Starting phenix.real_space_refine
on Mon May 12 23:50:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k10_36782/05_2025/8k10_36782_neut.cif"
  }
  resolution = 3.2
  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=   0.057
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      64      5.16       5
     C    6176      2.51       5
     N    1510      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9478
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4627
          Classifications: {'peptide': 588}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 568}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 61
    Chain: "B"
      Number of atoms: 4627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4627
          Classifications: {'peptide': 588}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PCIS': 3, 'PTRANS': 16, 'TRANS': 568}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 91
          Unresolved non-hydrogen angles: 117
          Unresolved non-hydrogen dihedrals: 88
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'PHE:plan': 2, 'TRP:plan': 1, 'TYR:plan': 4}
          Unresolved non-hydrogen planarities: 61
    Chain: "O"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "B"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 6.80, per 1000 atoms: 0.72
  Number of scatterers: 9478
  At special positions: 0
  Unit cell: (100.86, 74.62, 128.74, 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      64     16.00
     O    1728      8.00
     N    1510      7.00
     C    6176      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 117 " - pdb=" SG  CYS A 207 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 256 " distance=2.03
    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 117 " - pdb=" SG  CYS B 207 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 197 " - pdb=" SG  CYS B 256 " 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
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG O   1 " - " NAG O   2 "
    NAG-ASN
      " NAG A 901 " - " ASN A  27 "
      " NAG A 902 " - " ASN A  60 "
      " NAG A 903 " - " ASN A 123 "
      " NAG A 904 " - " ASN A 141 "
      " NAG B 901 " - " ASN B  27 "
      " NAG B 902 " - " ASN B  60 "
      " NAG B 903 " - " ASN B 123 "
      " NAG B 904 " - " ASN B 141 "
      " NAG C   1 " - " ASN A 165 "
      " NAG D   1 " - " ASN B  54 "
      " NAG E   1 " - " ASN B 165 "
      " NAG O   1 " - " ASN A  54 "
  Time building additional restraints: 2.95
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2244

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      45.7% alpha, 19.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 289 through 317
      removed outlier: 4.102A  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 462 through 479
    Processing helix  chain 'A' and resid 499 through 505
      removed outlier: 3.609A  pdb=" N   ILE A 503 " --> pdb=" O   ALA A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.705A  pdb=" N   ILE A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 569
      removed outlier: 3.623A  pdb=" N   LEU A 562 " --> pdb=" O   MET A 558 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ALA A 565 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 596
      removed outlier: 3.911A  pdb=" N   THR A 580 " --> pdb=" O   PHE A 576 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   PHE A 582 " --> pdb=" O   PHE A 578 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   MET A 583 " --> pdb=" O   ASP A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 626
      removed outlier: 4.369A  pdb=" N   PHE A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 652
      removed outlier: 3.916A  pdb=" N   SER A 638 " --> pdb=" O   TRP A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 709
      removed outlier: 3.889A  pdb=" N   MET A 709 " --> pdb=" O   TYR A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 740
      removed outlier: 3.524A  pdb=" N   LEU A 719 " --> pdb=" O   ALA A 715 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 767
      removed outlier: 3.509A  pdb=" N   PHE A 761 " --> pdb=" O   VAL A 757 " (cutoff:3.500A)
    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
    Processing helix  chain 'B' and resid 289 through 317
      removed outlier: 4.171A  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 462 through 479
    Processing helix  chain 'B' and resid 499 through 505
      removed outlier: 3.609A  pdb=" N   ILE B 503 " --> pdb=" O   ALA B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.705A  pdb=" N   ILE B 510 " --> pdb=" O   ASN B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 548 through 569
      removed outlier: 3.622A  pdb=" N   LEU B 562 " --> pdb=" O   MET B 558 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   ALA B 565 " --> pdb=" O   GLY B 561 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 576 through 596
      removed outlier: 4.131A  pdb=" N   THR B 580 " --> pdb=" O   PHE B 576 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   PHE B 582 " --> pdb=" O   PHE B 578 " (cutoff:3.500A)
      removed outlier: 5.573A  pdb=" N   MET B 583 " --> pdb=" O   ASP B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 626
      removed outlier: 4.369A  pdb=" N   PHE B 626 " --> pdb=" O   LEU B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 652
      removed outlier: 3.916A  pdb=" N   SER B 638 " --> pdb=" O   TRP B 634 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 709
      removed outlier: 3.889A  pdb=" N   MET B 709 " --> pdb=" O   TYR B 705 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 740
      removed outlier: 3.524A  pdb=" N   LEU B 719 " --> pdb=" O   ALA B 715 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 745 through 767
      removed outlier: 3.509A  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
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31
      removed outlier: 3.815A  pdb=" N   VAL A  57 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU A 126 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 43
      removed outlier: 3.952A  pdb=" N   GLY A  64 " --> pdb=" O   MET A 151 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 100
      removed outlier: 6.160A  pdb=" N   LYS A 106 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 161 through 166
    Processing sheet with id=AA5, first strand: chain 'A' and resid 172 through 176
    Processing sheet with id=AA6, first strand: chain 'B' and resid 27 through 31
      removed outlier: 3.814A  pdb=" N   VAL B  57 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   GLU B 126 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 43
      removed outlier: 3.952A  pdb=" N   GLY B  64 " --> pdb=" O   MET B 151 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 97 through 100
      removed outlier: 6.160A  pdb=" N   LYS B 106 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 155 through 156
    Processing sheet with id=AB1, first strand: chain 'B' and resid 161 through 166

    563 hydrogen bonds defined for protein.
