Starting phenix.real_space_refine
on Wed Sep 17 07:31:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7li7_23362/09_2025/7li7_23362.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.035
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      34      5.16       5
     C    4101      2.51       5
     N     960      2.21       5
     O    1082      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6177
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4292
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4292
          Classifications: {'peptide': 537}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 514}
    Chain: "B"
      Number of atoms: 913
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 913
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 114}
    Chain: "C"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 830
          Classifications: {'peptide': 110}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 101}
    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: "A"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 114
          Unusual residues: {'CLR': 1, 'D10': 1, 'D12': 3, 'HP6': 5, 'LNK': 1}
          Classifications: {'undetermined': 11}
          Link IDs: {None: 10}
  Time building chain proxies: 1.79, per 1000 atoms: 0.29
  Number of scatterers: 6177
  At special positions: 0
  Unit cell: (71.928, 73.224, 121.176, 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      34     16.00
     O    1082      8.00
     N     960      7.00
     C    4101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 200 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  41 " - pdb=" SG  CYS B 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 112 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG D   1 " - " NAG D   2 "
    NAG-ASN
      " NAG D   1 " - " ASN A 208 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 356.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1396

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      54.0% alpha, 11.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 84 through 97
    Processing helix  chain 'A' and resid 98 through 113
      Proline residue:  A 106  - end of helix
    Processing helix  chain 'A' and resid 114 through 118
      removed outlier: 3.758A  pdb=" N   LEU A 118 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 144
      Proline residue:  A 131  - end of helix
      removed outlier: 3.841A  pdb=" N   GLU A 136 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 154
      removed outlier: 3.849A  pdb=" N   TRP A 151 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 158
    Processing helix  chain 'A' and resid 159 through 190
      removed outlier: 4.289A  pdb=" N   TYR A 163 " --> pdb=" O   LYS A 159 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   THR A 178 " --> pdb=" O   SER A 174 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   ILE A 179 " --> pdb=" O   TYR A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 235
      removed outlier: 3.615A  pdb=" N   HIS A 235 " --> pdb=" O   PHE A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 242
    Processing helix  chain 'A' and resid 252 through 271
    Processing helix  chain 'A' and resid 273 through 282
      removed outlier: 3.730A  pdb=" N   TRP A 282 " --> pdb=" O   GLY A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 300
      removed outlier: 4.143A  pdb=" N   TYR A 289 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 313
    Processing helix  chain 'A' and resid 325 through 338
    Processing helix  chain 'A' and resid 342 through 349
    Processing helix  chain 'A' and resid 356 through 391
    Processing helix  chain 'A' and resid 403 through 417
      removed outlier: 4.240A  pdb=" N   PHE A 407 " --> pdb=" O   PRO A 403 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A 411 " --> pdb=" O   PHE A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 448
      removed outlier: 3.836A  pdb=" N   VAL A 446 " --> pdb=" O   GLY A 442 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 454
      removed outlier: 3.608A  pdb=" N   GLU A 453 " --> pdb=" O   ALA A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 4.125A  pdb=" N   LYS A 460 " --> pdb=" O   HIS A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 484
      removed outlier: 3.708A  pdb=" N   VAL A 479 " --> pdb=" O   PHE A 475 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   THR A 480 " --> pdb=" O   GLY A 476 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   PHE A 483 " --> pdb=" O   VAL A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 486 through 496
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 517 through 530
      removed outlier: 4.456A  pdb=" N   ASP A 524 " --> pdb=" O   GLN A 520 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   VAL A 525 " --> pdb=" O   PHE A 521 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLU A 527 " --> pdb=" O   ARG A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 536 through 541
    Processing helix  chain 'A' and resid 543 through 559
      removed outlier: 3.768A  pdb=" N   ILE A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 585
    Processing helix  chain 'A' and resid 587 through 600
    Processing helix  chain 'A' and resid 603 through 612
    Processing sheet with id=AA1, first strand: chain 'B' and resid 24 through 25
    Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 39
      removed outlier: 3.711A  pdb=" N   ILE B  39 " --> pdb=" O   MET B 100 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.559A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 77 through 79
      removed outlier: 3.559A  pdb=" N   ARG B  69 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 7.083A  pdb=" N   TRP B  55 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   ARG B  69 " --> pdb=" O   MET B  53 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   MET B  53 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 25 through 27
      removed outlier: 3.515A  pdb=" N   ALA C  39 " --> pdb=" O   ILE C  99 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   PHE C  95 " --> pdb=" O   CYS C  43 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR C  94 " --> pdb=" O   SER C  91 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.241A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   PHE C 111 " --> pdb=" O   PHE C  60 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.241A  pdb=" N   LEU C  31 " --> pdb=" O   GLU C 129 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   THR C 126 " --> pdb=" O   TYR C 110 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR C 110 " --> pdb=" O   THR C 126 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR C 121 " --> pdb=" O   GLN C 114 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 50 through 51
      removed outlier: 3.587A  pdb=" N   ASN C  51 " --> pdb=" O   ILE C  54 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 72 through 73

    319 hydrogen bonds defined for protein.
