Starting phenix.real_space_refine
on Tue Mar  3 14:13:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7slq_25198/03_2026/7slq_25198.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     P      53      5.49       5
     S      14      5.16       5
     C    3269      2.51       5
     N     958      2.21       5
     O    1157      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  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: 5451
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1862
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1862
          Classifications: {'peptide': 237}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 67
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 57
          Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 48
    Chain: "B"
      Number of atoms: 2473
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 321, 2473
          Classifications: {'peptide': 321}
          Incomplete info: {'truncation_to_alanine': 32}
          Link IDs: {'PTRANS': 10, 'TRANS': 310}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 125
          Unresolved non-hydrogen angles: 149
          Unresolved non-hydrogen dihedrals: 102
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 2, 'ARG:plan': 2, 'GLN:plan1': 5}
          Unresolved non-hydrogen planarities: 72
    Chain: "R"
      Number of atoms: 1090
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 1090
          Unusual residues: {'G5J': 1}
          Classifications: {'RNA': 50, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 16, 'rna3p_pyr': 21}
          Link IDs: {'rna2p': 12, 'rna3p': 37, None: 1}
            Not linked:
              pdbres="G5J R   1 "
              pdbres="  G R   2 "
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 26
          Classifications: {'peptide': 1}
  Time building chain proxies: 1.39, per 1000 atoms: 0.25
  Number of scatterers: 5451
  At special positions: 0
  Unit cell: (82.39, 92.02, 103.79, 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      14     16.00
     P      53     15.00
     O    1157      8.00
     N     958      7.00
     C    3269      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.62
  Conformation dependent library (CDL) restraints added in 166.3 milliseconds
  

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1054

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 4 sheets defined
      48.9% alpha, 12.7% beta
      13 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 432 through 436
      removed outlier: 3.502A  pdb=" N   ARG A 435 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 442
      removed outlier: 4.131A  pdb=" N   TRP A 441 " --> pdb=" O   LYS A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 465
      removed outlier: 4.008A  pdb=" N   LYS A 464 " --> pdb=" O   SER A 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 476 through 492
      removed outlier: 3.852A  pdb=" N   HIS A 481 " --> pdb=" O   SER A 477 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER A 482 " --> pdb=" O   ARG A 478 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   TYR A 490 " --> pdb=" O   ASN A 486 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   LEU A 491 " --> pdb=" O   ILE A 487 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   SER A 492 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 531
      removed outlier: 3.793A  pdb=" N   SER A 530 " --> pdb=" O   SER A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 570
      removed outlier: 3.533A  pdb=" N   ALA A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 583 through 606
      removed outlier: 7.969A  pdb=" N   ASP A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 8.839A  pdb=" N   GLU A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 622 through 627
      removed outlier: 3.757A  pdb=" N   LYS A 627 " --> pdb=" O   GLY A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.628A  pdb=" N   TYR A 634 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 646 through 651
    Processing helix  chain 'B' and resid 30 through 46
    Processing helix  chain 'B' and resid 47 through 54
    Processing helix  chain 'B' and resid 55 through 63
    Processing helix  chain 'B' and resid 71 through 76
      removed outlier: 3.526A  pdb=" N   SER B  76 " --> pdb=" O   SER B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 4.069A  pdb=" N   LYS B  82 " --> pdb=" O   ASN B  78 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 94
    Processing helix  chain 'B' and resid 121 through 125
    Processing helix  chain 'B' and resid 137 through 147
      removed outlier: 3.580A  pdb=" N   ILE B 141 " --> pdb=" O   ASN B 137 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   LYS B 147 " --> pdb=" O   ARG B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 186
      removed outlier: 3.923A  pdb=" N   ALA B 180 " --> pdb=" O   LYS B 176 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU B 184 " --> pdb=" O   ALA B 180 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 413
    Processing helix  chain 'B' and resid 467 through 477
      removed outlier: 3.673A  pdb=" N   ALA B 477 " --> pdb=" O   ASP B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 508
    Processing helix  chain 'B' and resid 526 through 546
    Processing helix  chain 'B' and resid 552 through 571
    Processing sheet with id=AA1, first strand: chain 'A' and resid 554 through 557
      removed outlier: 6.288A  pdb=" N   MET A 470 " --> pdb=" O   VAL A 554 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   VAL A 556 " --> pdb=" O   MET A 470 " (cutoff:3.500A)
      removed outlier: 6.104A  pdb=" N   GLY A 472 " --> pdb=" O   VAL A 556 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   VAL A 447 " --> pdb=" O   VAL A 471 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   LEU A 473 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ASP A 449 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
      removed outlier: 6.563A  pdb=" N   ASP A 446 " --> pdb=" O   ASP A 576 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   VAL A 578 " --> pdb=" O   ASP A 446 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   LEU A 448 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   CYS A 580 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 7.551A  pdb=" N   LEU A 450 " --> pdb=" O   CYS A 580 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ASP A 576 " --> pdb=" O   ILE A 612 " (cutoff:3.500A)
      removed outlier: 8.084A  pdb=" N   VAL A 614 " --> pdb=" O   ASP A 576 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   VAL A 578 " --> pdb=" O   VAL A 614 " (cutoff:3.500A)
      removed outlier: 8.539A  pdb=" N   GLU A 616 " --> pdb=" O   VAL A 578 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   CYS A 580 " --> pdb=" O   GLU A 616 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   SER A 660 " --> pdb=" O   HIS A 682 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 69 through 70
      removed outlier: 3.673A  pdb=" N   VAL B  69 " --> pdb=" O   ILE B 109 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 151 through 155
      removed outlier: 3.755A  pdb=" N   TYR B 153 " --> pdb=" O   GLU B 172 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   ARG B 377 " --> pdb=" O   GLU B 130 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 481 through 485