    1635 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: 3.48

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2857
        1.34 -     1.46: 2219
        1.46 -     1.58: 4510
        1.58 -     1.71: 0
        1.71 -     1.83: 96
  Bond restraints: 9682
  Sorted by residual:
  bond pdb=" N   VAL B 182 "
       pdb=" CA  VAL B 182 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.037 1.24e-02 6.50e+03 8.72e+00
  bond pdb=" N   VAL A 182 "
       pdb=" CA  VAL A 182 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.24e-02 6.50e+03 8.53e+00
  bond pdb=" N   VAL A 288 "
       pdb=" CA  VAL A 288 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.19e-02 7.06e+03 7.15e+00
  bond pdb=" N   THR A 289 "
       pdb=" CA  THR A 289 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.14e-02 7.69e+03 6.64e+00
  bond pdb=" N   THR B 289 "
       pdb=" CA  THR B 289 "
    ideal  model  delta    sigma   weight residual
    1.456  1.485 -0.029 1.14e-02 7.69e+03 6.60e+00
  ... (remaining 9677 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 12651
        1.70 -     3.39: 455
        3.39 -     5.09: 48
        5.09 -     6.79: 10
        6.79 -     8.49: 4
  Bond angle restraints: 13168
  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  124.39   -4.41 1.11e+00 8.12e-01 1.58e+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  124.37   -4.39 1.11e+00 8.12e-01 1.56e+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  124.35   -4.37 1.11e+00 8.12e-01 1.55e+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  124.22   -4.24 1.11e+00 8.12e-01 1.46e+01
  angle pdb=" CA  GLN B 577 "
        pdb=" C   GLN B 577 "
        pdb=" O   GLN B 577 "
      ideal   model   delta    sigma   weight residual
     120.90  117.47    3.43 1.07e+00 8.73e-01 1.03e+01
  ... (remaining 13163 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.19: 5051
       16.19 -    32.38: 638
       32.38 -    48.57: 171
       48.57 -    64.77: 46
       64.77 -    80.96: 10
  Dihedral angle restraints: 5916
    sinusoidal: 2460
      harmonic: 3456
  Sorted by residual:
  dihedral pdb=" CB  CYS A 117 "
           pdb=" SG  CYS A 117 "
           pdb=" SG  CYS A 207 "
           pdb=" CB  CYS A 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.67  -30.67     1      1.00e+01 1.00e-02 1.34e+01
  dihedral pdb=" CB  CYS B 117 "
           pdb=" SG  CYS B 117 "
           pdb=" SG  CYS B 207 "
           pdb=" CB  CYS B 207 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.67  -30.67     1      1.00e+01 1.00e-02 1.34e+01
  dihedral pdb=" CA  LEU A 691 "
           pdb=" CB  LEU A 691 "
           pdb=" CG  LEU A 691 "
           pdb=" CD1 LEU A 691 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.40   59.60     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1144
       0.046 -    0.091: 322
       0.091 -    0.137: 99
       0.137 -    0.183: 33
       0.183 -    0.228: 8
  Chirality restraints: 1606
  Sorted by residual:
  chirality pdb=" CB  VAL A 288 "
            pdb=" CA  VAL A 288 "
            pdb=" CG1 VAL A 288 "
            pdb=" CG2 VAL A 288 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.40   -0.23 2.00e-01 2.50e+01 1.30e+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
  chirality pdb=" CB  THR B 311 "
            pdb=" CA  THR B 311 "
            pdb=" OG1 THR B 311 "
            pdb=" CG2 THR B 311 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1603 not shown)

  Planarity restraints: 1636
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 308 "    0.070 2.00e-02 2.50e+03   4.39e-02 3.85e+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 "   -0.036 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 "    0.008 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 B 304 "   -0.040 2.00e-02 2.50e+03   2.56e-02 1.15e+01
        pdb=" CG  PHE B 304 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 304 "    0.026 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 304 "    0.028 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 304 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 304 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 304 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 1633 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1024
        2.75 -     3.29: 9372
        3.29 -     3.82: 15464
        3.82 -     4.36: 17587
        4.36 -     4.90: 30611
  Nonbonded interactions: 74058
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 194 "
            pdb=" OG1 THR B 226 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   ALA A 194 "
            pdb=" OG1 THR A 226 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" NZ  LYS A  26 "
            pdb=" NH2 ARG B  85 "
     model   vdw
     2.218 3.200
