Starting phenix.real_space_refine
on Tue Feb 11 11:56:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k12_36784/02_2025/8k12_36784_neut.cif"
  }
  resolution = 3.3
  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=  -0.000 sd=   0.046
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      48      5.16       5
     C    3730      2.51       5
     N     872      2.21       5
     O     942      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5592
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 2796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2796
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 349}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 2796
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 357, 2796
          Classifications: {'peptide': 357}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 7, 'TRANS': 349}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 66
          Unresolved non-hydrogen angles: 85
          Unresolved non-hydrogen dihedrals: 63
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'TYR:plan': 4, 'PHE:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 48
  Time building chain proxies: 4.56, per 1000 atoms: 0.82
  Number of scatterers: 5592
  At special positions: 0
  Unit cell: (99.22, 71.34, 77.08, 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      48     16.00
     O     942      8.00
     N     872      7.00
     C    3730      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 484 " - pdb=" SG  CYS A 570 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 490 " - pdb=" SG  CYS A 787 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 484 " - pdb=" SG  CYS B 570 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 490 " - pdb=" SG  CYS B 787 " 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: 1.38
  Conformation dependent library (CDL) restraints added in 665.6 milliseconds
  

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1348

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 0 sheets defined
      80.1% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 289 through 317
      removed outlier: 3.991A  pdb=" N   TYR A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   PHE A 307 " --> pdb=" O   ILE A 303 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   TYR A 308 " --> pdb=" O   PHE A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 451 through 479
      removed outlier: 3.554A  pdb=" N   LEU A 462 " --> pdb=" O   VAL A 458 " (cutoff:3.500A)
      Proline residue:  A 463  - end of helix
    Processing helix  chain 'A' and resid 499 through 505
      removed outlier: 3.620A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.836A  pdb=" N   ILE A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU A 517 " --> pdb=" O   GLY A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 547 through 568
      removed outlier: 3.709A  pdb=" N   GLY A 561 " --> pdb=" O   LEU A 557 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ALA A 565 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS A 568 " --> pdb=" O   SER A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 596
      removed outlier: 3.671A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
      removed outlier: 5.157A  pdb=" N   MET A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 625
    Processing helix  chain 'A' and resid 630 through 652
      removed outlier: 4.128A  pdb=" N   SER A 638 " --> pdb=" O   TRP A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
    Processing helix  chain 'A' and resid 713 through 740
      removed outlier: 3.562A  pdb=" N   LEU A 719 " --> pdb=" O   ALA A 715 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE A 734 " --> pdb=" O   PHE A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 767
    Processing helix  chain 'A' and resid 776 through 781
    Processing helix  chain 'A' and resid 782 through 784
      No H-bonds generated for 'chain 'A' and resid 782 through 784'
    Processing helix  chain 'A' and resid 794 through 816
      removed outlier: 3.666A  pdb=" N   ILE A 805 " --> pdb=" O   PHE A 801 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 317
      removed outlier: 3.996A  pdb=" N   TYR B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   PHE B 307 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TYR B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 479
      removed outlier: 3.554A  pdb=" N   LEU B 462 " --> pdb=" O   VAL B 458 " (cutoff:3.500A)
      Proline residue:  B 463  - end of helix
    Processing helix  chain 'B' and resid 499 through 505
      removed outlier: 3.620A  pdb=" N   ILE B 503 " --> pdb=" O   ALA B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.835A  pdb=" N   ILE B 510 " --> pdb=" O   ASN B 506 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU B 517 " --> pdb=" O   GLY B 513 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 547 through 568
      removed outlier: 3.709A  pdb=" N   GLY B 561 " --> pdb=" O   LEU B 557 " (cutoff:3.500A)
      removed outlier: 4.265A  pdb=" N   ALA B 565 " --> pdb=" O   GLY B 561 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   HIS B 568 " --> pdb=" O   SER B 564 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 577 through 596
      removed outlier: 3.670A  pdb=" N   PHE B 582 " --> pdb=" O   PHE B 578 " (cutoff:3.500A)
      removed outlier: 5.156A  pdb=" N   MET B 583 " --> pdb=" O   ASP B 579 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR B 584 " --> pdb=" O   THR B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 603 through 625
    Processing helix  chain 'B' and resid 630 through 652
      removed outlier: 4.128A  pdb=" N   SER B 638 " --> pdb=" O   TRP B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
    Processing helix  chain 'B' and resid 713 through 740
      removed outlier: 3.562A  pdb=" N   LEU B 719 " --> pdb=" O   ALA B 715 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ILE B 734 " --> pdb=" O   PHE B 730 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 767
      removed outlier: 3.501A  pdb=" N   PHE B 761 " --> pdb=" O   VAL B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 776 through 781
    Processing helix  chain 'B' and resid 782 through 784
      No H-bonds generated for 'chain 'B' and resid 782 through 784'
    Processing helix  chain 'B' and resid 794 through 816
      removed outlier: 3.666A  pdb=" N   ILE B 805 " --> pdb=" O   PHE B 801 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LEU B 814 " --> pdb=" O   SER B 810 " (cutoff:3.500A)

    419 hydrogen bonds defined for protein.
