Starting phenix.real_space_refine
on Wed Sep 17 06:23:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jie_61503/09_2025/9jie_61503.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.019
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      16      5.16       5
     C    3730      2.51       5
     N    1002      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5900
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1186
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1197
    Chain: "B"
      Number of atoms: 1186
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
      Conformer: "B"
        Number of residues, atoms: 152, 1174
          Classifications: {'peptide': 152}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 143}
          bond proxies already assigned to first conformer: 1197
    Chain: "C"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 961
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "D"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 803
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 961
          Classifications: {'peptide': 124}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
    Chain: "L"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 803
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 102}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N  ASER A 474 " occ=0.26
      ... (10 atoms not shown)
      pdb=" OG BSER A 474 " occ=0.74
    residue:
      pdb=" N  ASER A 502 " occ=0.52
      ... (10 atoms not shown)
      pdb=" OG BSER A 502 " occ=0.48
    residue:
      pdb=" N  ASER B 474 " occ=0.30
      ... (10 atoms not shown)
      pdb=" OG BSER B 474 " occ=0.70
    residue:
      pdb=" N  ASER B 502 " occ=0.52
      ... (10 atoms not shown)
      pdb=" OG BSER B 502 " occ=0.48
  Time building chain proxies: 2.34, per 1000 atoms: 0.40
  Number of scatterers: 5900
  At special positions: 0
  Unit cell: (92.95, 116.35, 87.75, 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      16     16.00
     O    1152      8.00
     N    1002      7.00
     C    3730      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  89 " distance=2.38
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  89 " distance=2.35

  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: 0.49
  Conformation dependent library (CDL) restraints added in 535.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1384

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 18 sheets defined
      2.1% alpha, 49.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 501 through 503
      No H-bonds generated for 'chain 'A' and resid 501 through 503'
    Processing helix  chain 'B' and resid 501 through 503
      No H-bonds generated for 'chain 'B' and resid 501 through 503'
    Processing helix  chain 'C' and resid 28 through 32
      removed outlier: 3.539A  pdb=" N   SER C  31 " --> pdb=" O   THR C  28 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 28 through 32
    Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 454
    Processing sheet with id=AA2, first strand: chain 'A' and resid 497 through 499
      removed outlier: 4.139A  pdb=" N   SER A 472 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 5.260A  pdb=" N   HIS A 479 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   SER A 573 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
      removed outlier: 8.078A  pdb=" N   SER A 557 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   VAL A 524 " --> pdb=" O   TRP A 562 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 497 through 499
      removed outlier: 5.347A  pdb=" N   TRP A 461 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 7.431A  pdb=" N   GLY A 590 " --> pdb=" O   TRP A 461 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   THR A 463 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   GLY A 588 " --> pdb=" O   THR A 463 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   ILE A 586 " --> pdb=" O   PRO A 465 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   PHE A 536 " --> pdb=" O   GLY A 545 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 453 through 454
    Processing sheet with id=AA5, first strand: chain 'B' and resid 497 through 499
      removed outlier: 4.111A  pdb=" N   SER B 472 " --> pdb=" O   HIS B 479 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   HIS B 479 " --> pdb=" O   SER B 472 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   SER B 484 " --> pdb=" O   LEU B 570 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU B 570 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER B 573 " --> pdb=" O   SER B 557 " (cutoff:3.500A)
      removed outlier: 8.089A  pdb=" N   SER B 557 " --> pdb=" O   SER B 573 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TRP B 562 " --> pdb=" O   VAL B 524 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   VAL B 524 " --> pdb=" O   TRP B 562 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 497 through 499
      removed outlier: 4.100A  pdb=" N   SER B 466 " --> pdb=" O   VAL B 584 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   VAL B 584 " --> pdb=" O   SER B 466 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   PHE B 536 " --> pdb=" O   GLY B 545 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.541A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   LEU C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ILE C  34 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN C  39 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   TYR C 113 " --> pdb=" O   ARG C  98 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.541A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.579A  pdb=" N   LEU C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 7.035A  pdb=" N   ILE C  34 " --> pdb=" O   LEU C  50 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN C  39 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 9 through 12
      removed outlier: 6.845A  pdb=" N   TRP D  36 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   LEU D  48 " --> pdb=" O   TRP D  36 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 9 through 12
    Processing sheet with id=AB3, first strand: chain 'D' and resid 18 through 23
    Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AB5, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.576A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   LEU H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ILE H  34 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN H  39 " --> pdb=" O   LEU H  93 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   TYR H 113 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 58 through 60
      removed outlier: 6.576A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   LEU H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   ILE H  34 " --> pdb=" O   LEU H  50 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN H  39 " --> pdb=" O   LEU H  93 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 9 through 12
      removed outlier: 6.741A  pdb=" N   TRP L  36 " --> pdb=" O   LEU L  48 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   LEU L  48 " --> pdb=" O   TRP L  36 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'L' and resid 9 through 12
    Processing sheet with id=AB9, first strand: chain 'L' and resid 18 through 23