  nonbonded pdb=" OD1 ASN A 165 "
            pdb=" OG1 THR A 279 "
     model   vdw
     2.243 3.040
  nonbonded pdb=" OD1 ASN B 165 "
            pdb=" OG1 THR B 279 "
     model   vdw
     2.243 3.040
  ... (remaining 74053 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'O'
}

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:             3.380
  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:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     26.990
  Find NCS groups from input model:        0.350
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
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   0.064   9706  Z= 0.282
  Angle     :  0.733   8.552  13232  Z= 0.432
  Chirality :  0.050   0.228   1606
  Planarity :  0.004   0.044   1624
  Dihedral  : 15.767  80.958   3648
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 23.14 %
    Favored  : 76.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.24), residues: 1152
  helix:  1.76 (0.22), residues: 516
  sheet:  1.64 (0.28), residues: 272
  loop : -1.93 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 773 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.040   0.003   PHE B 304 
 TYR   0.078   0.003   TYR B 308 
 ARG   0.001   0.000   ARG B 114 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00526 (   12)
  link_NAG-ASN         : angle       2.92283 (   36)
  link_BETA1-4         : bond        0.00300 (    4)
  link_BETA1-4         : angle       0.94404 (   12)
  hydrogen bonds       : bond        0.11408 (  563)
  hydrogen bonds       : angle       5.25002 ( 1635)
  SS BOND              : bond        0.00381 (    8)
  SS BOND              : angle       1.53476 (   16)
  covalent geometry    : bond        0.00511 ( 9682)
  covalent geometry    : angle       0.71602 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 128
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.7034 (tpp80) cc_final: 0.6649 (mtm-85)
REVERT: A  297 MET cc_start: 0.7435 (mtt) cc_final: 0.7113 (tpp)
REVERT: B   61 ARG cc_start: 0.6910 (tpp80) cc_final: 0.6580 (mtm-85)
REVERT: B  297 MET cc_start: 0.7533 (mtt) cc_final: 0.7165 (tpp)
  outliers start: 4
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2280
  time to fit residues: 43.2231
Evaluate side-chains
  111 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.3980
   chunk 87 optimal weight:    7.9990
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 90 optimal weight:    0.0870
   chunk 35 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 105 optimal weight:   10.0000
   overall best weight:    1.0964

-------------------------------------------------------------------------------
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 = 0.4491 r_free = 0.4491 target = 0.217682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.168697 restraints weight = 11081.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3984 rms_B_bonded: 3.70
r_work: 0.3649 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.0821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9706  Z= 0.158
  Angle     :  0.554   7.597  13232  Z= 0.285
  Chirality :  0.042   0.167   1606
  Planarity :  0.003   0.028   1624
  Dihedral  :  6.023  51.881   1590
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 24.41 %
    Favored  : 73.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.32 (0.24), residues: 1152
  helix:  2.25 (0.21), residues: 520
  sheet:  1.40 (0.29), residues: 280
  loop : -1.81 (0.30), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 773 
 HIS   0.004   0.001   HIS A  55 
 PHE   0.019   0.002   PHE A 304 
 TYR   0.014   0.001   TYR B 173 
 ARG   0.007   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00452 (   12)
  link_NAG-ASN         : angle       2.67752 (   36)
  link_BETA1-4         : bond        0.00477 (    4)
  link_BETA1-4         : angle       0.96359 (   12)
  hydrogen bonds       : bond        0.04482 (  563)
  hydrogen bonds       : angle       4.46573 ( 1635)
  SS BOND              : bond        0.00354 (    8)
  SS BOND              : angle       1.10209 (   16)
  covalent geometry    : bond        0.00366 ( 9682)
  covalent geometry    : angle       0.53519 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 137
  time to evaluate  : 0.969 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8279 (ttm-80)
REVERT: A  297 MET cc_start: 0.7695 (mtt) cc_final: 0.7148 (tpp)
REVERT: A  736 MET cc_start: 0.7258 (mmm) cc_final: 0.6729 (mtt)
REVERT: B  297 MET cc_start: 0.7704 (mtt) cc_final: 0.7177 (tpp)
REVERT: B  817 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7379 (tp)
  outliers start: 20
  outliers final: 7
  residues processed: 151
  average time/residue: 0.1755
  time to fit residues: 39.5414
Evaluate side-chains
