Starting phenix.real_space_refine
on Tue Mar  3 19:36:07 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d2w_27152/03_2026/8d2w_27152.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      34      5.16       5
     C    4501      2.51       5
     N    1026      2.21       5
     O    1296      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6858
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3442
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 115
      Conformer: "B"
        Number of residues, atoms: 460, 3417
          Classifications: {'peptide': 460}
          Incomplete info: {'truncation_to_alanine': 49}
          Link IDs: {'PTRANS': 20, 'TRANS': 439}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 186
          Unresolved non-hydrogen angles: 224
          Unresolved non-hydrogen dihedrals: 157
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 6, 'GLN:plan1': 6, 'HIS:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 115
          bond proxies already assigned to first conformer: 3476
    Chain: "B"
      Number of atoms: 1404
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
      Conformer: "B"
        Number of residues, atoms: 201, 1393
          Classifications: {'peptide': 201}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 14, 'TRANS': 186}
          Unresolved non-hydrogen bonds: 60
          Unresolved non-hydrogen angles: 71
          Unresolved non-hydrogen dihedrals: 49
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASN:plan1': 4, 'GLN:plan1': 3, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 31
          bond proxies already assigned to first conformer: 1419
    Chain: "C"
      Number of atoms: 1419
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 203, 1408
          Classifications: {'peptide': 203}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 12, 'TRANS': 190}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 1436
    Chain: "A"
      Number of atoms: 553
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
      Conformer: "B"
        Number of residues, atoms: 15, 448
          Unusual residues: {'LMT': 14, 'ZGS': 1}
          Classifications: {'undetermined': 15}
          Link IDs: {None: 14}
          Unresolved non-hydrogen bonds: 84
          Unresolved non-hydrogen angles: 126
          Unresolved non-hydrogen dihedrals: 179
          Unresolved non-hydrogen chiralities: 35
          bond proxies already assigned to first conformer: 346
    Chain: "C"
      Number of atoms: 35
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 35
          Unusual residues: {'LMT': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Classifications: {'water': 5}
          Link IDs: {None: 4}
  Residues with excluded nonbonded symmetry interactions: 7
    residue:
      pdb=" N  ATRP A 346 " occ=0.50
      ... (26 atoms not shown)
      pdb=" CH2BTRP A 346 " occ=0.50
    residue:
      pdb=" N  APHE A 449 " occ=0.50
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 449 " occ=0.50
    residue:
      pdb=" N  AARG B 191 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG B 191 " occ=0.50
    residue:
      pdb=" N  AARG C  13 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG C  13 " occ=0.50
    residue:
      pdb=" C1 ALMT A 602 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 602 " occ=0.50
    residue:
      pdb=" C1 ALMT A 603 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 603 " occ=0.50
    residue:
      pdb=" C1 ALMT A 610 " occ=0.50
      ... (68 atoms not shown)
      pdb=" O6BBLMT A 610 " occ=0.50
  Time building chain proxies: 2.99, per 1000 atoms: 0.44
  Number of scatterers: 6858
  At special positions: 0
  Unit cell: (69.208, 73.428, 141.792, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      34     16.00
     P       1     15.00
     O    1296      8.00
     N    1026      7.00
     C    4501      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  86 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 186 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 139 " - pdb=" SG  CYS C 186 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 495.5 milliseconds
  