    1257 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.33

  Time building geometry restraints manager: 1.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1678
        1.35 -     1.46: 1456
        1.46 -     1.58: 2522
        1.58 -     1.70: 0
        1.70 -     1.82: 72
  Bond restraints: 5728
  Sorted by residual:
  bond pdb=" N   THR B 289 "
       pdb=" CA  THR B 289 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.31e-02 5.83e+03 7.52e+00
  bond pdb=" N   THR A 289 "
       pdb=" CA  THR A 289 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.31e-02 5.83e+03 7.32e+00
  bond pdb=" N   ILE B 586 "
       pdb=" CA  ILE B 586 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.39e+00
  bond pdb=" N   ILE A 586 "
       pdb=" CA  ILE A 586 "
    ideal  model  delta    sigma   weight residual
    1.461  1.490 -0.030 1.19e-02 7.06e+03 6.15e+00
  bond pdb=" N   LEU B 592 "
       pdb=" CA  LEU B 592 "
    ideal  model  delta    sigma   weight residual
    1.459  1.488 -0.028 1.19e-02 7.06e+03 5.72e+00
  ... (remaining 5723 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.21: 7212
        1.21 -     2.42: 430
        2.42 -     3.64: 114
        3.64 -     4.85: 30
        4.85 -     6.06: 10
  Bond angle restraints: 7796
  Sorted by residual:
  angle pdb=" C   SER A 295 "
        pdb=" N   GLY A 296 "
        pdb=" CA  GLY A 296 "
      ideal   model   delta    sigma   weight residual
     119.98  124.36   -4.38 1.11e+00 8.12e-01 1.56e+01
  angle pdb=" C   SER B 295 "
        pdb=" N   GLY B 296 "
        pdb=" CA  GLY B 296 "
      ideal   model   delta    sigma   weight residual
     119.98  124.34   -4.36 1.11e+00 8.12e-01 1.55e+01
  angle pdb=" C   LEU A 301 "
        pdb=" N   GLY A 302 "
        pdb=" CA  GLY A 302 "
      ideal   model   delta    sigma   weight residual
     119.98  124.33   -4.35 1.11e+00 8.12e-01 1.54e+01
  angle pdb=" C   LEU B 301 "
        pdb=" N   GLY B 302 "
        pdb=" CA  GLY B 302 "
      ideal   model   delta    sigma   weight residual
     119.98  124.21   -4.23 1.11e+00 8.12e-01 1.45e+01
  angle pdb=" N   GLN A 596 "
        pdb=" CA  GLN A 596 "
        pdb=" C   GLN A 596 "
      ideal   model   delta    sigma   weight residual
     113.20  109.19    4.01 1.21e+00 6.83e-01 1.10e+01
  ... (remaining 7791 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.04: 2875
       16.04 -    32.07: 297
       32.07 -    48.11: 80
       48.11 -    64.15: 20
       64.15 -    80.18: 4
  Dihedral angle restraints: 3276
    sinusoidal: 1196
      harmonic: 2080
  Sorted by residual:
  dihedral pdb=" CA  PHE A 576 "
           pdb=" C   PHE A 576 "
           pdb=" N   GLN A 577 "
           pdb=" CA  GLN A 577 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.93  -28.07     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  PHE B 576 "
           pdb=" C   PHE B 576 "
           pdb=" N   GLN B 577 "
           pdb=" CA  GLN B 577 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -151.94  -28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  MET B 559 "
           pdb=" C   MET B 559 "
           pdb=" N   GLU B 560 "
           pdb=" CA  GLU B 560 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.07   16.93     0      5.00e+00 4.00e-02 1.15e+01
  ... (remaining 3273 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 660
       0.042 -    0.085: 192
       0.085 -    0.127: 43
       0.127 -    0.169: 29
       0.169 -    0.212: 10
  Chirality restraints: 934
  Sorted by residual:
  chirality pdb=" CA  ILE B 586 "
            pdb=" N   ILE B 586 "
            pdb=" C   ILE B 586 "
            pdb=" CB  ILE B 586 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.12e+00
  chirality pdb=" CA  ILE A 586 "
            pdb=" N   ILE A 586 "
            pdb=" C   ILE A 586 "
            pdb=" CB  ILE A 586 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  THR A 311 "
            pdb=" CA  THR A 311 "
            pdb=" OG1 THR A 311 "
            pdb=" CG2 THR A 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.21 2.00e-01 2.50e+01 1.06e+00
  ... (remaining 931 not shown)

  Planarity restraints: 942
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 308 "    0.070 2.00e-02 2.50e+03   4.41e-02 3.89e+01
        pdb=" CG  TYR A 308 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 308 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 308 "   -0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 308 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 308 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 308 "   -0.009 2.00e-02 2.50e+03