  128 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    4.9990
   chunk 104 optimal weight:    9.9990
   chunk 19 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 85 optimal weight:    5.9990
   chunk 94 optimal weight:    0.8980
   chunk 89 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 506 ASN
** A 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 796 HIS
B 506 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.216560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.169904 restraints weight = 11204.935|
|-----------------------------------------------------------------------------|
r_work (start): 0.3998 rms_B_bonded: 3.67
r_work: 0.3658 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7794
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   9706  Z= 0.203
  Angle     :  0.566   7.081  13232  Z= 0.293
  Chirality :  0.044   0.165   1606
  Planarity :  0.003   0.031   1624
  Dihedral  :  5.634  41.654   1590
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.25 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.45 (0.24), residues: 1152
  helix:  2.45 (0.21), residues: 514
  sheet:  1.32 (0.29), residues: 280
  loop : -1.69 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 773 
 HIS   0.004   0.001   HIS B  55 
 PHE   0.016   0.002   PHE B 516 
 TYR   0.015   0.001   TYR B 173 
 ARG   0.005   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00445 (   12)
  link_NAG-ASN         : angle       2.55131 (   36)
  link_BETA1-4         : bond        0.00182 (    4)
  link_BETA1-4         : angle       1.03002 (   12)
  hydrogen bonds       : bond        0.04195 (  563)
  hydrogen bonds       : angle       4.43104 ( 1635)
  SS BOND              : bond        0.00426 (    8)
  SS BOND              : angle       1.10741 (   16)
  covalent geometry    : bond        0.00487 ( 9682)
  covalent geometry    : angle       0.54875 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 127
  time to evaluate  : 1.014 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8324 (ttm-80)
REVERT: A  214 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.7290 (p0)
REVERT: A  297 MET cc_start: 0.7736 (mtt) cc_final: 0.7246 (tpp)
REVERT: B   61 ARG cc_start: 0.7074 (tpp-160) cc_final: 0.6443 (mtm-85)
REVERT: B  100 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.8326 (ttm-80)
REVERT: B  214 ASN cc_start: 0.8769 (OUTLIER) cc_final: 0.7366 (p0)
REVERT: B  297 MET cc_start: 0.7766 (mtt) cc_final: 0.7383 (tpp)
REVERT: B  817 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7426 (tp)
  outliers start: 47
  outliers final: 26
  residues processed: 163
  average time/residue: 0.1802
  time to fit residues: 43.6873
Evaluate side-chains
  142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 111
  time to evaluate  : 1.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  283 LEU
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  574 THR
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 37 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 14 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 104 GLN
B 796 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.217825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.169996 restraints weight = 11181.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.4011 rms_B_bonded: 3.43
r_work: 0.3703 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9706  Z= 0.146
  Angle     :  0.514   6.663  13232  Z= 0.266
  Chirality :  0.042   0.176   1606
  Planarity :  0.003   0.030   1624
  Dihedral  :  5.220  37.118   1590
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.73 %
    Allowed  : 24.41 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.54 (0.24), residues: 1152
  helix:  2.56 (0.21), residues: 514
  sheet:  1.30 (0.29), residues: 280
  loop : -1.66 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 773 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.019   0.001   PHE B 801 
 TYR   0.013   0.001   TYR B 173 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00440 (   12)
  link_NAG-ASN         : angle       2.37852 (   36)
  link_BETA1-4         : bond        0.00286 (    4)
  link_BETA1-4         : angle       1.02991 (   12)
  hydrogen bonds       : bond        0.03809 (  563)
  hydrogen bonds       : angle       4.25047 ( 1635)
  SS BOND              : bond        0.00329 (    8)
  SS BOND              : angle       1.05879 (   16)
  covalent geometry    : bond        0.00339 ( 9682)
  covalent geometry    : angle       0.49783 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 126
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8272 (ttm-80)
REVERT: A  297 MET cc_start: 0.7653 (mtt) cc_final: 0.7250 (tpp)
REVERT: B  100 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8262 (ttm-80)