    900 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: 1.02

  Time building geometry restraints manager: 0.84 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1814
        1.34 -     1.46: 1597
        1.46 -     1.58: 2889
        1.58 -     1.69: 0
        1.69 -     1.81: 49
  Bond restraints: 6349
  Sorted by residual:
  bond pdb=" C1  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.41e+00
  bond pdb=" N   SER C  48 "
       pdb=" CA  SER C  48 "
    ideal  model  delta    sigma   weight residual
    1.458  1.482 -0.024 1.90e-02 2.77e+03 1.64e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C   GLU C  47 "
       pdb=" N   SER C  48 "
    ideal  model  delta    sigma   weight residual
    1.329  1.345 -0.016 1.40e-02 5.10e+03 1.35e+00
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.21e+00
  ... (remaining 6344 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 8434
        1.88 -     3.75: 125
        3.75 -     5.63: 49
        5.63 -     7.50: 3
        7.50 -     9.38: 1
  Bond angle restraints: 8612
  Sorted by residual:
  angle pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
        pdb=" CA  SER C  48 "
      ideal   model   delta    sigma   weight residual
     121.70  131.08   -9.38 1.80e+00 3.09e-01 2.71e+01
  angle pdb=" N   TRP A 197 "
        pdb=" CA  TRP A 197 "
        pdb=" C   TRP A 197 "
      ideal   model   delta    sigma   weight residual
     114.56  111.00    3.56 1.27e+00 6.20e-01 7.84e+00
  angle pdb=" C13 CLR A 710 "
        pdb=" C17 CLR A 710 "
        pdb=" C20 CLR A 710 "
      ideal   model   delta    sigma   weight residual
     119.60  112.55    7.05 3.00e+00 1.11e-01 5.52e+00
  angle pdb=" C20 CLR A 710 "
        pdb=" C22 CLR A 710 "
        pdb=" C23 CLR A 710 "
      ideal   model   delta    sigma   weight residual
     115.57  108.76    6.81 3.00e+00 1.11e-01 5.16e+00
  angle pdb=" CA  GLU C  47 "
        pdb=" C   GLU C  47 "
        pdb=" N   SER C  48 "
      ideal   model   delta    sigma   weight residual
     115.49  118.10   -2.61 1.24e+00 6.50e-01 4.42e+00
  ... (remaining 8607 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 3379
       17.81 -    35.61: 284
       35.61 -    53.42: 40
       53.42 -    71.23: 5
       71.23 -    89.03: 2
  Dihedral angle restraints: 3710
    sinusoidal: 1510
      harmonic: 2200
  Sorted by residual:
  dihedral pdb=" CB  GLU A 453 "
           pdb=" CG  GLU A 453 "
           pdb=" CD  GLU A 453 "
           pdb=" OE1 GLU A 453 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.03  -89.03     1      3.00e+01 1.11e-03 1.05e+01
  dihedral pdb=" CB  GLU A 136 "
           pdb=" CG  GLU A 136 "
           pdb=" CD  GLU A 136 "
           pdb=" OE1 GLU A 136 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -84.87   84.87     1      3.00e+01 1.11e-03 9.71e+00
  dihedral pdb=" CA  ARG A 596 "
           pdb=" CB  ARG A 596 "
           pdb=" CG  ARG A 596 "
           pdb=" CD  ARG A 596 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  122.06   57.94     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 3707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.234: 945
       0.234 -    0.469: 2
       0.469 -    0.703: 0
       0.703 -    0.937: 0
       0.937 -    1.171: 1
  Chirality restraints: 948
  Sorted by residual:
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.23   -1.17 2.00e-02 2.50e+03 3.43e+03
  chirality pdb=" C14 CLR A 710 "
            pdb=" C13 CLR A 710 "
            pdb=" C15 CLR A 710 "
            pdb=" C8  CLR A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.32   -2.67    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" C9  CLR A 710 "
            pdb=" C10 CLR A 710 "
            pdb=" C11 CLR A 710 "
            pdb=" C8  CLR A 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.45   -2.70    0.25 2.00e-01 2.50e+01 1.55e+00
  ... (remaining 945 not shown)

  Planarity restraints: 1048
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 402 "   -0.023 5.00e-02 4.00e+02   3.44e-02 1.89e+00
        pdb=" N   PRO A 403 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 403 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 403 "   -0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C 100 "   -0.021 5.00e-02 4.00e+02   3.18e-02 1.62e+00
        pdb=" N   PRO C 101 "    0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO C 101 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 101 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 589 "   -0.016 5.00e-02 4.00e+02   2.41e-02 9.26e-01
        pdb=" N   PRO A 590 "    0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO A 590 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A 590 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1045 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1874