        pdb=" OH  TYR A 308 "    0.078 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 308 "   -0.070 2.00e-02 2.50e+03   4.39e-02 3.85e+01
        pdb=" CG  TYR B 308 "    0.007 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 308 "    0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 308 "    0.031 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 308 "    0.036 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 308 "    0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 308 "    0.010 2.00e-02 2.50e+03
        pdb=" OH  TYR B 308 "   -0.078 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 304 "    0.040 2.00e-02 2.50e+03   2.56e-02 1.14e+01
        pdb=" CG  PHE A 304 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 304 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 304 "   -0.028 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 304 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 304 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 304 "    0.031 2.00e-02 2.50e+03
  ... (remaining 939 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 580
        2.75 -     3.29: 6039
        3.29 -     3.82: 9252
        3.82 -     4.36: 10919
        4.36 -     4.90: 17906
  Nonbonded interactions: 44696
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 293 "
            pdb=" O   PRO A 493 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OH  TYR A 486 "
            pdb=" O   VAL A 569 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OH  TYR B 486 "
            pdb=" O   VAL B 569 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   ASN B 501 "
            pdb=" OG  SER B 505 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ASN A 501 "
            pdb=" OG  SER A 505 "
     model   vdw
     2.263 3.040
  ... (remaining 44691 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.060
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   5728  Z= 0.305
  Angle     :  0.710   6.061   7796  Z= 0.470
  Chirality :  0.050   0.212    934
  Planarity :  0.004   0.044    942
  Dihedral  : 14.817  80.183   1916
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  : 16.22 %
    Favored  : 83.28 %
  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:  1.25 (0.31), residues: 694
  helix:  1.47 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.48 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.003   TRP A 317 
 HIS   0.002   0.001   HIS B 492 
 PHE   0.040   0.002   PHE A 304 
 TYR   0.078   0.004   TYR A 308 
 ARG   0.001   0.000   ARG A 785 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 286
  time to evaluate  : 1.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LEU cc_start: 0.7758 (mt) cc_final: 0.7508 (mt)
REVERT: A  562 LEU cc_start: 0.6917 (tt) cc_final: 0.6697 (tt)
REVERT: A  791 ASP cc_start: 0.7372 (m-30) cc_final: 0.7104 (t0)
REVERT: A  794 ASP cc_start: 0.6138 (p0) cc_final: 0.5749 (p0)
REVERT: B  308 TYR cc_start: 0.8073 (m-80) cc_final: 0.6944 (m-80)
REVERT: B  462 LEU cc_start: 0.7815 (mt) cc_final: 0.7584 (mt)
REVERT: B  562 LEU cc_start: 0.6933 (tt) cc_final: 0.6708 (tt)
REVERT: B  791 ASP cc_start: 0.7429 (m-30) cc_final: 0.7043 (t0)
REVERT: B  794 ASP cc_start: 0.6038 (p0) cc_final: 0.5748 (p0)
  outliers start: 3
  outliers final: 0
  residues processed: 286
  average time/residue: 0.1438
  time to fit residues: 55.3701
Evaluate side-chains
  172 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.649 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 29 optimal weight:    0.5980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 28 optimal weight:    0.4980
   chunk 54 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 526 ASN
A 527 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 HIS
B 526 ASN
B 527 HIS
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 796 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4475 r_free = 0.4475 target = 0.167295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.136551 restraints weight = 11477.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.4037 rms_B_bonded: 3.55
r_work: 0.3893 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.3663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5728  Z= 0.223
  Angle     :  0.708  11.224   7796  Z= 0.357
  Chirality :  0.042   0.149    934
  Planarity :  0.004   0.027    942