REVERT: B  297 MET cc_start: 0.7747 (mtt) cc_final: 0.7365 (tpp)
REVERT: B  817 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7428 (tp)
  outliers start: 38
  outliers final: 18
  residues processed: 155
  average time/residue: 0.1713
  time to fit residues: 39.5039
Evaluate side-chains
  139 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 118
  time to evaluate  : 0.979 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  175 LYS
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  812 LEU
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 104 optimal weight:    9.9990
   chunk 113 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 115 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 45 optimal weight:    9.9990
   chunk 76 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 87 optimal weight:   10.0000
   overall best weight:    1.6986

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.216120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.168881 restraints weight = 11176.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3992 rms_B_bonded: 3.70
r_work: 0.3654 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1827

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   9706  Z= 0.191
  Angle     :  0.576  13.060  13232  Z= 0.289
  Chirality :  0.043   0.186   1606
  Planarity :  0.003   0.030   1624
  Dihedral  :  5.094  36.137   1590
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 24.41 %
    Favored  : 71.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.54 (0.24), residues: 1152
  helix:  2.54 (0.21), residues: 514
  sheet:  1.29 (0.29), residues: 280
  loop : -1.62 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 773 
 HIS   0.004   0.001   HIS B 492 
 PHE   0.019   0.002   PHE A 801 
 TYR   0.014   0.001   TYR B 173 
 ARG   0.005   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00405 (   12)
  link_NAG-ASN         : angle       2.32031 (   36)
  link_BETA1-4         : bond        0.00237 (    4)
  link_BETA1-4         : angle       1.08939 (   12)
  hydrogen bonds       : bond        0.03923 (  563)
  hydrogen bonds       : angle       4.29941 ( 1635)
  SS BOND              : bond        0.00415 (    8)
  SS BOND              : angle       1.14125 (   16)
  covalent geometry    : bond        0.00458 ( 9682)
  covalent geometry    : angle       0.56184 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 123
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8332 (ttm-80)
REVERT: A  297 MET cc_start: 0.7681 (mtt) cc_final: 0.7341 (tpp)
REVERT: B   61 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6467 (mpp-170)
REVERT: B  100 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.8313 (ttm-80)
REVERT: B  297 MET cc_start: 0.7737 (mtt) cc_final: 0.7375 (tpp)
REVERT: B  514 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7115 (tt)
REVERT: B  586 ILE cc_start: 0.8530 (tt) cc_final: 0.8297 (tp)
  outliers start: 39
  outliers final: 30
  residues processed: 154
  average time/residue: 0.1740
  time to fit residues: 39.7726
Evaluate side-chains
  148 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 115
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain A residue  802 LEU
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  137 LEU
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  475 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  514 LEU
Chi-restraints excluded: chain B residue  549 LEU
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  574 THR
Chi-restraints excluded: chain B residue  589 LEU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 48 optimal weight:    0.0010
   chunk 4 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 55 optimal weight:    0.6980
   chunk 63 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 113 optimal weight:    0.3980
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 575 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.219537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.172623 restraints weight = 11159.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.4032 rms_B_bonded: 3.55
r_work: 0.3711 rms_B_bonded: 3.97 restraints_weight: 0.5000
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9706  Z= 0.107
  Angle     :  0.539  15.985  13232  Z= 0.264
  Chirality :  0.041   0.173   1606
  Planarity :  0.003   0.029   1624
  Dihedral  :  4.718  34.520   1590
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 25.88 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.58 (0.24), residues: 1152
  helix:  2.60 (0.21), residues: 514
  sheet:  1.35 (0.29), residues: 280
  loop : -1.68 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 773 
 HIS   0.002   0.001   HIS B  55 
 PHE   0.018   0.001   PHE A 801 