        2.82 -     3.34: 5815
        3.34 -     3.86: 10355
        3.86 -     4.38: 11298
        4.38 -     4.90: 19568
  Nonbonded interactions: 48910
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 110 "
            pdb=" O   VAL A 397 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   ASN A 112 "
            pdb=" NZ  LYS A 319 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   THR A 600 "
            pdb=" NE  ARG A 607 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OD1 ASN A 101 "
            pdb=" NE2 GLN A 332 "
     model   vdw
     2.311 3.120
  nonbonded pdb=" O   SER A 190 "
            pdb=" OG  SER A 190 "
     model   vdw
     2.313 3.040
  ... (remaining 48905 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.270
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.120
  Find NCS groups from input model:        0.030
  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:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
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      :  0.002   0.065   6355  Z= 0.121
  Angle     :  0.644  11.827   8624  Z= 0.305
  Chirality :  0.056   1.171    948
  Planarity :  0.003   0.034   1047
  Dihedral  : 12.289  89.034   2305
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.70 (0.27), residues: 759
  helix: -0.80 (0.24), residues: 370
  sheet: -1.58 (0.54), residues: 81
  loop : -3.08 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 152 
 TYR   0.012   0.001   TYR A 176 
 PHE   0.016   0.001   PHE A 474 
 TRP   0.006   0.001   TRP A 204 
 HIS   0.001   0.000   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 ( 6349)
  covalent geometry    : angle       0.61140 ( 8612)
  SS BOND              : bond        0.00107 (    3)
  SS BOND              : angle       0.27710 (    6)
  hydrogen bonds       : bond        0.13463 (  315)
  hydrogen bonds       : angle       5.43678 (  900)
  Misc. bond           : bond        0.00023 (    1)
  link_BETA1-4         : bond        0.06491 (    1)
  link_BETA1-4         : angle      10.90698 (    3)
  link_NAG-ASN         : bond        0.00491 (    1)
  link_NAG-ASN         : angle       0.99914 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.4133 (mmmt) cc_final: 0.3539 (mmtp)
REVERT: A  260 MET cc_start: 0.6096 (mmm) cc_final: 0.4406 (tmm)
REVERT: A  267 TYR cc_start: 0.7045 (t80) cc_final: 0.6839 (t80)
REVERT: A  456 HIS cc_start: 0.7952 (p-80) cc_final: 0.7737 (p90)
REVERT: A  463 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6779 (mm-30)
REVERT: A  478 LEU cc_start: 0.6966 (tt) cc_final: 0.6669 (tp)
REVERT: A  514 TRP cc_start: 0.6695 (m100) cc_final: 0.6023 (m-10)
REVERT: B   29 GLU cc_start: 0.8859 (mp0) cc_final: 0.8552 (mp0)
REVERT: B   88 THR cc_start: 0.9257 (m) cc_final: 0.8963 (p)
REVERT: B  125 PHE cc_start: 0.8290 (m-80) cc_final: 0.7888 (m-10)
REVERT: C   33 VAL cc_start: 0.8265 (m) cc_final: 0.8057 (p)
REVERT: C   66 GLN cc_start: 0.7811 (mp10) cc_final: 0.7283 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1012
  time to fit residues: 19.8424
Evaluate side-chains
  117 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN
B  58 GLN
B 132 GLN
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  62 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.205413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 78)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.198164 restraints weight = 7694.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.178686 restraints weight = 12069.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.178675 restraints weight = 11194.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.178855 restraints weight = 10062.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.179083 restraints weight = 9205.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
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      :  0.004   0.080   6355  Z= 0.154
  Angle     :  0.559   9.458   8624  Z= 0.292
  Chirality :  0.041   0.194    948
  Planarity :  0.005   0.064   1047
  Dihedral  :  5.859  59.748    995
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.14 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.93 (0.29), residues: 759
  helix: -0.02 (0.25), residues: 364
  sheet: -1.75 (0.52), residues: 91
  loop : -2.71 (0.33), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 596 
 TYR   0.016   0.002   TYR B  99 
 PHE   0.020   0.001   PHE A 474 
 TRP   0.025   0.001   TRP A 317 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6349)
  covalent geometry    : angle       0.55889 ( 8612)
  SS BOND              : bond        0.00392 (    3)
  SS BOND              : angle       0.92740 (    6)
