: -1.31 (0.49), residues: 102
  sheet: -3.12 (0.23), residues: 410
  loop : -2.95 (0.24), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 317 
 PHE   0.008   0.001   PHE A 170 
 TYR   0.014   0.001   TYR C 108 
 ARG   0.003   0.000   ARG A 421 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  163)
  hydrogen bonds       : angle       6.60531 (  438)
  SS BOND              : bond        0.00307 (    3)
  SS BOND              : angle       0.63941 (    6)
  covalent geometry    : bond        0.00356 ( 8271)
  covalent geometry    : angle       0.61387 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 102
  time to evaluate  : 1.002 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6866 (t60) cc_final: 0.6015 (t60)
REVERT: A  142 MET cc_start: 0.6485 (OUTLIER) cc_final: 0.5219 (tmt)
REVERT: A  255 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7280 (mpp)
REVERT: A  275 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7278 (tm-30)
REVERT: A  328 ASN cc_start: 0.8584 (OUTLIER) cc_final: 0.8295 (m-40)
REVERT: A  343 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8416 (p90)
REVERT: A  347 TYR cc_start: 0.8561 (m-80) cc_final: 0.8361 (m-80)
REVERT: A  448 ASN cc_start: 0.7972 (t0) cc_final: 0.7484 (t0)
REVERT: A  460 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8472 (mt0)
REVERT: A  499 MET cc_start: 0.7535 (OUTLIER) cc_final: 0.7123 (tmm)
REVERT: A  595 ILE cc_start: 0.8392 (mm) cc_final: 0.8064 (mt)
REVERT: A  729 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7688 (ttp80)
REVERT: A  745 HIS cc_start: 0.6359 (OUTLIER) cc_final: 0.5842 (m90)
REVERT: A  778 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7872 (mt)
REVERT: B   66 GLU cc_start: 0.7180 (mp0) cc_final: 0.6980 (mp0)
  outliers start: 54
  outliers final: 25
  residues processed: 146
  average time/residue: 0.1882
  time to fit residues: 38.6622
Evaluate side-chains
  134 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  302 HIS
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 18 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 5 optimal weight:   20.0000
   chunk 30 optimal weight:    8.9990
   chunk 15 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 744 GLN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.151524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.110405 restraints weight = 10814.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.113917 restraints weight = 5743.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.114663 restraints weight = 3643.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   8274  Z= 0.160
  Angle     :  0.613  13.436  11256  Z= 0.324
  Chirality :  0.045   0.161   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  7.861  58.760   1163
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.04 %
    Favored  : 88.76 %
  Rotamer:
    Outliers :  6.28 %
    Allowed  : 30.14 %
    Favored  : 63.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.25 (0.24), residues: 996
  helix: -1.17 (0.48), residues: 109
  sheet: -2.98 (0.23), residues: 413
  loop : -2.98 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.009   0.001   HIS A 745 
 PHE   0.009   0.001   PHE A 170 
 TYR   0.013   0.001   TYR C 108 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03999 (  163)
  hydrogen bonds       : angle       6.03194 (  438)
  SS BOND              : bond        0.00268 (    3)
  SS BOND              : angle       0.67492 (    6)
  covalent geometry    : bond        0.00376 ( 8271)
  covalent geometry    : angle       0.61329 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 103
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6903 (t60) cc_final: 0.5992 (t60)
REVERT: A  142 MET cc_start: 0.6477 (OUTLIER) cc_final: 0.5197 (tmt)
REVERT: A  255 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7311 (mpp)
REVERT: A  328 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8291 (m-40)
REVERT: A  343 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8588 (p90)
REVERT: A  448 ASN cc_start: 0.8035 (t0) cc_final: 0.7526 (t0)
REVERT: A  460 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8503 (mt0)
REVERT: A  499 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6897 (tmm)
REVERT: A  595 ILE cc_start: 0.8411 (mm) cc_final: 0.8094 (mt)
REVERT: A  729 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7759 (ttp80)
REVERT: A  754 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6563 (t80)
REVERT: A  778 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7867 (mt)
  outliers start: 55
  outliers final: 32
  residues processed: 146
  average time/residue: 0.1990
  time to fit residues: 41.6917
Evaluate side-chains
  143 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 102
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  137 GLU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 77 optimal weight:    2.9990
   chunk 84 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 57 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 13 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 129 ASN
A 217 GLN
B  58 ASN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.153339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.111063 restraints weight = 10683.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.114192 restraints weight = 5541.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.116138 restraints weight = 3752.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8085
moved from start:          0.1400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.124
  Angle     :  0.576  10.551  11256  Z= 0.302
  Chirality :  0.044   0.158   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  7.302  59.742   1159
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  9.34 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  7.42 %
    Allowed  : 27.97 %
    Favored  : 64.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.24), residues: 996
  helix: -0.97 (0.49), residues: 109
  sheet: -2.91 (0.23), residues: 413
  loop : -2.90 (0.24), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.008   0.001   PHE A 276 
 TYR   0.013   0.001   TYR C 108 
 ARG   0.001   0.000   ARG B 150 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03293 (  163)
  hydrogen bonds       : angle       5.55769 (  438)