    240 hydrogen bonds defined for protein.
    594 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: 1.13

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.12 -     1.26: 949
        1.26 -     1.40: 1547
        1.40 -     1.53: 3247
        1.53 -     1.67: 289
        1.67 -     1.80: 24
  Bond restraints: 6056
  Sorted by residual:
  bond pdb=" C   TRP A 461 "
       pdb=" O   TRP A 461 "
    ideal  model  delta    sigma   weight residual
    1.235  1.125  0.111 1.13e-02 7.83e+03 9.63e+01
  bond pdb=" C   VAL A 462 "
       pdb=" O   VAL A 462 "
    ideal  model  delta    sigma   weight residual
    1.238  1.157  0.081 1.28e-02 6.10e+03 4.00e+01
  bond pdb=" CA  GLY A 582 "
       pdb=" C   GLY A 582 "
    ideal  model  delta    sigma   weight residual
    1.515  1.434  0.081 1.43e-02 4.89e+03 3.19e+01
  bond pdb=" C   PRO B 465 "
       pdb=" N   SER B 466 "
    ideal  model  delta    sigma   weight residual
    1.332  1.409 -0.077 1.40e-02 5.10e+03 3.02e+01
  bond pdb=" C   ALA B 487 "
       pdb=" O   ALA B 487 "
    ideal  model  delta    sigma   weight residual
    1.234  1.161  0.074 1.36e-02 5.41e+03 2.93e+01
  ... (remaining 6051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 8090
        1.64 -     3.28: 140
        3.28 -     4.92: 24
        4.92 -     6.57: 19
        6.57 -     8.21: 7
  Bond angle restraints: 8280
  Sorted by residual:
  angle pdb=" CA  GLY A 582 "
        pdb=" C   GLY A 582 "
        pdb=" O   GLY A 582 "
      ideal   model   delta    sigma   weight residual
     121.52  113.31    8.21 1.43e+00 4.89e-01 3.29e+01
  angle pdb=" CA  ALA B 487 "
        pdb=" C   ALA B 487 "
        pdb=" O   ALA B 487 "
      ideal   model   delta    sigma   weight residual
     121.87  115.57    6.30 1.16e+00 7.43e-01 2.95e+01
  angle pdb=" O   TRP B 461 "
        pdb=" C   TRP B 461 "
        pdb=" N   VAL B 462 "
      ideal   model   delta    sigma   weight residual
     123.27  117.09    6.18 1.16e+00 7.43e-01 2.84e+01
  angle pdb=" CA  ALA A 568 "
        pdb=" C   ALA A 568 "
        pdb=" O   ALA A 568 "
      ideal   model   delta    sigma   weight residual
     120.66  114.67    5.99 1.15e+00 7.56e-01 2.72e+01
  angle pdb=" C   VAL A 459 "
        pdb=" N   VAL A 460 "
        pdb=" CA  VAL A 460 "
      ideal   model   delta    sigma   weight residual
     122.91  129.13   -6.22 1.43e+00 4.89e-01 1.89e+01
  ... (remaining 8275 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 3137
       17.07 -    34.14: 257
       34.14 -    51.21: 72
       51.21 -    68.28: 11
       68.28 -    85.35: 9
  Dihedral angle restraints: 3486
    sinusoidal: 1280
      harmonic: 2206
  Sorted by residual:
  dihedral pdb=" CB  CYS L  22 "
           pdb=" SG  CYS L  22 "
           pdb=" SG  CYS L  89 "
           pdb=" CB  CYS L  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  178.35  -85.35     1      1.00e+01 1.00e-02 8.82e+01
  dihedral pdb=" CB  CYS D  22 "
           pdb=" SG  CYS D  22 "
           pdb=" SG  CYS D  89 "
           pdb=" CB  CYS D  89 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.37  -74.37     1      1.00e+01 1.00e-02 7.01e+01
  dihedral pdb=" CA  GLY A 582 "
           pdb=" C   GLY A 582 "
           pdb=" N   PRO A 583 "
           pdb=" CA  PRO A 583 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -35.74   35.74     0      5.00e+00 4.00e-02 5.11e+01
  ... (remaining 3483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 676
       0.041 -    0.082: 161
       0.082 -    0.123: 66
       0.123 -    0.164: 5
       0.164 -    0.205: 2
  Chirality restraints: 910
  Sorted by residual:
  chirality pdb=" CB  VAL A 462 "
            pdb=" CA  VAL A 462 "
            pdb=" CG1 VAL A 462 "
            pdb=" CG2 VAL A 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CB  VAL A 460 "
            pdb=" CA  VAL A 460 "
            pdb=" CG1 VAL A 460 "
            pdb=" CG2 VAL A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.35e-01
  chirality pdb=" CB  THR A 576 "
            pdb=" CA  THR A 576 "
            pdb=" OG1 THR A 576 "
            pdb=" CG2 THR A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.41    0.14 2.00e-01 2.50e+01 5.18e-01
  ... (remaining 907 not shown)