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 10 sheets defined
      45.5% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 46
    Processing helix  chain 'A' and resid 47 through 67
      removed outlier: 3.998A  pdb=" N   GLN A  51 " --> pdb=" O   GLY A  47 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   GLN A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ILE A  63 " --> pdb=" O   PHE A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 100
      removed outlier: 4.021A  pdb=" N   ALA A  88 " --> pdb=" O   ARG A  84 " (cutoff:3.500A)
      Proline residue:  A  92  - end of helix
    Processing helix  chain 'A' and resid 109 through 128
      Proline residue:  A 118  - end of helix
      removed outlier: 3.715A  pdb=" N   TRP A 128 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 162
      Proline residue:  A 158  - end of helix
    Processing helix  chain 'A' and resid 163 through 165
      No H-bonds generated for 'chain 'A' and resid 163 through 165'
    Processing helix  chain 'A' and resid 169 through 200
    Processing helix  chain 'A' and resid 232 through 262
      removed outlier: 3.512A  pdb=" N   VAL A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 288
    Processing helix  chain 'A' and resid 288 through 311
    Processing helix  chain 'A' and resid 312 through 319
    Processing helix  chain 'A' and resid 325 through 352
      Proline residue:  A 342  - end of helix
      removed outlier: 3.770A  pdb=" N   THR A 349 " --> pdb=" O   GLN A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 371
      removed outlier: 3.664A  pdb=" N   THR A 361 " --> pdb=" O   VAL A 357 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   VAL A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   VAL A 365 " --> pdb=" O   THR A 361 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'A' and resid 377 through 414
      removed outlier: 3.535A  pdb=" N   TYR A 382 " --> pdb=" O   LEU A 378 " (cutoff:3.500A)
      Proline residue:  A 399  - end of helix
      Proline residue:  A 404  - end of helix
    Processing helix  chain 'A' and resid 419 through 451
      removed outlier: 3.542A  pdb=" N   TYR A 425 " --> pdb=" O   GLU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 473
      removed outlier: 3.574A  pdb=" N   LEU A 465 " --> pdb=" O   GLY A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 488
      removed outlier: 3.570A  pdb=" N   SER A 488 " --> pdb=" O   LEU A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 507
      removed outlier: 3.644A  pdb=" N   GLN A 497 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   GLY A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 5.522A  pdb=" N   ASN A 499 " --> pdb=" O   LYS A 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 123
    Processing helix  chain 'C' and resid 28 through 31
    Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 12
      removed outlier: 5.976A  pdb=" N   LYS B  11 " --> pdb=" O   ASN B 102 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   VAL B  32 " --> pdb=" O   TYR B  48 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   TYR B  48 " --> pdb=" O   VAL B  32 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   TRP B  34 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 112 through 114
      removed outlier: 4.858A  pdb=" N   ALA B 127 " --> pdb=" O   ILE B 174 " (cutoff:3.500A)
      removed outlier: 7.185A  pdb=" N   ILE B 174 " --> pdb=" O   ALA B 127 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   VAL B 129 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   LEU B 172 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
      removed outlier: 5.534A  pdb=" N   PHE B 131 " --> pdb=" O   ALA B 170 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ALA B 170 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 5.434A  pdb=" N   MET B 168 " --> pdb=" O   PRO B 133 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 149
      removed outlier: 4.658A  pdb=" N   TRP B 143 " --> pdb=" O   GLN B 149 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.646A  pdb=" N   GLU C   5 " --> pdb=" O   LYS C  23 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 35
    Processing sheet with id=AA7, first strand: chain 'C' and resid 89 through 91
    Processing sheet with id=AA8, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 123
      removed outlier: 5.886A  pdb=" N   TRP C 170 " --> pdb=" O   GLY C 143 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   LEU C 169 " --> pdb=" O   ASN C 166 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 185 through 187

    384 hydrogen bonds defined for protein.
    1088 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.28