  hydrogen bonds       : bond        0.03267 (  315)
  hydrogen bonds       : angle       4.48784 (  900)
  Misc. bond           : bond        0.00015 (    1)
  link_BETA1-4         : bond        0.00613 (    1)
  link_BETA1-4         : angle       0.44383 (    3)
  link_NAG-ASN         : bond        0.00726 (    1)
  link_NAG-ASN         : angle       0.34493 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.4897 (mmmt) cc_final: 0.4468 (mmtt)
REVERT: B   32 LYS cc_start: 0.6376 (mmpt) cc_final: 0.6082 (mmmt)
REVERT: B   57 LYS cc_start: 0.9061 (tttm) cc_final: 0.8678 (ttmm)
REVERT: B   99 TYR cc_start: 0.8872 (m-80) cc_final: 0.8479 (m-10)
REVERT: C  103 GLU cc_start: 0.7894 (mp0) cc_final: 0.7684 (mp0)
  outliers start: 2
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0890
  time to fit residues: 15.9729
Evaluate side-chains
  115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 12 optimal weight:    0.1980
   chunk 4 optimal weight:    0.9990
   chunk 41 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 14 optimal weight:    0.6980
   chunk 36 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 38 optimal weight:    0.6980
   chunk 73 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  61 GLN
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.201399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.192830 restraints weight = 7632.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.191780 restraints weight = 11918.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.177747 restraints weight = 12612.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.176844 restraints weight = 16724.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.176949 restraints weight = 13213.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.2680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6355  Z= 0.139
  Angle     :  0.558   9.638   8624  Z= 0.289
  Chirality :  0.041   0.154    948
  Planarity :  0.004   0.064   1047
  Dihedral  :  5.903  59.897    995
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  5.30 %
    Favored  : 94.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.44 (0.30), residues: 759
  helix:  0.22 (0.26), residues: 375
  sheet: -1.49 (0.54), residues: 91
  loop : -2.31 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.013   0.001   TYR A  95 
 PHE   0.018   0.001   PHE A 474 
 TRP   0.019   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6349)
  covalent geometry    : angle       0.55813 ( 8612)
  SS BOND              : bond        0.00254 (    3)
  SS BOND              : angle       0.77265 (    6)
  hydrogen bonds       : bond        0.03213 (  315)
  hydrogen bonds       : angle       4.33001 (  900)
  Misc. bond           : bond        0.00022 (    1)
  link_BETA1-4         : bond        0.00449 (    1)
  link_BETA1-4         : angle       0.54370 (    3)
  link_NAG-ASN         : bond        0.00619 (    1)
  link_NAG-ASN         : angle       0.54832 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 136
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  201 LYS cc_start: 0.5154 (mmmt) cc_final: 0.4620 (mmtt)
REVERT: A  456 HIS cc_start: 0.6947 (p90) cc_final: 0.6707 (p90)
REVERT: C   62 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8378 (tt0)
REVERT: C  106 ASP cc_start: 0.8321 (m-30) cc_final: 0.7975 (m-30)
  outliers start: 2
  outliers final: 0
  residues processed: 137
  average time/residue: 0.0797
  time to fit residues: 14.5480
Evaluate side-chains
  113 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 112
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 4 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 50 optimal weight:    0.3980
   chunk 31 optimal weight:    0.0170
   chunk 0 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 132 GLN
C  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.198128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.189200 restraints weight = 7484.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.168997 restraints weight = 12041.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.168676 restraints weight = 13922.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.168846 restraints weight = 11832.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.169094 restraints weight = 10853.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
moved from start:          0.3041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6355  Z= 0.138
  Angle     :  0.552   9.578   8624  Z= 0.288
  Chirality :  0.040   0.160    948
  Planarity :  0.004   0.066   1047
  Dihedral  :  6.029  59.791    995
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.96 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.30), residues: 759
  helix:  0.41 (0.27), residues: 368