  Planarity restraints: 1058
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 461 "   -0.050 2.00e-02 2.50e+03   9.62e-02 9.26e+01
        pdb=" C   TRP B 461 "    0.167 2.00e-02 2.50e+03
        pdb=" O   TRP B 461 "   -0.060 2.00e-02 2.50e+03
        pdb=" N   VAL B 462 "   -0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C  98 "    0.573 9.50e-02 1.11e+02   2.57e-01 4.03e+01
        pdb=" NE  ARG C  98 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG C  98 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG C  98 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG C  98 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG H  72 "    0.470 9.50e-02 1.11e+02   2.11e-01 2.72e+01
        pdb=" NE  ARG H  72 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ  ARG H  72 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG H  72 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG H  72 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1055 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 454
        2.74 -     3.28: 5712
        3.28 -     3.82: 10254
        3.82 -     4.36: 12303
        4.36 -     4.90: 21205
  Nonbonded interactions: 49928
  Sorted by model distance:
  nonbonded pdb=" OG  SER L  35 "
            pdb=" O   ILE L  49 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   PRO A 465 "
            pdb=" OG  SER A 484 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   PRO B 465 "
            pdb=" OG  SER B 484 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" N   VAL L  34 "
            pdb=" OD1 ASN L  52 "
     model   vdw
     2.342 3.120
  nonbonded pdb=" OG  SER A 456 "
            pdb=" O   GLY A 593 "
     model   vdw
     2.348 3.040
  ... (remaining 49923 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: 0.01
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 446 through 473 or resid 475 through 501 or resid 503 thro \ 
ugh 597))
  selection = (chain 'B' and (resid 446 through 473 or resid 475 through 501 or resid 503 thro \ 
ugh 597))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'H'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'L'
}