 TYR   0.012   0.001   TYR A 308 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00425 (   12)
  link_NAG-ASN         : angle       2.09774 (   36)
  link_BETA1-4         : bond        0.00345 (    4)
  link_BETA1-4         : angle       1.02284 (   12)
  hydrogen bonds       : bond        0.03480 (  563)
  hydrogen bonds       : angle       4.12667 ( 1635)
  SS BOND              : bond        0.00388 (    8)
  SS BOND              : angle       0.89157 (   16)
  covalent geometry    : bond        0.00230 ( 9682)
  covalent geometry    : angle       0.52715 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.993 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6527 (mpp-170)
REVERT: A  297 MET cc_start: 0.7594 (mtt) cc_final: 0.7238 (tpp)
REVERT: B   61 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6605 (mpp-170)
REVERT: B  100 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8187 (ttm-80)
REVERT: B  297 MET cc_start: 0.7616 (mtt) cc_final: 0.7375 (tpp)
REVERT: B  586 ILE cc_start: 0.8539 (tt) cc_final: 0.8273 (tp)
  outliers start: 27
  outliers final: 16
  residues processed: 155
  average time/residue: 0.1718
  time to fit residues: 39.5706
Evaluate side-chains
  138 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  175 LYS
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 14 optimal weight:    0.8980
   chunk 100 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 106 optimal weight:    0.4980
   chunk 115 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 97 optimal weight:    0.3980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4485 r_free = 0.4485 target = 0.216091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.165341 restraints weight = 11267.179|
|-----------------------------------------------------------------------------|
r_work (start): 0.3970 rms_B_bonded: 3.66
r_work: 0.3663 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9706  Z= 0.120
  Angle     :  0.564  15.191  13232  Z= 0.271
  Chirality :  0.041   0.168   1606
  Planarity :  0.003   0.027   1624
  Dihedral  :  4.585  32.782   1590
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 26.37 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.61 (0.24), residues: 1152
  helix:  2.63 (0.21), residues: 514
  sheet:  1.36 (0.29), residues: 280
  loop : -1.66 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 773 
 HIS   0.003   0.001   HIS B  55 
 PHE   0.021   0.001   PHE B 801 
 TYR   0.011   0.001   TYR A 308 
 ARG   0.004   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00401 (   12)
  link_NAG-ASN         : angle       2.03310 (   36)
  link_BETA1-4         : bond        0.00325 (    4)
  link_BETA1-4         : angle       1.04765 (   12)
  hydrogen bonds       : bond        0.03474 (  563)
  hydrogen bonds       : angle       4.08267 ( 1635)
  SS BOND              : bond        0.00197 (    8)
  SS BOND              : angle       0.98454 (   16)
  covalent geometry    : bond        0.00271 ( 9682)
  covalent geometry    : angle       0.55342 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 MET cc_start: 0.7682 (mtt) cc_final: 0.7127 (tpp)
REVERT: A  574 THR cc_start: 0.8031 (p) cc_final: 0.7782 (p)
REVERT: B   61 ARG cc_start: 0.7109 (tpp80) cc_final: 0.6463 (mtm-85)
REVERT: B  100 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8162 (ttm-80)
REVERT: B  297 MET cc_start: 0.7660 (mtt) cc_final: 0.7221 (tpp)
REVERT: B  586 ILE cc_start: 0.8308 (tt) cc_final: 0.8081 (tp)
  outliers start: 23
  outliers final: 19
  residues processed: 143
  average time/residue: 0.1715
  time to fit residues: 36.7033
Evaluate side-chains
  138 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0770
   chunk 64 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   chunk 99 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 74 optimal weight:    0.7980
   chunk 33 optimal weight:    0.0980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.4738

-------------------------------------------------------------------------------
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 = 0.4523 r_free = 0.4523 target = 0.218382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.165180 restraints weight = 11424.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3977 rms_B_bonded: 4.36
r_work: 0.3691 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9706  Z= 0.104
  Angle     :  0.547  14.549  13232  Z= 0.263
  Chirality :  0.041   0.165   1606
  Planarity :  0.003   0.027   1624
  Dihedral  :  4.343  30.128   1590
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 26.96 %
    Favored  : 70.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.68 (0.24), residues: 1152
  helix:  2.67 (0.21), residues: 514
  sheet:  1.45 (0.29), residues: 280