  Dihedral  :  4.364  28.025    748
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 24.25 %
    Favored  : 73.08 %
  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:  1.79 (0.30), residues: 694
  helix:  1.88 (0.20), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.54 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP B 700 
 HIS   0.008   0.001   HIS B 527 
 PHE   0.043   0.003   PHE B 811 
 TYR   0.022   0.002   TYR B 717 
 ARG   0.002   0.000   ARG B 785 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 186
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 TYR cc_start: 0.8095 (m-80) cc_final: 0.7670 (m-80)
REVERT: A  462 LEU cc_start: 0.8509 (mt) cc_final: 0.8300 (mt)
REVERT: A  472 GLN cc_start: 0.8838 (tp40) cc_final: 0.8569 (tp40)
REVERT: A  791 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7284 (t0)
REVERT: B  308 TYR cc_start: 0.8061 (m-80) cc_final: 0.7664 (m-80)
REVERT: B  472 GLN cc_start: 0.8885 (tp40) cc_final: 0.8661 (tp40)
REVERT: B  612 CYS cc_start: 0.9071 (t) cc_final: 0.8684 (p)
REVERT: B  709 MET cc_start: 0.7839 (tpp) cc_final: 0.7463 (tpp)
REVERT: B  791 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7209 (t0)
  outliers start: 16
  outliers final: 7
  residues processed: 195
  average time/residue: 0.1477
  time to fit residues: 39.1178
Evaluate side-chains
  174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.635 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  821 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    8.9990
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0970
   chunk 21 optimal weight:    5.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 HIS
B 527 HIS
** B 575 ASN ** 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 = 0.4434 r_free = 0.4434 target = 0.163989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.133522 restraints weight = 11781.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 3.51
r_work: 0.3876 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5728  Z= 0.210
  Angle     :  0.616   8.438   7796  Z= 0.316
  Chirality :  0.040   0.154    934
  Planarity :  0.003   0.026    942
  Dihedral  :  4.338  23.566    748
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  4.18 %
    Allowed  : 24.08 %
    Favored  : 71.74 %
  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:  1.93 (0.30), residues: 694
  helix:  2.02 (0.20), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.68 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 700 
 HIS   0.008   0.001   HIS A 527 
 PHE   0.022   0.002   PHE A 761 
 TYR   0.009   0.001   TYR B 486 
 ARG   0.001   0.000   ARG B 785 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 175
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 TYR cc_start: 0.8153 (m-80) cc_final: 0.7745 (m-80)
REVERT: A  450 PHE cc_start: 0.3057 (OUTLIER) cc_final: 0.2189 (t80)
REVERT: A  462 LEU cc_start: 0.8467 (mt) cc_final: 0.8206 (mt)
REVERT: A  472 GLN cc_start: 0.8840 (tp40) cc_final: 0.8496 (tp40)
REVERT: A  637 PHE cc_start: 0.8518 (t80) cc_final: 0.8306 (m-80)
REVERT: A  736 MET cc_start: 0.8565 (mpp) cc_final: 0.8269 (ptp)
REVERT: A  791 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7258 (t0)
REVERT: A  807 MET cc_start: 0.8032 (tpp) cc_final: 0.7814 (tpp)
REVERT: B  308 TYR cc_start: 0.8112 (m-80) cc_final: 0.7709 (m-80)
REVERT: B  450 PHE cc_start: 0.2796 (OUTLIER) cc_final: 0.1862 (t80)
REVERT: B  472 GLN cc_start: 0.8874 (tp40) cc_final: 0.8603 (tp40)
REVERT: B  709 MET cc_start: 0.7858 (tpp) cc_final: 0.7440 (tpp)
REVERT: B  791 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7169 (t0)
  outliers start: 25
  outliers final: 13
  residues processed: 191
  average time/residue: 0.1284
  time to fit residues: 34.1190
Evaluate side-chains
  178 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 161
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  821 LEU
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  803 SER
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  821 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 27 optimal weight:    8.9990
   chunk 35 optimal weight:   10.0000
   overall best weight:    1.7388

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
A 796 HIS
B 527 HIS
** B 575 ASN ** 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 = 0.4406 r_free = 0.4406 target = 0.161499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.130355 restraints weight = 12171.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3982 rms_B_bonded: 3.56
r_work: 0.3842 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.4613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5728  Z= 0.237