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=0.26 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:             6.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     9.040
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.353   6058  Z= 0.443
  Angle     :  0.677  12.947   8284  Z= 0.381
  Chirality :  0.042   0.205    910
  Planarity :  0.013   0.257   1058
  Dihedral  : 14.159  74.981   2096
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 14.44 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.78 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.56 (0.32), residues: 772
  helix: -4.11 (0.36), residues: 12
  sheet: -0.84 (0.28), residues: 362
  loop :  0.46 (0.34), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG C  72 
 TYR   0.013   0.001   TYR H 113 
 PHE   0.004   0.001   PHE C  27 
 TRP   0.041   0.002   TRP A 561 
 HIS   0.002   0.001   HIS B 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 ( 6056)
  covalent geometry    : angle       0.64543 ( 8280)
  SS BOND              : bond        0.33590 (    2)
  SS BOND              : angle       9.27486 (    4)
  hydrogen bonds       : bond        0.27198 (  194)
  hydrogen bonds       : angle      10.34665 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 72
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  554 ASP cc_start: 0.6665 (m-30) cc_final: 0.6460 (m-30)
REVERT: B  455 ARG cc_start: 0.5856 (mtm-85) cc_final: 0.5626 (mtt-85)
  outliers start: 5
  outliers final: 4
  residues processed: 77
  average time/residue: 0.2417
  time to fit residues: 20.5057
Evaluate side-chains
  68 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 64
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue  104 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 471 GLN
B 471 GLN
B 491 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.174587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.155278 restraints weight = 25991.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.4110 rms_B_bonded: 3.95
r_work: 0.3942 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.3942
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3940
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3940 r_free = 0.3940    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3940
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.1791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6058  Z= 0.214
  Angle     :  0.676   8.709   8284  Z= 0.347
  Chirality :  0.046   0.176    910
  Planarity :  0.005   0.041   1058
  Dihedral  :  5.631  32.680    858
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 16.35 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.44 (0.32), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.66 (0.29), residues: 346
  loop :  0.22 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  98 
 TYR   0.021   0.002   TYR A 546 
 PHE   0.015   0.002   PHE L  63 
 TRP   0.023   0.003   TRP B 561 
 HIS   0.006   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 ( 6056)
  covalent geometry    : angle       0.67352 ( 8280)
  SS BOND              : bond        0.00644 (    2)
  SS BOND              : angle       2.66672 (    4)
  hydrogen bonds       : bond        0.05226 (  194)
  hydrogen bonds       : angle       6.94440 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.191 
Fit side-chains
REVERT: B  455 ARG cc_start: 0.6629 (mtm-85) cc_final: 0.6418 (mtt-85)
REVERT: H   32 TYR cc_start: 0.8276 (m-80) cc_final: 0.8036 (m-80)
  outliers start: 23
  outliers final: 14
  residues processed: 80
  average time/residue: 0.2893
  time to fit residues: 25.2592
Evaluate side-chains
  77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   23 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   18 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 57 optimal weight:    0.0270
   chunk 10 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0370
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.3916

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.178163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.158006 restraints weight = 31304.418|
|-----------------------------------------------------------------------------|
r_work (start): 0.4138 rms_B_bonded: 5.02
r_work (final): 0.4138
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4138 r_free = 0.4138    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4138 r_free = 0.4138    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4138
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6058  Z= 0.138
  Angle     :  0.587   8.012   8284  Z= 0.300
  Chirality :  0.043   0.164    910
  Planarity :  0.004   0.036   1058
  Dihedral  :  5.190  30.457    858
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.62 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.60 (0.29), residues: 346
  loop :  0.14 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  98 
 TYR   0.011   0.001   TYR A 546 
 PHE   0.008   0.001   PHE L  63 
 TRP   0.027   0.002   TRP B 561 
 HIS   0.004   0.001   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6056)
  covalent geometry    : angle       0.58550 ( 8280)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       1.87359 (    4)
  hydrogen bonds       : bond        0.04132 (  194)
  hydrogen bonds       : angle       6.32808 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  543 LYS cc_start: 0.7291 (tptt) cc_final: 0.7027 (tttm)
REVERT: B  455 ARG cc_start: 0.5603 (mtm-85) cc_final: 0.5401 (mtt-85)
REVERT: L   35 SER cc_start: 0.5219 (OUTLIER) cc_final: 0.4721 (p)
  outliers start: 22
  outliers final: 10
  residues processed: 78
  average time/residue: 0.3594
  time to fit residues: 30.0920
Evaluate side-chains
  71 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 60
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   18 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0980
   chunk 67 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9990
   chunk 9 optimal weight:    0.2980
   overall best weight:    0.4380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.178307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.158290 restraints weight = 28450.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.4145 rms_B_bonded: 4.32
r_work: 0.3963 rms_B_bonded: 4.90 restraints_weight: 0.5000
r_work (final): 0.3963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3958 r_free = 0.3958    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3958 r_free = 0.3958    target_work(ls_wunit_k1) = 0.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6910
moved from start:          0.2202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6058  Z= 0.149
  Angle     :  0.604  11.813   8284  Z= 0.305
  Chirality :  0.043   0.166    910
  Planarity :  0.004   0.038   1058
  Dihedral  :  5.189  30.399    857
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 19.21 %
    Favored  : 77.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.62 (0.27), residues: 356
  loop :  0.05 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H 100 
 TYR   0.010   0.001   TYR B 550 
 PHE   0.008   0.001   PHE L  63 
 TRP   0.030   0.002   TRP B 561 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 6056)
  covalent geometry    : angle       0.60289 ( 8280)
  SS BOND              : bond        0.00280 (    2)
  SS BOND              : angle       1.60053 (    4)
  hydrogen bonds       : bond        0.03956 (  194)
  hydrogen bonds       : angle       6.19914 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 62
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  543 LYS cc_start: 0.7504 (tptt) cc_final: 0.7304 (tttm)
REVERT: H   32 TYR cc_start: 0.8307 (m-80) cc_final: 0.8039 (m-80)
REVERT: L   35 SER cc_start: 0.5494 (OUTLIER) cc_final: 0.5050 (p)
  outliers start: 23
  outliers final: 16
  residues processed: 80
  average time/residue: 0.3014
  time to fit residues: 26.2888
Evaluate side-chains
  78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 61
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 57 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0870
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 67 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0470
   chunk 71 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   overall best weight:    0.4456