  SS BOND              : bond        0.00240 (    3)
  SS BOND              : angle       0.58017 (    6)
  covalent geometry    : bond        0.00286 ( 8271)
  covalent geometry    : angle       0.57571 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 108
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6872 (t60) cc_final: 0.5958 (t60)
REVERT: A  142 MET cc_start: 0.6439 (OUTLIER) cc_final: 0.5160 (tmt)
REVERT: A  255 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7319 (mpp)
REVERT: A  328 ASN cc_start: 0.8509 (OUTLIER) cc_final: 0.8263 (m-40)
REVERT: A  343 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8507 (p90)
REVERT: A  448 ASN cc_start: 0.8025 (t0) cc_final: 0.7539 (t0)
REVERT: A  460 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8472 (mt0)
REVERT: A  499 MET cc_start: 0.7419 (OUTLIER) cc_final: 0.6935 (tmm)
REVERT: A  595 ILE cc_start: 0.8376 (mm) cc_final: 0.8053 (mt)
REVERT: A  729 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7785 (ttp80)
REVERT: A  754 PHE cc_start: 0.7104 (OUTLIER) cc_final: 0.6536 (t80)
REVERT: A  778 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7743 (mt)
  outliers start: 65
  outliers final: 37
  residues processed: 158
  average time/residue: 0.1794
  time to fit residues: 39.8822
Evaluate side-chains
  146 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 100
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  343 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue   40 SER
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 92 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 37 optimal weight:    0.4980
   chunk 94 optimal weight:    9.9990
   chunk 89 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.173244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.134316 restraints weight = 10606.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.134870 restraints weight = 6069.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.135771 restraints weight = 5465.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.1540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8274  Z= 0.157
  Angle     :  0.604   9.345  11256  Z= 0.318
  Chirality :  0.045   0.159   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  7.230  59.445   1153
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.75 %
    Favored  : 88.05 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 27.85 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.11 (0.24), residues: 996
  helix: -0.92 (0.49), residues: 109
  sheet: -2.90 (0.23), residues: 418
  loop : -2.91 (0.25), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 317 
 PHE   0.008   0.001   PHE A 406 
 TYR   0.013   0.001   TYR A 537 
 ARG   0.003   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03595 (  163)
  hydrogen bonds       : angle       5.47670 (  438)
  SS BOND              : bond        0.00264 (    3)
  SS BOND              : angle       0.65852 (    6)
  covalent geometry    : bond        0.00371 ( 8271)
  covalent geometry    : angle       0.60393 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 104
  time to evaluate  : 0.951 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6868 (t60) cc_final: 0.5874 (t60)
REVERT: A  142 MET cc_start: 0.6643 (OUTLIER) cc_final: 0.5339 (tmt)
REVERT: A  255 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.7572 (mpp)
REVERT: A  328 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8223 (m-40)
REVERT: A  448 ASN cc_start: 0.7944 (t0) cc_final: 0.7493 (t0)
REVERT: A  460 GLN cc_start: 0.9069 (OUTLIER) cc_final: 0.8498 (mt0)
REVERT: A  499 MET cc_start: 0.7242 (OUTLIER) cc_final: 0.6651 (ttm)
REVERT: A  595 ILE cc_start: 0.8447 (mm) cc_final: 0.8133 (mt)
REVERT: A  668 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8534 (mp)
REVERT: A  729 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7793 (ttp80)
REVERT: A  745 HIS cc_start: 0.6306 (OUTLIER) cc_final: 0.5864 (m90)
REVERT: A  754 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6585 (t80)
REVERT: A  778 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.7932 (mt)
  outliers start: 63
  outliers final: 40
  residues processed: 156
  average time/residue: 0.1842
  time to fit residues: 40.3734
Evaluate side-chains
  151 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 101
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 48 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 86 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.163215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.122637 restraints weight = 10696.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.124789 restraints weight = 5905.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.125272 restraints weight = 4136.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032   8274  Z= 0.199
  Angle     :  0.656  11.423  11256  Z= 0.341
  Chirality :  0.046   0.161   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  7.126  58.696   1150
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 13.35 %
    Favored  : 86.45 %
  Rotamer:
    Outliers :  7.19 %
    Allowed  : 27.85 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.17 (0.24), residues: 996
  helix: -0.98 (0.49), residues: 109
  sheet: -2.92 (0.23), residues: 422
  loop : -2.96 (0.25), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 311 
 HIS   0.007   0.001   HIS A 745 
 PHE   0.010   0.001   PHE A 276 
 TYR   0.014   0.001   TYR C 108 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03940 (  163)
  hydrogen bonds       : angle       5.57688 (  438)
  SS BOND              : bond        0.00290 (    3)
  SS BOND              : angle       0.70414 (    6)
  covalent geometry    : bond        0.00474 ( 8271)
  covalent geometry    : angle       0.65603 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 102
  time to evaluate  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6825 (t60) cc_final: 0.5710 (t60)
REVERT: A  142 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5279 (tmt)
REVERT: A  255 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7615 (mpp)
REVERT: A  328 ASN cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (m-40)
REVERT: A  448 ASN cc_start: 0.8069 (t0) cc_final: 0.7611 (t0)
REVERT: A  460 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8532 (mt0)