  Time building geometry restraints manager: 0.69 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 990
        1.30 -     1.43: 1870
        1.43 -     1.56: 4019
        1.56 -     1.68: 110
        1.68 -     1.81: 48
  Bond restraints: 7037
  Sorted by residual:
  bond pdb=" C1BALMT A 603 "
       pdb=" O5BALMT A 603 "
    ideal  model  delta    sigma   weight residual
    1.393  1.519 -0.126 2.00e-02 2.50e+03 3.98e+01
  bond pdb=" C1B LMT A 604 "
       pdb=" O5B LMT A 604 "
    ideal  model  delta    sigma   weight residual
    1.393  1.517 -0.124 2.00e-02 2.50e+03 3.82e+01
  bond pdb=" C1BBLMT A 602 "
       pdb=" O5BBLMT A 602 "
    ideal  model  delta    sigma   weight residual
    1.393  1.514 -0.121 2.00e-02 2.50e+03 3.67e+01
  bond pdb=" C1B LMT A 611 "
       pdb=" O5B LMT A 611 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.62e+01
  bond pdb=" C1B LMT A 605 "
       pdb=" O5B LMT A 605 "
    ideal  model  delta    sigma   weight residual
    1.393  1.513 -0.120 2.00e-02 2.50e+03 3.61e+01
  ... (remaining 7032 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.95: 9361
        4.95 -     9.89: 212
        9.89 -    14.84: 3
       14.84 -    19.79: 3
       19.79 -    24.74: 3
  Bond angle restraints: 9582
  Sorted by residual:
  angle pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.34  152.08  -24.74 3.00e+00 1.11e-01 6.80e+01
  angle pdb=" C09 ZGS A 601 "
        pdb=" C10 ZGS A 601 "
        pdb=" C11 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.16  151.03  -23.87 3.00e+00 1.11e-01 6.33e+01
  angle pdb=" C06 ZGS A 601 "
        pdb=" C07 ZGS A 601 "
        pdb=" C08 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.52  151.32  -23.80 3.00e+00 1.11e-01 6.29e+01
  angle pdb=" C04 ZGS A 601 "
        pdb=" C05 ZGS A 601 "
        pdb=" C06 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     110.70  129.66  -18.96 3.00e+00 1.11e-01 3.99e+01
  angle pdb=" C02 ZGS A 601 "
        pdb=" C03 ZGS A 601 "
        pdb=" C04 ZGS A 601 "
      ideal   model   delta    sigma   weight residual
     127.67  111.44   16.23 3.00e+00 1.11e-01 2.93e+01
  ... (remaining 9577 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.54: 4151
       29.54 -    59.08: 248
       59.08 -    88.62: 93
       88.62 -   118.15: 137
      118.15 -   147.69: 5
  Dihedral angle restraints: 4634
    sinusoidal: 2166
      harmonic: 2468
  Sorted by residual:
  dihedral pdb=" C23 ZGS A 601 "
           pdb=" O24 ZGS A 601 "
           pdb=" P25 ZGS A 601 "
           pdb=" O26 ZGS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     177.58  -34.73 -147.69     1      3.00e+01 1.11e-03 1.97e+01
  dihedral pdb=" C5B LMT C 301 "
           pdb=" C1B LMT C 301 "
           pdb=" O5B LMT C 301 "
           pdb=" O1B LMT C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.61  173.64  121.97     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" C2B LMT C 301 "
           pdb=" C1B LMT C 301 "
           pdb=" O5B LMT C 301 "
           pdb=" C5B LMT C 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.12   64.84 -121.96     1      3.00e+01 1.11e-03 1.63e+01
  ... (remaining 4631 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 849
       0.050 -    0.100: 225
       0.100 -    0.150: 68
       0.150 -    0.200: 9
       0.200 -    0.250: 5
  Chirality restraints: 1156
  Sorted by residual:
  chirality pdb=" C1BALMT A 602 "
            pdb=" C2BALMT A 602 "
            pdb=" O1BALMT A 602 "
            pdb=" O5BALMT A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.45    0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" C1B LMT A 607 "
            pdb=" C2B LMT A 607 "
            pdb=" O1B LMT A 607 "
            pdb=" O5B LMT A 607 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.43    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" C1B LMT A 608 "
            pdb=" C2B LMT A 608 "
            pdb=" O1B LMT A 608 "
            pdb=" O5B LMT A 608 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.20   -2.42    0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 1153 not shown)