  Angle     :  0.633   9.806   7796  Z= 0.315
  Chirality :  0.039   0.161    934
  Planarity :  0.003   0.025    942
  Dihedral  :  4.334  23.398    748
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 24.92 %
    Favored  : 69.40 %
  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:  2.05 (0.30), residues: 694
  helix:  2.08 (0.20), residues: 550
  sheet:  None (None), residues: 0
  loop : -1.58 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 700 
 HIS   0.004   0.001   HIS A 527 
 PHE   0.021   0.002   PHE A 811 
 TYR   0.009   0.001   TYR B 485 
 ARG   0.001   0.000   ARG B 529 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 166
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 PHE cc_start: 0.3313 (OUTLIER) cc_final: 0.2482 (t80)
REVERT: A  462 LEU cc_start: 0.8467 (mt) cc_final: 0.8211 (mt)
REVERT: A  472 GLN cc_start: 0.8830 (tp40) cc_final: 0.8462 (tp40)
REVERT: A  736 MET cc_start: 0.8621 (mpp) cc_final: 0.8303 (ptp)
REVERT: A  791 ASP cc_start: 0.8289 (OUTLIER) cc_final: 0.7278 (t0)
REVERT: B  450 PHE cc_start: 0.3127 (OUTLIER) cc_final: 0.2229 (t80)
REVERT: B  472 GLN cc_start: 0.8880 (tp40) cc_final: 0.8600 (tp40)
REVERT: B  709 MET cc_start: 0.7902 (tpp) cc_final: 0.7454 (tpp)
REVERT: B  791 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.7234 (t0)
  outliers start: 34
  outliers final: 10
  residues processed: 183
  average time/residue: 0.1334
  time to fit residues: 33.6420
Evaluate side-chains
  168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 154
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  803 SER
Chi-restraints excluded: chain B residue  805 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 68 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 12 optimal weight:    0.8980
   chunk 62 optimal weight:   10.0000
   chunk 69 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 56 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.2582

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
B 527 HIS
** B 575 ASN ** 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 = 0.4413 r_free = 0.4413 target = 0.162237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.131465 restraints weight = 11893.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 3.55
r_work: 0.3849 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.4869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5728  Z= 0.203
  Angle     :  0.624  10.784   7796  Z= 0.309
  Chirality :  0.039   0.163    934
  Planarity :  0.003   0.026    942
  Dihedral  :  4.364  23.316    748
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.42 %
    Favored  : 68.90 %
  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:  2.07 (0.30), residues: 694
  helix:  2.10 (0.20), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.43 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 700 
 HIS   0.013   0.001   HIS A 527 
 PHE   0.031   0.002   PHE A 811 
 TYR   0.013   0.001   TYR A 573 
 ARG   0.001   0.000   ARG A 529 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 166
  time to evaluate  : 0.547 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  308 TYR cc_start: 0.8335 (m-80) cc_final: 0.7873 (m-10)
REVERT: A  450 PHE cc_start: 0.3558 (OUTLIER) cc_final: 0.2722 (t80)
REVERT: A  462 LEU cc_start: 0.8451 (mt) cc_final: 0.8176 (mt)
REVERT: A  472 GLN cc_start: 0.8823 (tp40) cc_final: 0.8400 (tp40)
REVERT: A  514 LEU cc_start: 0.8883 (tt) cc_final: 0.8643 (tt)
REVERT: A  736 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8319 (ptp)
REVERT: A  791 ASP cc_start: 0.8313 (OUTLIER) cc_final: 0.7295 (t0)
REVERT: B  308 TYR cc_start: 0.8327 (m-80) cc_final: 0.8074 (m-10)
REVERT: B  450 PHE cc_start: 0.3298 (OUTLIER) cc_final: 0.2469 (t80)
REVERT: B  472 GLN cc_start: 0.8877 (tp40) cc_final: 0.8497 (tp40)
REVERT: B  709 MET cc_start: 0.7937 (tpp) cc_final: 0.7449 (tpp)
REVERT: B  775 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7908 (mmmt)
REVERT: B  791 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.7268 (t0)
  outliers start: 28
  outliers final: 13
  residues processed: 177
  average time/residue: 0.1337
  time to fit residues: 32.3371
Evaluate side-chains
  174 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 155
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  549 LEU