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.178919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.158815 restraints weight = 31713.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.4149 rms_B_bonded: 5.03
r_work (final): 0.4149
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4149
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4149 r_free = 0.4149    target_work(ls_wunit_k1) = 0.159         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4149
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6058  Z= 0.149
  Angle     :  0.596   9.647   8284  Z= 0.303
  Chirality :  0.043   0.160    910
  Planarity :  0.004   0.042   1058
  Dihedral  :  5.180  30.437    857
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  4.29 %
    Allowed  : 19.37 %
    Favored  : 76.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.55 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.59 (0.27), residues: 356
  loop :  0.01 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 100 
 TYR   0.010   0.001   TYR B 550 
 PHE   0.007   0.001   PHE L  63 
 TRP   0.030   0.002   TRP B 561 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 6056)
  covalent geometry    : angle       0.59563 ( 8280)
  SS BOND              : bond        0.00248 (    2)
  SS BOND              : angle       1.41771 (    4)
  hydrogen bonds       : bond        0.03840 (  194)
  hydrogen bonds       : angle       6.12163 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 62
  time to evaluate  : 0.162 
Fit side-chains
REVERT: C  116 GLN cc_start: 0.7351 (tp40) cc_final: 0.7021 (mp10)
REVERT: H   32 TYR cc_start: 0.7863 (m-80) cc_final: 0.7525 (m-80)
REVERT: L   35 SER cc_start: 0.5127 (OUTLIER) cc_final: 0.4658 (p)
  outliers start: 27
  outliers final: 20
  residues processed: 83
  average time/residue: 0.3071
  time to fit residues: 27.7494
Evaluate side-chains
  82 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   18 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.0070
   chunk 69 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0980
   chunk 49 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.4198

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4385 r_free = 0.4385 target = 0.179287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.159300 restraints weight = 27865.602|
|-----------------------------------------------------------------------------|
r_work (start): 0.4156 rms_B_bonded: 4.36
r_work: 0.3978 rms_B_bonded: 4.86 restraints_weight: 0.5000
r_work (final): 0.3978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3975
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3975 r_free = 0.3975    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3975 r_free = 0.3975    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3975
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6058  Z= 0.144
  Angle     :  0.589   8.743   8284  Z= 0.300
  Chirality :  0.043   0.156    910
  Planarity :  0.004   0.039   1058
  Dihedral  :  5.111  29.890    857
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.16 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.50 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.51 (0.27), residues: 360
  loop :  0.00 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 100 
 TYR   0.010   0.001   TYR L  37 
 PHE   0.007   0.001   PHE L  63 
 TRP   0.032   0.002   TRP B 561 
 HIS   0.004   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6056)
  covalent geometry    : angle       0.58888 ( 8280)
  SS BOND              : bond        0.00221 (    2)
  SS BOND              : angle       1.28171 (    4)
  hydrogen bonds       : bond        0.03735 (  194)
  hydrogen bonds       : angle       5.96969 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.154 
Fit side-chains
REVERT: H   32 TYR cc_start: 0.8282 (m-80) cc_final: 0.7957 (m-80)
REVERT: L   35 SER cc_start: 0.5439 (OUTLIER) cc_final: 0.5002 (p)
  outliers start: 24
  outliers final: 19
  residues processed: 79
  average time/residue: 0.2946
  time to fit residues: 25.2784
Evaluate side-chains
  83 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 63
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.0670
   chunk 6 optimal weight:    0.3980
   chunk 9 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 74 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 10 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.5718