    191 hydrogen bonds defined for protein.
    555 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 0.82

  Time building geometry restraints manager: 0.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1016
        1.33 -     1.45: 1622
        1.45 -     1.57: 2902
        1.57 -     1.69: 106
        1.69 -     1.81: 22
  Bond restraints: 5668
  Sorted by residual:
  bond pdb=" C3' G5J R   1 "
       pdb=" O3' G5J R   1 "
    ideal  model  delta    sigma   weight residual
    1.404  1.737 -0.333 2.00e-02 2.50e+03 2.78e+02
  bond pdb=" C3' G5J R   1 "
       pdb=" C4' G5J R   1 "
    ideal  model  delta    sigma   weight residual
    1.526  1.248  0.278 2.00e-02 2.50e+03 1.93e+02
  bond pdb=" C1' G5J R   1 "
       pdb=" C2' G5J R   1 "
    ideal  model  delta    sigma   weight residual
    1.524  1.254  0.270 2.00e-02 2.50e+03 1.82e+02
  bond pdb=" C6  G5J R   1 "
       pdb=" O6  G5J R   1 "
    ideal  model  delta    sigma   weight residual
    1.226  1.433 -0.207 2.00e-02 2.50e+03 1.07e+02
  bond pdb=" C2' G5J R   1 "
       pdb=" C3' G5J R   1 "
    ideal  model  delta    sigma   weight residual
    1.531  1.722 -0.191 2.00e-02 2.50e+03 9.15e+01
  ... (remaining 5663 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 7782
        3.39 -     6.78: 108
        6.78 -    10.17: 21
       10.17 -    13.56: 9
       13.56 -    16.95: 4
  Bond angle restraints: 7924
  Sorted by residual:
  angle pdb=" C   VAL B  99 "
        pdb=" N   VAL B 100 "
        pdb=" CA  VAL B 100 "
      ideal   model   delta    sigma   weight residual
     121.97  128.13   -6.16 1.00e+00 1.00e+00 3.80e+01
  angle pdb=" O3'   A R 298 "
        pdb=" C3'   A R 298 "
        pdb=" C2'   A R 298 "
      ideal   model   delta    sigma   weight residual
     109.50  118.39   -8.89 1.50e+00 4.44e-01 3.51e+01
  angle pdb=" N   TYR B  68 "
        pdb=" CA  TYR B  68 "
        pdb=" CB  TYR B  68 "
      ideal   model   delta    sigma   weight residual
     111.05  102.42    8.63 1.50e+00 4.44e-01 3.31e+01
  angle pdb=" O3A G5J R   1 "
        pdb=" PB  G5J R   1 "
        pdb=" O3B G5J R   1 "
      ideal   model   delta    sigma   weight residual
      92.82  109.77  -16.95 3.00e+00 1.11e-01 3.19e+01
  angle pdb=" C4'   G R 300 "
        pdb=" C3'   G R 300 "
        pdb=" O3'   G R 300 "
      ideal   model   delta    sigma   weight residual
     109.40  117.58   -8.18 1.50e+00 4.44e-01 2.98e+01
  ... (remaining 7919 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 3273
       35.50 -    71.00: 184
       71.00 -   106.51: 23
      106.51 -   142.01: 1
      142.01 -   177.51: 3
  Dihedral angle restraints: 3484
    sinusoidal: 1855
      harmonic: 1629