REVERT: A  469 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7071 (mmt180)
REVERT: A  499 MET cc_start: 0.7200 (OUTLIER) cc_final: 0.6633 (ttm)
REVERT: A  595 ILE cc_start: 0.8435 (mm) cc_final: 0.8128 (mt)
REVERT: A  717 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7924 (tt)
REVERT: A  729 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7776 (ttp80)
REVERT: A  745 HIS cc_start: 0.6416 (OUTLIER) cc_final: 0.6105 (m170)
REVERT: A  754 PHE cc_start: 0.7123 (OUTLIER) cc_final: 0.6633 (t80)
REVERT: A  778 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7977 (mt)
  outliers start: 63
  outliers final: 47
  residues processed: 150
  average time/residue: 0.1815
  time to fit residues: 38.3412
Evaluate side-chains
  158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 100
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  242 GLU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  642 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  668 LEU
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  745 HIS
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 67 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9980
   chunk 36 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 75 optimal weight:    0.9980
   chunk 37 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
B  58 ASN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.174663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.135037 restraints weight = 10658.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.137112 restraints weight = 7868.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.138268 restraints weight = 4582.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.122
  Angle     :  0.603   9.982  11256  Z= 0.309
  Chirality :  0.045   0.158   1199
  Planarity :  0.005   0.047   1484
  Dihedral  :  6.824  59.424   1150
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  8.73 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  7.76 %
    Allowed  : 27.51 %
    Favored  : 64.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.01 (0.24), residues: 996
  helix: -0.81 (0.50), residues: 109
  sheet: -2.83 (0.24), residues: 411
  loop : -2.87 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  33 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.008   0.001   PHE A 276 
 TYR   0.012   0.001   TYR C 108 
 ARG   0.001   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03146 (  163)
  hydrogen bonds       : angle       5.32998 (  438)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.52580 (    6)
  covalent geometry    : bond        0.00282 ( 8271)
  covalent geometry    : angle       0.60278 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 103
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6943 (t60) cc_final: 0.5698 (t60)
REVERT: A  142 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.5407 (tmt)
REVERT: A  255 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7587 (mpp)
REVERT: A  328 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8271 (m-40)
REVERT: A  448 ASN cc_start: 0.7978 (t0) cc_final: 0.7476 (t0)
REVERT: A  460 GLN cc_start: 0.9055 (OUTLIER) cc_final: 0.8490 (mt0)
REVERT: A  469 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.7050 (mmt180)
REVERT: A  499 MET cc_start: 0.7019 (OUTLIER) cc_final: 0.6462 (ttm)
REVERT: A  595 ILE cc_start: 0.8400 (mm) cc_final: 0.8104 (mt)
REVERT: A  598 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6267 (mp0)
REVERT: A  717 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7719 (tt)
REVERT: A  729 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7783 (ttp80)
REVERT: A  754 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6556 (t80)
REVERT: A  778 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7870 (mt)
REVERT: B   97 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7599 (mt-10)
  outliers start: 68
  outliers final: 43
  residues processed: 155
  average time/residue: 0.1776
  time to fit residues: 38.7141
Evaluate side-chains
  155 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 101
  time to evaluate  : 0.890 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 77 optimal weight:    0.9980
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.164802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.123957 restraints weight = 10717.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.125717 restraints weight = 8710.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.126694 restraints weight = 5187.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8274  Z= 0.161
  Angle     :  0.624  10.083  11256  Z= 0.323
  Chirality :  0.045   0.158   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.692  58.948   1147
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.85 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  7.65 %
    Allowed  : 27.17 %
    Favored  : 65.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.04 (0.24), residues: 996
  helix: -0.79 (0.50), residues: 108
  sheet: -2.84 (0.24), residues: 413
  loop : -2.90 (0.24), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.005   0.001   HIS A 317 
 PHE   0.009   0.001   PHE A 276 
 TYR   0.013   0.001   TYR C 108 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03532 (  163)
  hydrogen bonds       : angle       5.35156 (  438)
  SS BOND              : bond        0.00247 (    3)
  SS BOND              : angle       0.62142 (    6)
  covalent geometry    : bond        0.00381 ( 8271)
  covalent geometry    : angle       0.62438 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 102
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6806 (t60) cc_final: 0.5667 (t60)
REVERT: A  142 MET cc_start: 0.6745 (OUTLIER) cc_final: 0.5506 (tmt)
REVERT: A  255 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7585 (mpp)
REVERT: A  328 ASN cc_start: 0.8488 (OUTLIER) cc_final: 0.8253 (m-40)
REVERT: A  448 ASN cc_start: 0.8068 (t0) cc_final: 0.7588 (t0)
REVERT: A  460 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8519 (mt0)
REVERT: A  469 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7085 (mmt180)
REVERT: A  499 MET cc_start: 0.6995 (OUTLIER) cc_final: 0.6423 (ttm)
REVERT: A  595 ILE cc_start: 0.8399 (mm) cc_final: 0.8103 (mt)
REVERT: A  598 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6281 (mp0)