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.177638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.157581 restraints weight = 32202.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.4137 rms_B_bonded: 5.27
r_work: 0.3945 rms_B_bonded: 5.05 restraints_weight: 2.0000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3939 r_free = 0.3939    target_work(ls_wunit_k1) = 0.142         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6945
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6058  Z= 0.177
  Angle     :  0.621   9.205   8284  Z= 0.316
  Chirality :  0.044   0.154    910
  Planarity :  0.004   0.040   1058
  Dihedral  :  5.371  34.051    857
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 19.84 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.49 (0.27), residues: 346
  loop : -0.08 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H 100 
 TYR   0.013   0.002   TYR B 550 
 PHE   0.009   0.002   PHE L  63 
 TRP   0.032   0.002   TRP B 561 
 HIS   0.005   0.001   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6056)
  covalent geometry    : angle       0.62051 ( 8280)
  SS BOND              : bond        0.00355 (    2)
  SS BOND              : angle       1.44562 (    4)
  hydrogen bonds       : bond        0.04043 (  194)
  hydrogen bonds       : angle       6.15402 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 65
  time to evaluate  : 0.202 
Fit side-chains
REVERT: H   32 TYR cc_start: 0.8315 (m-80) cc_final: 0.7995 (m-80)
REVERT: L   35 SER cc_start: 0.5515 (OUTLIER) cc_final: 0.5084 (p)
  outliers start: 26
  outliers final: 21
  residues processed: 82
  average time/residue: 0.2870
  time to fit residues: 25.4840
Evaluate side-chains
  87 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain B residue  472 SER
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 38 optimal weight:    0.1980
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 50 optimal weight:    0.9990
   chunk 26 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9990
   chunk 20 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.177299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.156853 restraints weight = 35320.613|
|-----------------------------------------------------------------------------|
r_work (start): 0.4132 rms_B_bonded: 5.53
r_work: 0.3914 rms_B_bonded: 5.45 restraints_weight: 2.0000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3909 r_free = 0.3909    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.2660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6058  Z= 0.188
  Angle     :  0.630   9.371   8284  Z= 0.321
  Chirality :  0.044   0.157    910
  Planarity :  0.004   0.040   1058
  Dihedral  :  5.489  36.762    857
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 20.32 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.53 (0.27), residues: 346
  loop : -0.11 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H 100 
 TYR   0.013   0.002   TYR L  37 
 PHE   0.009   0.002   PHE L  63 
 TRP   0.034   0.002   TRP B 561 
 HIS   0.005   0.002   HIS A 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 6056)
  covalent geometry    : angle       0.62972 ( 8280)
  SS BOND              : bond        0.00376 (    2)
  SS BOND              : angle       1.49433 (    4)
  hydrogen bonds       : bond        0.04100 (  194)
  hydrogen bonds       : angle       6.18292 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 63
  time to evaluate  : 0.145 
Fit side-chains
REVERT: H   32 TYR cc_start: 0.8336 (m-80) cc_final: 0.8019 (m-80)
REVERT: L   35 SER cc_start: 0.5555 (OUTLIER) cc_final: 0.5130 (p)
  outliers start: 24
  outliers final: 21
  residues processed: 80
  average time/residue: 0.2984
  time to fit residues: 26.0263
Evaluate side-chains
  85 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  552 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain B residue  466 SER
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   37 VAL
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   64 VAL
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain D residue   35 SER
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   37 VAL
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 40 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 33 optimal weight:    0.1980
   chunk 39 optimal weight:    0.1980
   chunk 16 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0040
   chunk 51 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.2190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4413 r_free = 0.4413 target = 0.182068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.162218 restraints weight = 30204.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.4189 rms_B_bonded: 4.96
r_work (final): 0.4189
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4189
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4189 r_free = 0.4189    target_work(ls_wunit_k1) = 0.162         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.4189
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.2687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6058  Z= 0.105
  Angle     :  0.558   7.621   8284  Z= 0.284
  Chirality :  0.043   0.152    910
  Planarity :  0.004   0.039   1058
  Dihedral  :  4.888  29.135    857
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.87 %
    Favored  : 95.13 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 22.54 %
    Favored  : 75.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.51 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.50 (0.27), residues: 360
  loop : -0.02 (0.33), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 100 
 TYR   0.007   0.001   TYR B 469 
 PHE   0.006   0.001   PHE B 536 
 TRP   0.034   0.002   TRP B 561 
 HIS   0.002   0.001   HIS B 516 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 6056)
  covalent geometry    : angle       0.55742 ( 8280)
  SS BOND              : bond        0.00029 (    2)
  SS BOND              : angle       0.84060 (    4)
  hydrogen bonds       : bond        0.03157 (  194)
  hydrogen bonds       : angle       5.63974 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.208 
Fit side-chains
REVERT: L   35 SER cc_start: 0.5074 (OUTLIER) cc_final: 0.4613 (p)
  outliers start: 12
  outliers final: 8
  residues processed: 69
  average time/residue: 0.3365
  time to fit residues: 25.1208
Evaluate side-chains
  69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 60
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 50 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 60 optimal weight:    0.4980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 585 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.177254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.156616 restraints weight = 36691.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.4130 rms_B_bonded: 5.56
r_work: 0.3909 rms_B_bonded: 5.50 restraints_weight: 2.0000
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3904
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3904 r_free = 0.3904    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3904
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6989
moved from start:          0.2781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   6058  Z= 0.206
  Angle     :  0.641   9.081   8284  Z= 0.328
  Chirality :  0.045   0.171    910
  Planarity :  0.005   0.038   1058
  Dihedral  :  5.412  35.078    856
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.92 %
    Favored  : 94.08 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 22.54 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.59 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.50 (0.27), residues: 354
  loop : -0.14 (0.32), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 100 
 TYR   0.016   0.002   TYR B 550 
 PHE   0.009   0.002   PHE L  63 
 TRP   0.036   0.003   TRP B 561 
 HIS   0.006   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00481 ( 6056)
  covalent geometry    : angle       0.64071 ( 8280)
  SS BOND              : bond        0.00388 (    2)
  SS BOND              : angle       1.48971 (    4)
  hydrogen bonds       : bond        0.04220 (  194)
  hydrogen bonds       : angle       6.08787 (  594)