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  736 MET
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  812 LEU
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 24 optimal weight:    8.9990
   chunk 3 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.162614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.132644 restraints weight = 11918.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.4007 rms_B_bonded: 3.48
r_work: 0.3863 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.5019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5728  Z= 0.189
  Angle     :  0.605   9.321   7796  Z= 0.304
  Chirality :  0.038   0.161    934
  Planarity :  0.002   0.026    942
  Dihedral  :  4.336  23.364    748
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 11.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 26.25 %
    Favored  : 68.90 %
  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:  2.18 (0.31), residues: 694
  helix:  2.19 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.44 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 799 
 HIS   0.007   0.001   HIS B 527 
 PHE   0.031   0.002   PHE A 732 
 TYR   0.008   0.001   TYR B 486 
 ARG   0.001   0.000   ARG A 785 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 159
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 PHE cc_start: 0.3575 (OUTLIER) cc_final: 0.2751 (t80)
REVERT: A  462 LEU cc_start: 0.8426 (mt) cc_final: 0.8174 (mt)
REVERT: A  472 GLN cc_start: 0.8782 (tp40) cc_final: 0.8383 (tp40)
REVERT: A  709 MET cc_start: 0.7912 (tpp) cc_final: 0.7463 (tpp)
REVERT: A  736 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8336 (ptp)
REVERT: A  791 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7305 (t0)
REVERT: B  450 PHE cc_start: 0.3653 (OUTLIER) cc_final: 0.2729 (t80)
REVERT: B  472 GLN cc_start: 0.8827 (tp40) cc_final: 0.8453 (tp40)
REVERT: B  709 MET cc_start: 0.7890 (tpp) cc_final: 0.7398 (tpp)
REVERT: B  775 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7979 (mmmt)
REVERT: B  791 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7248 (t0)
  outliers start: 29
  outliers final: 13
  residues processed: 173
  average time/residue: 0.1453
  time to fit residues: 34.6319
Evaluate side-chains
  168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 149
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  615 ILE
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  736 MET
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 52 optimal weight:    0.8980
   chunk 34 optimal weight:    0.9990
   chunk 33 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS
** B 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.162042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.132098 restraints weight = 11905.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3997 rms_B_bonded: 3.51
r_work: 0.3862 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.5241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5728  Z= 0.201
  Angle     :  0.640  14.477   7796  Z= 0.321
  Chirality :  0.039   0.165    934
  Planarity :  0.003   0.026    942
  Dihedral  :  4.343  23.016    748
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 27.42 %
    Favored  : 68.73 %
  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:  2.22 (0.31), residues: 694
  helix:  2.19 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.34 (0.50), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 799 
 HIS   0.012   0.001   HIS B 527 
 PHE   0.047   0.002   PHE A 618 
 TYR   0.025   0.001   TYR B 573 
 ARG   0.001   0.000   ARG A 529 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 PHE cc_start: 0.3842 (OUTLIER) cc_final: 0.3002 (t80)
REVERT: A  472 GLN cc_start: 0.8792 (tp40) cc_final: 0.8369 (tp40)
REVERT: A  709 MET cc_start: 0.7938 (tpp) cc_final: 0.7476 (tpp)
REVERT: A  761 PHE cc_start: 0.8781 (m-10) cc_final: 0.8492 (m-80)
REVERT: A  791 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7300 (t0)
REVERT: B  450 PHE cc_start: 0.3597 (OUTLIER) cc_final: 0.2748 (t80)
REVERT: B  472 GLN cc_start: 0.8825 (tp40) cc_final: 0.8495 (tp40)
REVERT: B  573 TYR cc_start: 0.6998 (m-10) cc_final: 0.6565 (t80)
REVERT: B  709 MET cc_start: 0.7906 (tpp) cc_final: 0.7425 (tpp)
REVERT: B  775 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.7976 (mmmt)
REVERT: B  791 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7225 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 172
  average time/residue: 0.1569