  Planarity restraints: 1130
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP C  46 "   -0.038 5.00e-02 4.00e+02   5.84e-02 5.46e+00
        pdb=" N   PRO C  47 "    0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO C  47 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO C  47 "   -0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B  75 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.96e+00
        pdb=" N   PRO B  76 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B  76 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B  76 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 374 "    0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 375 "   -0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 375 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 375 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1127 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1748
        2.80 -     3.33: 6113
        3.33 -     3.85: 11558
        3.85 -     4.38: 12697
        4.38 -     4.90: 22836
  Nonbonded interactions: 54952
  Sorted by model distance:
  nonbonded pdb=" O   TYR A  43 "
            pdb=" OH  TYR A 159 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OD1 ASP A  67 "
            pdb=" OH  TYR A 452 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" OH  TYR A 425 "
            pdb=" O   HOH A 701 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" O   TYR A 452 "
            pdb=" ND2 ASN C  99 "
     model   vdw
     2.322 3.120
  nonbonded pdb=" O3' LMT A 607 "
            pdb=" O6'BLMT A 610 "
     model   vdw
     2.329 3.040
  ... (remaining 54947 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=0.98
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:             3.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.900
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7515
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      :  0.012   0.126   7041  Z= 0.612
  Angle     :  1.386  24.737   9590  Z= 0.547
  Chirality :  0.053   0.250   1156
  Planarity :  0.006   0.058   1130
  Dihedral  : 29.930 147.692   3050
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.54 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.55 %
    Favored  : 91.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.42 (0.27), residues: 868
  helix:  0.47 (0.24), residues: 385
  sheet: -0.76 (0.43), residues: 150
  loop : -2.76 (0.30), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  40 
 TYR   0.013   0.001   TYR A 251 
 PHE   0.025   0.002   PHE B  89 
 TRP   0.015   0.002   TRP C  33 
 HIS   0.001   0.000   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.01232 ( 7037)
  covalent geometry    : angle       1.38684 ( 9582)
  SS BOND              : bond        0.00219 (    4)
  SS BOND              : angle       0.72782 (    8)
  hydrogen bonds       : bond        0.09925 (  371)
  hydrogen bonds       : angle       5.81154 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6932 (ttm-80)
REVERT: A  159 TYR cc_start: 0.8601 (t80) cc_final: 0.8345 (t80)
REVERT: A  173 ARG cc_start: 0.7234 (mtt180) cc_final: 0.6781 (mtt-85)
REVERT: A  199 VAL cc_start: 0.8805 (t) cc_final: 0.8386 (m)
REVERT: A  288 HIS cc_start: 0.7354 (t-90) cc_final: 0.6739 (t-90)
REVERT: A  296 MET cc_start: 0.6885 (mmt) cc_final: 0.6637 (mmp)
REVERT: A  413 GLN cc_start: 0.8528 (mm110) cc_final: 0.8013 (mt0)
  outliers start: 5
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0915
  time to fit residues: 16.4247
Evaluate side-chains
  97 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.0970
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:   20.0000
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
A 152 GLN
A 319 ASN
A 413 GLN
B 190 ASN
C  74 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.171633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.135353 restraints weight = 29002.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3571 rms_B_bonded: 6.33
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3571
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3571 r_free = 0.3571    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3571
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   7041  Z= 0.188
  Angle     :  0.886  10.130   9590  Z= 0.377
  Chirality :  0.051   0.315   1156
  Planarity :  0.005   0.056   1130
  Dihedral  : 20.158 157.456   1869
  Min Nonbonded Distance : 2.204

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.72 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.26 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.83 (0.28), residues: 868
  helix:  1.36 (0.25), residues: 382
  sheet: -1.10 (0.41), residues: 175
  loop : -2.72 (0.31), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 104 
 TYR   0.011   0.002   TYR A 291 
 PHE   0.022   0.002   PHE A 367 
 TRP   0.015   0.002   TRP A 140 
 HIS   0.001   0.001   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 7037)
  covalent geometry    : angle       0.88566 ( 9582)
  SS BOND              : bond        0.00218 (    4)
  SS BOND              : angle       0.70578 (    8)
  hydrogen bonds       : bond        0.03982 (  371)
  hydrogen bonds       : angle       4.62518 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7504 (ttm-80)
REVERT: A  172 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7975 (mt-10)
REVERT: A  173 ARG cc_start: 0.7135 (mtt180) cc_final: 0.6895 (mtt-85)
REVERT: B  110 GLN cc_start: 0.7203 (tt0) cc_final: 0.6938 (mt0)
REVERT: B  196 PHE cc_start: 0.8062 (m-80) cc_final: 0.7740 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 110
  average time/residue: 0.0817
  time to fit residues: 12.1272
Evaluate side-chains
  108 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain A residue  359 ILE
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain C residue  151 THR
Chi-restraints excluded: chain C residue  185 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 4 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 31 optimal weight:    0.0170
   chunk 54 optimal weight:    0.6980
   chunk 83 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0980
   chunk 76 optimal weight:    0.1980
   chunk 26 optimal weight:    0.6980
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.2018