  loop : -1.66 (0.31), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 759 
 HIS   0.002   0.001   HIS A  55 
 PHE   0.026   0.001   PHE A 801 
 TYR   0.013   0.001   TYR A 308 
 ARG   0.003   0.000   ARG B  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00396 (   12)
  link_NAG-ASN         : angle       1.91513 (   36)
  link_BETA1-4         : bond        0.00366 (    4)
  link_BETA1-4         : angle       1.02602 (   12)
  hydrogen bonds       : bond        0.03305 (  563)
  hydrogen bonds       : angle       3.98951 ( 1635)
  SS BOND              : bond        0.00230 (    8)
  SS BOND              : angle       0.96041 (   16)
  covalent geometry    : bond        0.00226 ( 9682)
  covalent geometry    : angle       0.53748 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.071 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6432 (mpp-170)
REVERT: A  297 MET cc_start: 0.7646 (mtt) cc_final: 0.7086 (tpp)
REVERT: A  574 THR cc_start: 0.7993 (p) cc_final: 0.7760 (p)
REVERT: B   61 ARG cc_start: 0.7051 (tpp80) cc_final: 0.6410 (mtm-85)
REVERT: B  297 MET cc_start: 0.7683 (mtt) cc_final: 0.7125 (tpp)
REVERT: B  562 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.7181 (mm)
REVERT: B  586 ILE cc_start: 0.8180 (tt) cc_final: 0.7890 (tp)
  outliers start: 22
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1751
  time to fit residues: 38.0211
Evaluate side-chains
  142 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  589 LEU
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  562 LEU
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 29 optimal weight:    8.9990
   chunk 104 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0570
   chunk 36 optimal weight:    5.9990
   overall best weight:    2.0106

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4607 r_free = 0.4607 target = 0.219933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4125 r_free = 0.4125 target = 0.168875 restraints weight = 11228.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 4.36
r_work: 0.3766 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   9706  Z= 0.215
  Angle     :  0.614  14.257  13232  Z= 0.301
  Chirality :  0.044   0.237   1606
  Planarity :  0.003   0.031   1624
  Dihedral  :  4.518  28.664   1590
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 26.37 %
    Favored  : 71.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.57 (0.24), residues: 1152
  helix:  2.61 (0.21), residues: 514
  sheet:  1.22 (0.29), residues: 286
  loop : -1.65 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 799 
 HIS   0.004   0.001   HIS B  55 
 PHE   0.027   0.002   PHE B  82 
 TYR   0.016   0.002   TYR A 173 
 ARG   0.005   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00340 (   12)
  link_NAG-ASN         : angle       2.10634 (   36)
  link_BETA1-4         : bond        0.00177 (    4)
  link_BETA1-4         : angle       1.15038 (   12)
  hydrogen bonds       : bond        0.03806 (  563)
  hydrogen bonds       : angle       4.24288 ( 1635)
  SS BOND              : bond        0.00363 (    8)
  SS BOND              : angle       1.39827 (   16)
  covalent geometry    : bond        0.00518 ( 9682)
  covalent geometry    : angle       0.60217 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 1.117 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8060 (ttm-80)
REVERT: A  297 MET cc_start: 0.7695 (mtt) cc_final: 0.7246 (tpp)
REVERT: A  577 GLN cc_start: 0.8041 (pm20) cc_final: 0.7704 (pm20)
REVERT: B   61 ARG cc_start: 0.7007 (tpp80) cc_final: 0.6499 (mtm-85)
REVERT: B  100 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8065 (ttm-80)
REVERT: B  297 MET cc_start: 0.7772 (mtt) cc_final: 0.7342 (tpp)
REVERT: B  586 ILE cc_start: 0.8328 (tt) cc_final: 0.8027 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 136
  average time/residue: 0.1827
  time to fit residues: 37.1392
Evaluate side-chains
  135 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  100 ARG
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  136 THR
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue  100 ARG
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 41 optimal weight:    8.9990
   chunk 115 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0040
   chunk 9 optimal weight:    0.3980
   chunk 1 optimal weight:    0.7980
   chunk 57 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.217086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.164934 restraints weight = 11454.607|
|-----------------------------------------------------------------------------|
r_work (start): 0.3976 rms_B_bonded: 3.98
r_work: 0.3670 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9706  Z= 0.112
  Angle     :  0.556  14.103  13232  Z= 0.269
  Chirality :  0.041   0.184   1606