  sheet: -1.40 (0.52), residues: 95
  loop : -2.30 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 462 
 TYR   0.014   0.001   TYR A 410 
 PHE   0.021   0.001   PHE A 474 
 TRP   0.018   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 6349)
  covalent geometry    : angle       0.55105 ( 8612)
  SS BOND              : bond        0.00347 (    3)
  SS BOND              : angle       1.02672 (    6)
  hydrogen bonds       : bond        0.03184 (  315)
  hydrogen bonds       : angle       4.34203 (  900)
  Misc. bond           : bond        0.00014 (    1)
  link_BETA1-4         : bond        0.00307 (    1)
  link_BETA1-4         : angle       0.64926 (    3)
  link_NAG-ASN         : bond        0.00481 (    1)
  link_NAG-ASN         : angle       0.55899 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.181 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5029 (mmmt) cc_final: 0.4680 (mmtt)
REVERT: A  456 HIS cc_start: 0.7215 (p90) cc_final: 0.6921 (p90)
REVERT: C   86 PHE cc_start: 0.8102 (m-80) cc_final: 0.7844 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0736
  time to fit residues: 12.8012
Evaluate side-chains
  108 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 67 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 1 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 57 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
A 217 ASN
A 235 HIS
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 569 ASN
B  58 GLN
B 132 GLN
C  62 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.188589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.181627 restraints weight = 7647.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.178536 restraints weight = 10714.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.178001 restraints weight = 16303.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 69)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.175350 restraints weight = 11992.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.173201 restraints weight = 15090.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.3720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.078   6355  Z= 0.205
  Angle     :  0.643   9.798   8624  Z= 0.337
  Chirality :  0.044   0.162    948
  Planarity :  0.005   0.056   1047
  Dihedral  :  6.465  59.413    995
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  2.96 %
    Favored  : 96.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.30), residues: 759
  helix:  0.28 (0.27), residues: 368
  sheet: -1.24 (0.51), residues: 100
  loop : -2.42 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 607 
 TYR   0.021   0.002   TYR B  99 
 PHE   0.024   0.002   PHE A 474 
 TRP   0.027   0.002   TRP A 541 
 HIS   0.004   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00503 ( 6349)
  covalent geometry    : angle       0.64195 ( 8612)
  SS BOND              : bond        0.00222 (    3)
  SS BOND              : angle       1.29575 (    6)
  hydrogen bonds       : bond        0.03704 (  315)
  hydrogen bonds       : angle       4.53959 (  900)
  Misc. bond           : bond        0.00031 (    1)
  link_BETA1-4         : bond        0.00378 (    1)
  link_BETA1-4         : angle       0.83170 (    3)
  link_NAG-ASN         : bond        0.00602 (    1)
  link_NAG-ASN         : angle       0.46073 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  141 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7522 (pp30)
REVERT: A  186 TYR cc_start: 0.8535 (m-10) cc_final: 0.8321 (m-10)
REVERT: A  201 LYS cc_start: 0.5483 (mmmt) cc_final: 0.4654 (mmmt)
REVERT: A  456 HIS cc_start: 0.6474 (p90) cc_final: 0.6177 (p90)
REVERT: A  576 ILE cc_start: 0.8682 (tp) cc_final: 0.8463 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0773
  time to fit residues: 13.1780
Evaluate side-chains
  111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 110
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.3980
   chunk 18 optimal weight:    0.5980
   chunk 55 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 46 optimal weight:    0.0370
   chunk 2 optimal weight:    0.4980
   overall best weight:    0.3258

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 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 = 0.4063 r_free = 0.4063 target = 0.197340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.190404 restraints weight = 7486.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 72)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.169951 restraints weight = 12027.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.169525 restraints weight = 14573.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.169699 restraints weight = 12431.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.170069 restraints weight = 10844.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7421