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

Flipped N/Q/H residues before XYZ refinement:
B  36 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.173614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.141080 restraints weight = 32389.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3659 rms_B_bonded: 5.60
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3657
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3657 r_free = 0.3657    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3657
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7041  Z= 0.124
  Angle     :  0.706  10.115   9590  Z= 0.314
  Chirality :  0.043   0.306   1156
  Planarity :  0.005   0.051   1130
  Dihedral  : 14.313 152.664   1869
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.14 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 15.77 %
    Favored  : 82.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.29), residues: 868
  helix:  1.75 (0.26), residues: 384
  sheet: -0.92 (0.40), residues: 176
  loop : -2.74 (0.31), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 104 
 TYR   0.010   0.001   TYR A 291 
 PHE   0.012   0.001   PHE B  89 
 TRP   0.011   0.001   TRP C  33 
 HIS   0.001   0.000   HIS A 156 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7037)
  covalent geometry    : angle       0.70594 ( 9582)
  SS BOND              : bond        0.00200 (    4)
  SS BOND              : angle       0.57559 (    8)
  hydrogen bonds       : bond        0.03574 (  371)
  hydrogen bonds       : angle       4.30824 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 105
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7663 (mmm-85) cc_final: 0.7286 (ttm-80)
REVERT: A  288 HIS cc_start: 0.6299 (t-170) cc_final: 0.5209 (t-170)
REVERT: A  291 TYR cc_start: 0.6469 (OUTLIER) cc_final: 0.6097 (t80)
REVERT: A  296 MET cc_start: 0.7293 (OUTLIER) cc_final: 0.6386 (tpp)
REVERT: A  319 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7680 (m-40)
REVERT: B  196 PHE cc_start: 0.7876 (m-80) cc_final: 0.7623 (m-80)
  outliers start: 10
  outliers final: 3
  residues processed: 110
  average time/residue: 0.0843
  time to fit residues: 12.5425
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 100
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  319 ASN
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  174 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 64 optimal weight:    5.9990
   chunk 23 optimal weight:    6.9990
   chunk 10 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 52 optimal weight:    0.9990
   chunk 84 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0030
   chunk 21 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.5792

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

Flipped N/Q/H residues before XYZ refinement:
B 134 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.171120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.137242 restraints weight = 31078.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 5.76
r_work (final): 0.3596
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3595
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3595 r_free = 0.3595    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3595
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   7041  Z= 0.157
  Angle     :  0.689  10.171   9590  Z= 0.314
  Chirality :  0.042   0.298   1156
  Planarity :  0.005   0.052   1130
  Dihedral  : 12.846 151.603   1869
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.31 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 16.61 %
    Favored  : 82.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.29), residues: 868
  helix:  1.81 (0.26), residues: 384
  sheet: -1.04 (0.41), residues: 174
  loop : -2.51 (0.32), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 104 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.026   0.002   PHE A 367 
 TRP   0.013   0.001   TRP C  95 
 HIS   0.006   0.003   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 7037)
  covalent geometry    : angle       0.68889 ( 9582)
  SS BOND              : bond        0.00247 (    4)
  SS BOND              : angle       0.59661 (    8)
  hydrogen bonds       : bond        0.03695 (  371)
  hydrogen bonds       : angle       4.35158 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7705 (mmm-85) cc_final: 0.7333 (ttm-80)
REVERT: A  296 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.6359 (tpp)
REVERT: B  196 PHE cc_start: 0.7827 (m-80) cc_final: 0.7611 (m-80)
  outliers start: 7
  outliers final: 4
  residues processed: 101
  average time/residue: 0.0876
  time to fit residues: 11.8085
Evaluate side-chains
  103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    4 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9980
   chunk 54 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 70 optimal weight:    0.7980
   chunk 85 optimal weight:    0.9990
   chunk 84 optimal weight:    7.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.168638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.136234 restraints weight = 33864.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3592 rms_B_bonded: 5.65
r_work (final): 0.3592
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3591
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3591 r_free = 0.3591    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3591
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   7041  Z= 0.182
  Angle     :  0.701  10.433   9590  Z= 0.324
  Chirality :  0.042   0.299   1156
  Planarity :  0.005   0.055   1130
  Dihedral  : 12.279 149.988   1869
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.96 %
    Favored  : 93.93 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 16.78 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.42 (0.29), residues: 868
  helix:  1.83 (0.26), residues: 379
  sheet: -1.07 (0.42), residues: 173
  loop : -2.54 (0.32), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 104 
 TYR   0.011   0.001   TYR A 251 
 PHE   0.024   0.002   PHE B  89 
 TRP   0.019   0.002   TRP C  95 
 HIS   0.003   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 ( 7037)
  covalent geometry    : angle       0.70131 ( 9582)
  SS BOND              : bond        0.00288 (    4)
  SS BOND              : angle       0.57923 (    8)
  hydrogen bonds       : bond        0.03814 (  371)
  hydrogen bonds       : angle       4.43622 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7353 (ttm-80)
REVERT: A  173 ARG cc_start: 0.6940 (mtt-85) cc_final: 0.6617 (mtt-85)
REVERT: A  291 TYR cc_start: 0.6909 (OUTLIER) cc_final: 0.6510 (t80)
REVERT: A  296 MET cc_start: 0.7307 (OUTLIER) cc_final: 0.6354 (tpp)
REVERT: B  196 PHE cc_start: 0.7998 (m-80) cc_final: 0.7752 (m-80)
  outliers start: 10
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0877
  time to fit residues: 12.4717
Evaluate side-chains
  109 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ARG
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain A residue  480 ILE
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 42 optimal weight:    0.3980
   chunk 40 optimal weight:    0.7980
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9990
   chunk 84 optimal weight:    0.0000
   chunk 1 optimal weight:    0.4980
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.5184