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

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

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1544 Ramachandran restraints generated.
    772 Oldfield, 0 Emsley, 772 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 60
  time to evaluate  : 0.203 
Fit side-chains
REVERT: L   35 SER cc_start: 0.5560 (OUTLIER) cc_final: 0.5129 (p)
  outliers start: 16
  outliers final: 15
  residues processed: 73
  average time/residue: 0.3197
  time to fit residues: 25.2390
Evaluate side-chains
  75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 59
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  519 THR
Chi-restraints excluded: chain A residue  557 SER
Chi-restraints excluded: chain A residue  577 THR
Chi-restraints excluded: chain B residue  490 ILE
Chi-restraints excluded: chain B residue  552 THR
Chi-restraints excluded: chain C residue   31 SER
Chi-restraints excluded: chain C residue   51 ILE
Chi-restraints excluded: chain C residue   83 VAL
Chi-restraints excluded: chain C residue   91 THR
Chi-restraints excluded: chain C residue  103 ILE
Chi-restraints excluded: chain C residue  104 VAL
Chi-restraints excluded: chain H residue   31 SER
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   83 VAL
Chi-restraints excluded: chain H residue  104 VAL
Chi-restraints excluded: chain L residue   35 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 13 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.176860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.156399 restraints weight = 34864.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.4128 rms_B_bonded: 5.45
r_work: 0.3911 rms_B_bonded: 5.40 restraints_weight: 2.0000
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3905
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3905 r_free = 0.3905    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3905 r_free = 0.3905    target_work(ls_wunit_k1) = 0.140         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
r_final: 0.3905
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6058  Z= 0.205
  Angle     :  0.646  10.039   8284  Z= 0.329
  Chirality :  0.045   0.170    910
  Planarity :  0.004   0.039   1058
  Dihedral  :  5.569  38.885    856
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.18 %
    Favored  : 93.82 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 22.22 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.60 (0.31), residues: 772
  helix:  None (None), residues: 0
  sheet: -0.50 (0.28), residues: 344
  loop : -0.18 (0.32), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 100 
 TYR   0.015   0.002   TYR L  37 
 PHE   0.009   0.002   PHE L  63 
 TRP   0.037   0.002   TRP B 561 
 HIS   0.005   0.002   HIS C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 ( 6056)
  covalent geometry    : angle       0.64538 ( 8280)
  SS BOND              : bond        0.00423 (    2)
  SS BOND              : angle       1.56553 (    4)
  hydrogen bonds       : bond        0.04196 (  194)
  hydrogen bonds       : angle       6.22213 (  594)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2071.14 seconds
wall clock time: 36 minutes 13.34 seconds (2173.34 seconds total)