moved from start:          0.3764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6355  Z= 0.124
  Angle     :  0.585   9.808   8624  Z= 0.304
  Chirality :  0.041   0.247    948
  Planarity :  0.004   0.068   1047
  Dihedral  :  6.342  59.984    995
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.19 (0.30), residues: 759
  helix:  0.41 (0.27), residues: 364
  sheet: -1.05 (0.53), residues: 95
  loop : -2.21 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  85 
 TYR   0.018   0.001   TYR A 107 
 PHE   0.019   0.001   PHE A 474 
 TRP   0.031   0.001   TRP A 317 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6349)
  covalent geometry    : angle       0.58373 ( 8612)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       1.38834 (    6)
  hydrogen bonds       : bond        0.03293 (  315)
  hydrogen bonds       : angle       4.42451 (  900)
  Misc. bond           : bond        0.00005 (    1)
  link_BETA1-4         : bond        0.00360 (    1)
  link_BETA1-4         : angle       0.95391 (    3)
  link_NAG-ASN         : bond        0.00546 (    1)
  link_NAG-ASN         : angle       1.44438 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5317 (mmmt) cc_final: 0.4561 (mmmt)
REVERT: A  456 HIS cc_start: 0.7145 (p90) cc_final: 0.6808 (p90)
REVERT: A  536 PHE cc_start: 0.7984 (t80) cc_final: 0.7158 (t80)
REVERT: C   62 GLN cc_start: 0.8704 (tp40) cc_final: 0.8466 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0842
  time to fit residues: 14.2661
Evaluate side-chains
  111 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 9 optimal weight:    0.2980
   chunk 34 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 40 optimal weight:    0.3980
   chunk 53 optimal weight:    5.9990
   chunk 41 optimal weight:    0.5980
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.194102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.184901 restraints weight = 7533.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 77)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.162355 restraints weight = 12629.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.162495 restraints weight = 12892.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.162214 restraints weight = 12603.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.162571 restraints weight = 12026.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7542
moved from start:          0.3955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6355  Z= 0.135
  Angle     :  0.571   9.587   8624  Z= 0.300
  Chirality :  0.041   0.204    948
  Planarity :  0.004   0.060   1047
  Dihedral  :  6.309  59.974    995
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.25 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.09 (0.30), residues: 759
  helix:  0.49 (0.27), residues: 365
  sheet: -0.97 (0.54), residues: 95
  loop : -2.17 (0.34), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.016   0.001   TYR A 107 
 PHE   0.019   0.001   PHE A 474 
 TRP   0.037   0.001   TRP A 317 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 6349)
  covalent geometry    : angle       0.56998 ( 8612)
  SS BOND              : bond        0.00157 (    3)
  SS BOND              : angle       1.48100 (    6)
  hydrogen bonds       : bond        0.03293 (  315)
  hydrogen bonds       : angle       4.42141 (  900)
  Misc. bond           : bond        0.00010 (    1)
  link_BETA1-4         : bond        0.00269 (    1)
  link_BETA1-4         : angle       0.67433 (    3)
  link_NAG-ASN         : bond        0.00696 (    1)
  link_NAG-ASN         : angle       0.91630 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5349 (mmmt) cc_final: 0.4586 (mmmt)
REVERT: A  267 TYR cc_start: 0.8136 (t80) cc_final: 0.7932 (t80)
REVERT: A  456 HIS cc_start: 0.7264 (p90) cc_final: 0.6876 (p90)
REVERT: A  536 PHE cc_start: 0.8369 (t80) cc_final: 0.8059 (t80)
REVERT: A  576 ILE cc_start: 0.8597 (tp) cc_final: 0.8352 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0829
  time to fit residues: 14.3574
Evaluate side-chains
  112 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 20 optimal weight:    0.2980
   chunk 35 optimal weight:    0.5980
   chunk 0 optimal weight:    9.9990
   chunk 72 optimal weight:    9.9990
   chunk 57 optimal weight:    0.0070
   chunk 5 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 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 = 0.4041 r_free = 0.4041 target = 0.195106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 118)---------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.185437 restraints weight = 7581.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.167167 restraints weight = 11474.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.165513 restraints weight = 12513.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.165234 restraints weight = 12296.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.165317 restraints weight = 12258.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3658