-------------------------------------------------------------------------------
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 = 0.3967 r_free = 0.3967 target = 0.169782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.137944 restraints weight = 38663.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 5.93
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3612
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3612 r_free = 0.3612    target_work(ls_wunit_k1) = 0.137         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3612
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   7041  Z= 0.145
  Angle     :  0.665  10.699   9590  Z= 0.306
  Chirality :  0.041   0.289   1156
  Planarity :  0.005   0.053   1130
  Dihedral  : 11.783 149.718   1869
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.49 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.11 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.29), residues: 868
  helix:  1.97 (0.26), residues: 379
  sheet: -1.01 (0.42), residues: 169
  loop : -2.48 (0.32), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  34 
 TYR   0.011   0.001   TYR A 358 
 PHE   0.027   0.001   PHE A 367 
 TRP   0.018   0.001   TRP A 103 
 HIS   0.004   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 7037)
  covalent geometry    : angle       0.66470 ( 9582)
  SS BOND              : bond        0.00246 (    4)
  SS BOND              : angle       0.51882 (    8)
  hydrogen bonds       : bond        0.03656 (  371)
  hydrogen bonds       : angle       4.34956 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 99
  time to evaluate  : 0.172 
Fit side-chains
REVERT: A  100 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7482 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6468 (t80)
REVERT: A  296 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6315 (tpp)
REVERT: B  196 PHE cc_start: 0.7958 (m-80) cc_final: 0.7725 (m-80)
  outliers start: 8
  outliers final: 3
  residues processed: 102
  average time/residue: 0.0885
  time to fit residues: 12.0725
Evaluate side-chains
  99 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 94
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 22 optimal weight:   10.0000
   chunk 56 optimal weight:    0.4980
   chunk 40 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.169569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.146110 restraints weight = 31183.098|
|-----------------------------------------------------------------------------|
r_work (start): 0.3692 rms_B_bonded: 3.26
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3689 r_free = 0.3689    target_work(ls_wunit_k1) = 0.145         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.2668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   7041  Z= 0.178
  Angle     :  0.684  10.744   9590  Z= 0.320
  Chirality :  0.042   0.295   1156
  Planarity :  0.005   0.054   1130
  Dihedral  : 11.705 151.464   1869
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.43 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 17.62 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.38 (0.29), residues: 868
  helix:  1.75 (0.26), residues: 386
  sheet: -1.09 (0.42), residues: 173
  loop : -2.42 (0.33), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  34 
 TYR   0.011   0.001   TYR B  48 
 PHE   0.025   0.002   PHE B  89 
 TRP   0.038   0.002   TRP A 103 
 HIS   0.005   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 7037)
  covalent geometry    : angle       0.68458 ( 9582)
  SS BOND              : bond        0.00269 (    4)
  SS BOND              : angle       0.52414 (    8)
  hydrogen bonds       : bond        0.03849 (  371)
  hydrogen bonds       : angle       4.44546 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7473 (mmm-85) cc_final: 0.7135 (ttm-80)
REVERT: A  173 ARG cc_start: 0.6735 (mtt-85) cc_final: 0.6402 (mtt-85)
REVERT: A  291 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6425 (t80)
REVERT: A  296 MET cc_start: 0.6956 (OUTLIER) cc_final: 0.6024 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 101
  average time/residue: 0.0921
  time to fit residues: 12.3385
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain A residue  439 SER
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 48 optimal weight:    0.4980
   chunk 79 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0170
   chunk 7 optimal weight:    0.4980
   chunk 25 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3969 r_free = 0.3969 target = 0.170972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 24)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.147780 restraints weight = 30526.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 3.25
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3712 r_free = 0.3712    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3712 r_free = 0.3712    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7041  Z= 0.149
  Angle     :  0.663  10.925   9590  Z= 0.307
  Chirality :  0.041   0.289   1156
  Planarity :  0.005   0.052   1130
  Dihedral  : 11.382 151.816   1869
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.28 %
    Favored  : 81.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.29), residues: 868
  helix:  1.83 (0.26), residues: 387
  sheet: -1.07 (0.42), residues: 168
  loop : -2.35 (0.33), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  34 
 TYR   0.010   0.001   TYR A 358 
 PHE   0.020   0.001   PHE A 367 
 TRP   0.042   0.002   TRP A 103 
 HIS   0.005   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 7037)
  covalent geometry    : angle       0.66313 ( 9582)
  SS BOND              : bond        0.00210 (    4)
  SS BOND              : angle       0.45848 (    8)
  hydrogen bonds       : bond        0.03680 (  371)
  hydrogen bonds       : angle       4.36897 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7426 (mmm-85) cc_final: 0.7081 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.6376 (t80)
REVERT: A  296 MET cc_start: 0.6975 (OUTLIER) cc_final: 0.6058 (tpp)
REVERT: C  198 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7368 (ptmt)
  outliers start: 10
  outliers final: 4
  residues processed: 104
  average time/residue: 0.0917
  time to fit residues: 12.8255
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue   72 SER
Chi-restraints excluded: chain B residue  112 SER
Chi-restraints excluded: chain B residue  141 VAL
Chi-restraints excluded: chain C residue  198 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 3 optimal weight:    0.0270
   chunk 42 optimal weight:    0.4980
   chunk 73 optimal weight:    0.0980
   chunk 62 optimal weight:    3.9990
   chunk 7 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0770
   chunk 51 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 37 optimal weight:    0.0020
   chunk 24 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.1404