REVERT: A  622 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7405 (tt)
REVERT: A  717 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7795 (tt)
REVERT: A  729 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7778 (ttp80)
REVERT: A  754 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6626 (t80)
REVERT: A  778 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7908 (mt)
  outliers start: 67
  outliers final: 49
  residues processed: 155
  average time/residue: 0.1821
  time to fit residues: 40.0312
Evaluate side-chains
  158 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 97
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  281 GLN
Chi-restraints excluded: chain A residue  328 ASN
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  371 THR
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  488 ASP
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  562 VAL
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  593 ASP
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  626 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  719 VAL
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain A residue  778 LEU
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  119 SER
Chi-restraints excluded: chain B residue  143 ILE
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  106 ILE
Chi-restraints excluded: chain C residue  132 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 63 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 34 optimal weight:    0.4980
   chunk 1 optimal weight:    0.3980
   chunk 16 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0870
   chunk 5 optimal weight:   20.0000
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4154 r_free = 0.4154 target = 0.178886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.139288 restraints weight = 10689.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.140209 restraints weight = 9812.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.141372 restraints weight = 6677.235|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8274  Z= 0.097
  Angle     :  0.569   9.025  11256  Z= 0.293
  Chirality :  0.044   0.154   1199
  Planarity :  0.004   0.048   1484
  Dihedral  :  6.325  59.819   1147
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  6.12 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  5.82 %
    Allowed  : 29.22 %
    Favored  : 64.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.73 (0.25), residues: 996
  helix: -0.49 (0.51), residues: 108
  sheet: -2.64 (0.24), residues: 413
  loop : -2.72 (0.25), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  33 
 HIS   0.002   0.001   HIS A 317 
 PHE   0.007   0.001   PHE A 276 
 TYR   0.011   0.001   TYR C 108 
 ARG   0.001   0.000   ARG A  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02657 (  163)
  hydrogen bonds       : angle       5.08721 (  438)
  SS BOND              : bond        0.00183 (    3)
  SS BOND              : angle       0.41962 (    6)
  covalent geometry    : bond        0.00222 ( 8271)
  covalent geometry    : angle       0.56927 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 104
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6719 (t60) cc_final: 0.5600 (t60)
REVERT: A  142 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.5559 (tmt)
REVERT: A  255 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7402 (mpp)
REVERT: A  448 ASN cc_start: 0.8017 (t0) cc_final: 0.7533 (t0)
REVERT: A  460 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.8394 (mt0)
REVERT: A  499 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6396 (ttm)
REVERT: A  595 ILE cc_start: 0.8370 (mm) cc_final: 0.8078 (mt)
REVERT: A  598 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6282 (mp0)
REVERT: A  622 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7257 (tt)
REVERT: A  717 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7690 (tt)
REVERT: A  729 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7775 (ttp80)
REVERT: A  754 PHE cc_start: 0.7046 (OUTLIER) cc_final: 0.6568 (t80)
  outliers start: 51
  outliers final: 35
  residues processed: 142
  average time/residue: 0.1802
  time to fit residues: 35.9791
Evaluate side-chains
  143 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 99
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  115 ASN
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  622 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  132 MET
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   65 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 90 optimal weight:    5.9990
   chunk 40 optimal weight:    0.7980
   chunk 60 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
A 115 ASN
A 745 HIS
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.175511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.135782 restraints weight = 10644.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.138450 restraints weight = 7266.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.139398 restraints weight = 4439.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8274  Z= 0.144
  Angle     :  0.614   9.624  11256  Z= 0.318
  Chirality :  0.045   0.157   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.227  59.164   1144
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 5.00
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.14 %
    Favored  : 89.66 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 30.14 %
    Favored  : 64.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.25), residues: 996
  helix: -0.42 (0.51), residues: 107
  sheet: -2.59 (0.24), residues: 411
  loop : -2.73 (0.25), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 311 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.007   0.001   PHE A 170 
 TYR   0.013   0.001   TYR C 108 
 ARG   0.001   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  163)
  hydrogen bonds       : angle       5.15162 (  438)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.59161 (    6)
  covalent geometry    : bond        0.00342 ( 8271)
  covalent geometry    : angle       0.61441 (11250)

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

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

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1992 Ramachandran restraints generated.