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.4018

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   6355  Z= 0.137
  Angle     :  0.574   9.571   8624  Z= 0.304
  Chirality :  0.041   0.201    948
  Planarity :  0.004   0.071   1047
  Dihedral  :  6.327  59.961    995
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.06 (0.30), residues: 759
  helix:  0.48 (0.27), residues: 365
  sheet: -0.95 (0.54), residues: 95
  loop : -2.12 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.017   0.001   TYR A 107 
 PHE   0.019   0.001   PHE A 556 
 TRP   0.042   0.001   TRP A 317 
 HIS   0.003   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6349)
  covalent geometry    : angle       0.57266 ( 8612)
  SS BOND              : bond        0.00046 (    3)
  SS BOND              : angle       1.46412 (    6)
  hydrogen bonds       : bond        0.03317 (  315)
  hydrogen bonds       : angle       4.39710 (  900)
  Misc. bond           : bond        0.00010 (    1)
  link_BETA1-4         : bond        0.00311 (    1)
  link_BETA1-4         : angle       0.75572 (    3)
  link_NAG-ASN         : bond        0.00601 (    1)
  link_NAG-ASN         : angle       1.01849 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5389 (mmmt) cc_final: 0.4616 (mmmt)
REVERT: A  456 HIS cc_start: 0.7109 (p90) cc_final: 0.6710 (p90)
REVERT: A  536 PHE cc_start: 0.8268 (t80) cc_final: 0.7992 (t80)
REVERT: B   53 MET cc_start: 0.8270 (tpp) cc_final: 0.8043 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.0753
  time to fit residues: 12.7798
Evaluate side-chains
  103 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 2 optimal weight:    0.0980
   chunk 5 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.190972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 90)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.182502 restraints weight = 7536.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 69)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.160168 restraints weight = 11748.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.160356 restraints weight = 11979.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.161156 restraints weight = 9663.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.161303 restraints weight = 9300.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7569
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   6355  Z= 0.158
  Angle     :  0.595   9.673   8624  Z= 0.315
  Chirality :  0.042   0.185    948
  Planarity :  0.005   0.071   1047
  Dihedral  :  6.450  59.773    995
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.30), residues: 759
  helix:  0.46 (0.27), residues: 370
  sheet: -0.87 (0.54), residues: 100
  loop : -2.13 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  38 
 TYR   0.019   0.002   TYR A 186 
 PHE   0.022   0.002   PHE A 556 
 TRP   0.042   0.002   TRP A 317 
 HIS   0.004   0.001   HIS A 143 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 6349)
  covalent geometry    : angle       0.59480 ( 8612)
  SS BOND              : bond        0.00620 (    3)
  SS BOND              : angle       0.85851 (    6)
  hydrogen bonds       : bond        0.03460 (  315)
  hydrogen bonds       : angle       4.49603 (  900)
  Misc. bond           : bond        0.00029 (    1)
  link_BETA1-4         : bond        0.00262 (    1)
  link_BETA1-4         : angle       0.75135 (    3)
  link_NAG-ASN         : bond        0.00649 (    1)
  link_NAG-ASN         : angle       0.78405 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5582 (mmmt) cc_final: 0.4764 (mmmt)
REVERT: A  291 ILE cc_start: 0.8729 (mm) cc_final: 0.8509 (mm)
REVERT: A  536 PHE cc_start: 0.8337 (t80) cc_final: 0.8073 (t80)
REVERT: A  576 ILE cc_start: 0.8666 (tp) cc_final: 0.8415 (tp)
REVERT: B   86 LYS cc_start: 0.7471 (ptmt) cc_final: 0.7164 (tttt)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.0808
  time to fit residues: 14.8489
Evaluate side-chains
  115 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 52 optimal weight:    8.9990
   chunk 20 optimal weight:    0.0270
   chunk 46 optimal weight:    0.2980
   chunk 13 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0870
   chunk 18 optimal weight:    0.3980
   chunk 71 optimal weight:    2.9990
   chunk 3 optimal weight:    0.0370
   overall best weight:    0.1694