  time to fit residues: 36.6681
Evaluate side-chains
  171 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 150
  time to evaluate  : 0.722 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  791 ASP
Chi-restraints excluded: chain A residue  803 SER
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  458 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  615 ILE
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  791 ASP
Chi-restraints excluded: chain B residue  805 ILE
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 67 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0030
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS
** B 575 ASN ** 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 = 0.4412 r_free = 0.4412 target = 0.163036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.133706 restraints weight = 11934.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.4036 rms_B_bonded: 3.49
r_work: 0.3914 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.5453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5728  Z= 0.180
  Angle     :  0.671  13.535   7796  Z= 0.327
  Chirality :  0.039   0.181    934
  Planarity :  0.003   0.027    942
  Dihedral  :  4.336  22.687    748
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 28.93 %
    Favored  : 67.73 %
  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:  2.18 (0.31), residues: 694
  helix:  2.15 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.29 (0.51), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 799 
 HIS   0.013   0.001   HIS B 527 
 PHE   0.052   0.002   PHE B 618 
 TYR   0.014   0.001   TYR B 573 
 ARG   0.002   0.000   ARG A 781 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 155
  time to evaluate  : 0.650 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  450 PHE cc_start: 0.3861 (OUTLIER) cc_final: 0.3053 (t80)
REVERT: A  472 GLN cc_start: 0.8753 (tp40) cc_final: 0.8337 (tp40)
REVERT: A  710 ARG cc_start: 0.7484 (mtt180) cc_final: 0.6646 (mtp-110)
REVERT: A  761 PHE cc_start: 0.8748 (m-10) cc_final: 0.8439 (m-80)
REVERT: A  791 ASP cc_start: 0.8239 (m-30) cc_final: 0.7303 (t0)
REVERT: B  472 GLN cc_start: 0.8791 (tp40) cc_final: 0.8464 (tp40)
REVERT: B  573 TYR cc_start: 0.6908 (m-10) cc_final: 0.6321 (t80)
REVERT: B  709 MET cc_start: 0.7883 (tpp) cc_final: 0.7381 (tpp)
REVERT: B  775 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.7974 (mmmt)
REVERT: B  791 ASP cc_start: 0.8254 (m-30) cc_final: 0.7278 (t0)
  outliers start: 20
  outliers final: 11
  residues processed: 167
  average time/residue: 0.1387
  time to fit residues: 31.6021
Evaluate side-chains
  159 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 0.617 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  450 PHE
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 37 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 61 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    7.9990
   chunk 52 optimal weight:    0.2980
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.160666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.130970 restraints weight = 12066.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3988 rms_B_bonded: 3.51
r_work: 0.3862 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5728  Z= 0.227
  Angle     :  0.687  14.130   7796  Z= 0.339
  Chirality :  0.040   0.174    934
  Planarity :  0.003   0.026    942
  Dihedral  :  4.406  22.565    748
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 29.77 %
    Favored  : 67.22 %
  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:  2.21 (0.31), residues: 694
  helix:  2.16 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.21 (0.52), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP B 799 
 HIS   0.013   0.002   HIS A 527 
 PHE   0.038   0.002   PHE B 618 
 TYR   0.013   0.001   TYR B 573 
 ARG   0.002   0.000   ARG B 688 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 146
  time to evaluate  : 0.652 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 GLN cc_start: 0.8844 (tp40) cc_final: 0.8408 (tp40)
REVERT: A  710 ARG cc_start: 0.7524 (mtt180) cc_final: 0.6740 (mtp-110)
REVERT: A  791 ASP cc_start: 0.8311 (m-30) cc_final: 0.7335 (t0)
REVERT: B  472 GLN cc_start: 0.8829 (tp40) cc_final: 0.8460 (tp40)
REVERT: B  709 MET cc_start: 0.7964 (tpp) cc_final: 0.7415 (tpp)
REVERT: B  710 ARG cc_start: 0.7469 (mtt180) cc_final: 0.6674 (mtp-110)
REVERT: B  775 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8007 (mmmt)