-------------------------------------------------------------------------------
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 = 0.4021 r_free = 0.4021 target = 0.175955 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.149750 restraints weight = 30479.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3705 rms_B_bonded: 4.35
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.147         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7041  Z= 0.107
  Angle     :  0.626  11.383   9590  Z= 0.289
  Chirality :  0.040   0.273   1156
  Planarity :  0.005   0.049   1130
  Dihedral  : 10.727 154.357   1869
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.61 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 18.79 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.02 (0.30), residues: 868
  helix:  2.04 (0.26), residues: 387
  sheet: -0.92 (0.40), residues: 186
  loop : -2.26 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 173 
 TYR   0.008   0.001   TYR A 159 
 PHE   0.013   0.001   PHE B  89 
 TRP   0.033   0.001   TRP A 103 
 HIS   0.004   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 7037)
  covalent geometry    : angle       0.62567 ( 9582)
  SS BOND              : bond        0.00179 (    4)
  SS BOND              : angle       0.43947 (    8)
  hydrogen bonds       : bond        0.03434 (  371)
  hydrogen bonds       : angle       4.21616 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.7706 (mmm-85) cc_final: 0.7283 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6137 (t80)
REVERT: A  296 MET cc_start: 0.7042 (OUTLIER) cc_final: 0.6192 (tpp)
REVERT: A  354 LYS cc_start: 0.7410 (ttpp) cc_final: 0.7034 (ttmt)
  outliers start: 6
  outliers final: 4
  residues processed: 102
  average time/residue: 0.0855
  time to fit residues: 11.8278
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 SER
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 27 optimal weight:    0.0870
   chunk 44 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   chunk 15 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0670
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.2896