  Planarity :  0.003   0.028   1624
  Dihedral  :  4.279  26.690   1590
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 26.86 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.65 (0.24), residues: 1152
  helix:  2.66 (0.21), residues: 514
  sheet:  1.43 (0.29), residues: 274
  loop : -1.63 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 634 
 HIS   0.003   0.001   HIS A  55 
 PHE   0.025   0.001   PHE B  82 
 TYR   0.015   0.001   TYR B 308 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00364 (   12)
  link_NAG-ASN         : angle       1.88793 (   36)
  link_BETA1-4         : bond        0.00358 (    4)
  link_BETA1-4         : angle       1.04148 (   12)
  hydrogen bonds       : bond        0.03406 (  563)
  hydrogen bonds       : angle       4.07923 ( 1635)
  SS BOND              : bond        0.00223 (    8)
  SS BOND              : angle       1.12135 (   16)
  covalent geometry    : bond        0.00249 ( 9682)
  covalent geometry    : angle       0.54583 (13168)

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 128
  time to evaluate  : 0.957 
Fit side-chains
   revert: symmetry clash
REVERT: A  297 MET cc_start: 0.7698 (mtt) cc_final: 0.7069 (tpp)
REVERT: A  577 GLN cc_start: 0.7983 (pm20) cc_final: 0.7634 (pm20)
REVERT: B   61 ARG cc_start: 0.6983 (tpp80) cc_final: 0.6392 (mtm-85)
REVERT: B  297 MET cc_start: 0.7691 (mtt) cc_final: 0.7190 (tpp)
REVERT: B  586 ILE cc_start: 0.8187 (tt) cc_final: 0.7912 (tp)
  outliers start: 22
  outliers final: 21
  residues processed: 145
  average time/residue: 0.1907
  time to fit residues: 41.8379
Evaluate side-chains
  144 residues out of total 1052 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 1.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  127 ILE
Chi-restraints excluded: chain A residue  214 ASN
Chi-restraints excluded: chain A residue  233 VAL
Chi-restraints excluded: chain A residue  242 SER
Chi-restraints excluded: chain A residue  289 THR
Chi-restraints excluded: chain A residue  498 SER
Chi-restraints excluded: chain A residue  717 TYR
Chi-restraints excluded: chain A residue  751 CYS
Chi-restraints excluded: chain B residue  116 LEU
Chi-restraints excluded: chain B residue  127 ILE
Chi-restraints excluded: chain B residue  136 THR
Chi-restraints excluded: chain B residue  214 ASN
Chi-restraints excluded: chain B residue  233 VAL
Chi-restraints excluded: chain B residue  242 SER
Chi-restraints excluded: chain B residue  289 THR
Chi-restraints excluded: chain B residue  498 SER
Chi-restraints excluded: chain B residue  717 TYR
Chi-restraints excluded: chain B residue  751 CYS
Chi-restraints excluded: chain B residue  817 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0270
   chunk 21 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 83 optimal weight:    3.9990
   chunk 102 optimal weight:   20.0000
   chunk 12 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.7240

-------------------------------------------------------------------------------
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 = 0.4509 r_free = 0.4509 target = 0.216988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.164693 restraints weight = 11424.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3973 rms_B_bonded: 3.98
r_work: 0.3667 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7624
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9706  Z= 0.119
  Angle     :  0.551  13.515  13232  Z= 0.267
  Chirality :  0.042   0.184   1606
  Planarity :  0.003   0.030   1624
  Dihedral  :  4.093  25.255   1590
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 26.86 %
    Favored  : 70.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.79 %
    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:  1.66 (0.24), residues: 1152
  helix:  2.72 (0.21), residues: 514
  sheet:  1.44 (0.29), residues: 276
  loop : -1.75 (0.31), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 773 
 HIS   0.003   0.001   HIS B  55 
 PHE   0.024   0.001   PHE B  82 
 TYR   0.012   0.001   TYR B 308 
 ARG   0.004   0.000   ARG A  85 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00351 (   12)
  link_NAG-ASN         : angle       1.82833 (   36)
  link_BETA1-4         : bond        0.00312 (    4)
  link_BETA1-4         : angle       1.05184 (   12)
  hydrogen bonds       : bond        0.03344 (  563)
  hydrogen bonds       : angle       4.01841 ( 1635)
  SS BOND              : bond        0.00214 (    8)
  SS BOND              : angle       1.16315 (   16)
  covalent geometry    : bond        0.00273 ( 9682)
  covalent geometry    : angle       0.54174 (13168)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4939.58 seconds
wall clock time: 86 minutes 27.05 seconds (5187.05 seconds total)