REVERT: B  791 ASP cc_start: 0.8318 (m-30) cc_final: 0.7312 (t0)
  outliers start: 18
  outliers final: 12
  residues processed: 158
  average time/residue: 0.1667
  time to fit residues: 35.5820
Evaluate side-chains
  158 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  805 ILE
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 66 optimal weight:    0.6980
   chunk 43 optimal weight:    4.9990
   chunk 27 optimal weight:    0.0870
   chunk 38 optimal weight:    9.9990
   chunk 39 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9990
   chunk 11 optimal weight:    9.9990
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4405 r_free = 0.4405 target = 0.162573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.133300 restraints weight = 12127.243|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 3.53
r_work: 0.3895 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.5642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5728  Z= 0.181
  Angle     :  0.697  13.855   7796  Z= 0.342
  Chirality :  0.039   0.176    934
  Planarity :  0.003   0.026    942
  Dihedral  :  4.395  22.174    748
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 12.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 30.60 %
    Favored  : 66.72 %
  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:  2.21 (0.31), residues: 694
  helix:  2.14 (0.21), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.13 (0.54), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 799 
 HIS   0.012   0.001   HIS B 527 
 PHE   0.036   0.002   PHE B 618 
 TYR   0.015   0.001   TYR B 573 
 ARG   0.001   0.000   ARG A 785 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 0.587 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  472 GLN cc_start: 0.8811 (tp40) cc_final: 0.8362 (tp40)
REVERT: A  710 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6698 (mtp-110)
REVERT: A  775 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7060 (mmmt)
REVERT: A  791 ASP cc_start: 0.8242 (m-30) cc_final: 0.7314 (t0)
REVERT: A  794 ASP cc_start: 0.7929 (t70) cc_final: 0.7454 (m-30)
REVERT: B  472 GLN cc_start: 0.8819 (tp40) cc_final: 0.8428 (tp40)
REVERT: B  709 MET cc_start: 0.7910 (tpp) cc_final: 0.7351 (tpp)
REVERT: B  710 ARG cc_start: 0.7462 (mtt180) cc_final: 0.6642 (mtp-110)
REVERT: B  775 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7904 (mmmt)
REVERT: B  791 ASP cc_start: 0.8241 (m-30) cc_final: 0.7285 (t0)
  outliers start: 16
  outliers final: 11
  residues processed: 154
  average time/residue: 0.1429
  time to fit residues: 29.7161
Evaluate side-chains
  158 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 0.626 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  562 LEU
Chi-restraints excluded: chain A residue  638 SER
Chi-restraints excluded: chain A residue  759 TRP
Chi-restraints excluded: chain A residue  775 LYS
Chi-restraints excluded: chain A residue  815 LEU
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  638 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  775 LYS
Chi-restraints excluded: chain B residue  815 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 4 optimal weight:    0.0470
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 17 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0570
   chunk 38 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
A 527 HIS
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 527 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4411 r_free = 0.4411 target = 0.163235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.134219 restraints weight = 12136.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 3.56
r_work: 0.3910 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5728  Z= 0.171
  Angle     :  0.665  13.722   7796  Z= 0.328
  Chirality :  0.039   0.167    934
  Planarity :  0.003   0.027    942
  Dihedral  :  4.330  21.491    748
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 30.10 %
    Favored  : 67.06 %
  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:  2.26 (0.31), residues: 694
  helix:  2.19 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.12 (0.54), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 799 
 HIS   0.012   0.001   HIS A 527 
 PHE   0.034   0.002   PHE B 618 
 TYR   0.008   0.001   TYR B 573 
 ARG   0.000   0.000   ARG A 529 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2924.17 seconds
wall clock time: 52 minutes 49.01 seconds (3169.01 seconds total)