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.174076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.145509 restraints weight = 37226.692|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 5.80
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3634
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3634 r_free = 0.3634    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3634
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7041  Z= 0.119
  Angle     :  0.633  11.352   9590  Z= 0.291
  Chirality :  0.040   0.275   1156
  Planarity :  0.005   0.049   1130
  Dihedral  : 10.567 155.558   1869
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.26 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 18.46 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.29), residues: 868
  helix:  2.05 (0.26), residues: 387
  sheet: -1.01 (0.42), residues: 169
  loop : -2.26 (0.33), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 173 
 TYR   0.009   0.001   TYR A 251 
 PHE   0.026   0.001   PHE A 367 
 TRP   0.032   0.001   TRP A 103 
 HIS   0.005   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 7037)
  covalent geometry    : angle       0.63286 ( 9582)
  SS BOND              : bond        0.00155 (    4)
  SS BOND              : angle       0.46636 (    8)
  hydrogen bonds       : bond        0.03475 (  371)
  hydrogen bonds       : angle       4.19615 ( 1088)

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

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

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1736 Ramachandran restraints generated.
    868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A  100 ARG cc_start: 0.8033 (mmm-85) cc_final: 0.7612 (ttm-80)
REVERT: A  291 TYR cc_start: 0.6669 (OUTLIER) cc_final: 0.6263 (t80)
REVERT: A  296 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6405 (tpp)
REVERT: A  354 LYS cc_start: 0.7576 (ttpp) cc_final: 0.7188 (ttmt)
  outliers start: 6
  outliers final: 3
  residues processed: 101
  average time/residue: 0.0933
  time to fit residues: 12.5596
Evaluate side-chains
  103 residues out of total 671 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 GLU
Chi-restraints excluded: chain A residue  291 TYR
Chi-restraints excluded: chain A residue  296 MET
Chi-restraints excluded: chain B residue    5 ASN
Chi-restraints excluded: chain B residue  141 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0870
   chunk 53 optimal weight:    0.0470
   chunk 2 optimal weight:    0.5980
   chunk 70 optimal weight:    0.5980
   chunk 56 optimal weight:    0.2980
   chunk 8 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0970
   overall best weight:    0.2254

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

Flipped N/Q/H residues before XYZ refinement:
** A 413 GLN ** 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 = 0.4006 r_free = 0.4006 target = 0.174433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153286 restraints weight = 34110.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3790 rms_B_bonded: 3.09
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3787
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3787 r_free = 0.3787    target_work(ls_wunit_k1) = 0.154         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3787
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7544
moved from start:          0.3034

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7041  Z= 0.111
  Angle     :  0.632  11.419   9590  Z= 0.290
  Chirality :  0.039   0.269   1156
  Planarity :  0.005   0.049   1130
  Dihedral  : 10.350 157.160   1869
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.49 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 18.79 %
    Favored  : 80.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.01 (0.29), residues: 868
  helix:  2.02 (0.26), residues: 391
  sheet: -0.88 (0.43), residues: 161
  loop : -2.18 (0.33), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  34 
 TYR   0.009   0.001   TYR A 159 
 PHE   0.013   0.001   PHE B  89 
 TRP   0.027   0.001   TRP A 103 
 HIS   0.005   0.002   HIS A 288 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 7037)
  covalent geometry    : angle       0.63244 ( 9582)
  SS BOND              : bond        0.00152 (    4)
  SS BOND              : angle       0.44410 (    8)
  hydrogen bonds       : bond        0.03379 (  371)
  hydrogen bonds       : angle       4.15555 ( 1088)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1446.30 seconds
wall clock time: 25 minutes 36.62 seconds (1536.62 seconds total)