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.200328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 106)---------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.178491 restraints weight = 7428.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.178057 restraints weight = 8460.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.178094 restraints weight = 8172.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.177846 restraints weight = 8670.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.177849 restraints weight = 7867.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.4123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6355  Z= 0.122
  Angle     :  0.591   9.657   8624  Z= 0.309
  Chirality :  0.042   0.224    948
  Planarity :  0.005   0.075   1047
  Dihedral  :  6.356  59.960    995
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.04 (0.31), residues: 759
  helix:  0.39 (0.26), residues: 373
  sheet: -0.83 (0.54), residues: 98
  loop : -2.04 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  59 
 TYR   0.018   0.001   TYR A 107 
 PHE   0.020   0.001   PHE A 428 
 TRP   0.045   0.001   TRP A 317 
 HIS   0.005   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6349)
  covalent geometry    : angle       0.58940 ( 8612)
  SS BOND              : bond        0.00173 (    3)
  SS BOND              : angle       1.19203 (    6)
  hydrogen bonds       : bond        0.03231 (  315)
  hydrogen bonds       : angle       4.38285 (  900)
  Misc. bond           : bond        0.00003 (    1)
  link_BETA1-4         : bond        0.00221 (    1)
  link_BETA1-4         : angle       0.68730 (    3)
  link_NAG-ASN         : bond        0.00698 (    1)
  link_NAG-ASN         : angle       1.36533 (    3)

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

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

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1518 Ramachandran restraints generated.
    759 Oldfield, 0 Emsley, 759 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  201 LYS cc_start: 0.5239 (mmmt) cc_final: 0.4619 (mmmt)
REVERT: A  456 HIS cc_start: 0.6863 (p90) cc_final: 0.6574 (p90)
REVERT: B   58 GLN cc_start: 0.8599 (tt0) cc_final: 0.8243 (mt0)
REVERT: B   86 LYS cc_start: 0.7044 (ptmt) cc_final: 0.6813 (tttt)
REVERT: C   62 GLN cc_start: 0.8710 (tp40) cc_final: 0.8299 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.0774
  time to fit residues: 12.9069
Evaluate side-chains
  104 residues out of total 642 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 26 optimal weight:    0.4980
   chunk 73 optimal weight:    2.9990
   chunk 57 optimal weight:    0.6980
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0270
   chunk 1 optimal weight:    0.7980
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 332 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.195160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.186426 restraints weight = 7511.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.166356 restraints weight = 11604.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.166202 restraints weight = 14048.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.166796 restraints weight = 11595.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.166818 restraints weight = 9999.076|
|-----------------------------------------------------------------------------|
r_work (final): 0.3685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.4209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6355  Z= 0.139
  Angle     :  0.599  11.651   8624  Z= 0.315
  Chirality :  0.043   0.210    948
  Planarity :  0.004   0.071   1047
  Dihedral  :  6.449  59.995    995
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.27 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.05 (0.31), residues: 759
  helix:  0.45 (0.27), residues: 368
  sheet: -0.81 (0.54), residues: 103
  loop : -2.15 (0.36), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  59 
 TYR   0.018   0.001   TYR A 186 
 PHE   0.022   0.001   PHE A 474 
 TRP   0.042   0.002   TRP A 317 
 HIS   0.004   0.001   HIS C 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6349)
  covalent geometry    : angle       0.59732 ( 8612)
  SS BOND              : bond        0.00131 (    3)
  SS BOND              : angle       1.61451 (    6)
  hydrogen bonds       : bond        0.03228 (  315)
  hydrogen bonds       : angle       4.41103 (  900)
  Misc. bond           : bond        0.00014 (    1)
  link_BETA1-4         : bond        0.00361 (    1)
  link_BETA1-4         : angle       0.80650 (    3)
  link_NAG-ASN         : bond        0.00679 (    1)
  link_NAG-ASN         : angle       0.90876 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1307.38 seconds
wall clock time: 23 minutes 21.67 seconds (1401.67 seconds total)