    996 Oldfield, 0 Emsley, 996 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 TRP cc_start: 0.6786 (t60) cc_final: 0.5577 (t60)
REVERT: A  142 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.5321 (tmt)
REVERT: A  255 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7422 (mpp)
REVERT: A  448 ASN cc_start: 0.8044 (t0) cc_final: 0.7571 (t0)
REVERT: A  460 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8483 (mt0)
REVERT: A  469 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7115 (mmt180)
REVERT: A  499 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6282 (ttm)
REVERT: A  595 ILE cc_start: 0.8410 (mm) cc_final: 0.8125 (mt)
REVERT: A  598 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6191 (mp0)
REVERT: A  717 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7725 (tt)
REVERT: A  729 ARG cc_start: 0.8471 (OUTLIER) cc_final: 0.7768 (ttp80)
REVERT: A  754 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6598 (t80)
  outliers start: 47
  outliers final: 34
  residues processed: 137
  average time/residue: 0.1892
  time to fit residues: 36.1712
Evaluate side-chains
  140 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 97
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   54 ILE
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   89 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  166 ASP
Chi-restraints excluded: chain A residue  197 GLU
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  239 ASN
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  255 MET
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  435 THR
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  460 GLN
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  499 MET
Chi-restraints excluded: chain A residue  573 GLU
Chi-restraints excluded: chain A residue  574 ARG
Chi-restraints excluded: chain A residue  598 GLU
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  603 THR
Chi-restraints excluded: chain A residue  616 ILE
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  660 SER
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  711 LYS
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  729 ARG
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  765 TYR
Chi-restraints excluded: chain B residue   27 THR
Chi-restraints excluded: chain B residue   31 SER
Chi-restraints excluded: chain B residue   38 LEU
Chi-restraints excluded: chain B residue  167 ILE
Chi-restraints excluded: chain C residue   34 LEU
Chi-restraints excluded: chain C residue   67 CYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  106 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    0.5980
   chunk 67 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0980
   chunk 80 optimal weight:    3.9990
   chunk 14 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 98 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 745 HIS
B  54 GLN
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.177882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.138799 restraints weight = 10666.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.140157 restraints weight = 8067.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.141627 restraints weight = 4999.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8274  Z= 0.115
  Angle     :  0.589   8.491  11256  Z= 0.304
  Chirality :  0.044   0.155   1199
  Planarity :  0.005   0.048   1484
  Dihedral  :  6.096  59.964   1144
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  :  7.13 %
    Favored  : 92.67 %
  Rotamer:
    Outliers :  5.14 %
    Allowed  : 30.48 %
    Favored  : 64.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.50 (0.25), residues: 996
  helix: -0.23 (0.52), residues: 106
  sheet: -2.56 (0.24), residues: 409
  loop : -2.52 (0.25), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  33 
 HIS   0.003   0.001   HIS A 317 
 PHE   0.008   0.001   PHE A 276 
 TYR   0.012   0.001   TYR C 108 
 ARG   0.001   0.000   ARG A 267 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02909 (  163)
  hydrogen bonds       : angle       5.05843 (  438)
  SS BOND              : bond        0.00194 (    3)
  SS BOND              : angle       0.50305 (    6)
  covalent geometry    : bond        0.00270 ( 8271)
  covalent geometry    : angle       0.58905 (11250)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3105.97 seconds
wall clock time: 54 minutes 41.16 seconds (3281.16 seconds total)