  Sorted by residual:
  dihedral pdb=" C5'   A R 298 "
           pdb=" C4'   A R 298 "
           pdb=" C3'   A R 298 "
           pdb=" O3'   A R 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00  105.99   41.01     1      8.00e+00 1.56e-02 3.68e+01
  dihedral pdb=" CA  ASN B 135 "
           pdb=" C   ASN B 135 "
           pdb=" N   VAL B 136 "
           pdb=" CA  VAL B 136 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.10  -24.90     0      5.00e+00 4.00e-02 2.48e+01
  dihedral pdb=" C3' G5J R   1 "
           pdb=" C4' G5J R   1 "
           pdb=" C5' G5J R   1 "
           pdb=" O5' G5J R   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     176.65   -0.86  177.51     1      3.00e+01 1.11e-03 2.13e+01
  ... (remaining 3481 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 875
       0.118 -    0.237: 54
       0.237 -    0.355: 2
       0.355 -    0.473: 2
       0.473 -    0.591: 1
  Chirality restraints: 934
  Sorted by residual:
  chirality pdb=" C3'   A R 298 "
            pdb=" C4'   A R 298 "
            pdb=" O3'   A R 298 "
            pdb=" C2'   A R 298 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.15   -0.59 2.00e-01 2.50e+01 8.75e+00
  chirality pdb=" CA  PRO A 427 "
            pdb=" N   PRO A 427 "
            pdb=" C   PRO A 427 "
            pdb=" CB  PRO A 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.31    0.41 2.00e-01 2.50e+01 4.23e+00
  chirality pdb=" C3' G5J R   1 "
            pdb=" C2' G5J R   1 "
            pdb=" C4' G5J R   1 "
            pdb=" O3' G5J R   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -3.10    0.39 2.00e-01 2.50e+01 3.80e+00
  ... (remaining 931 not shown)

  Planarity restraints: 815
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 549 "   -0.045 5.00e-02 4.00e+02   6.91e-02 7.63e+00
        pdb=" N   PRO A 550 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 550 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 550 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' G5J R   1 "   -0.031 2.00e-02 2.50e+03   1.47e-02 6.50e+00
        pdb=" C2  G5J R   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4  G5J R   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5  G5J R   1 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6  G5J R   1 "   -0.000 2.00e-02 2.50e+03
        pdb=" C8  G5J R   1 "    0.011 2.00e-02 2.50e+03
        pdb=" N1  G5J R   1 "    0.000 2.00e-02 2.50e+03
        pdb=" N2  G5J R   1 "    0.010 2.00e-02 2.50e+03
        pdb=" N3  G5J R   1 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7  G5J R   1 "    0.026 2.00e-02 2.50e+03
        pdb=" N9  G5J R   1 "    0.011 2.00e-02 2.50e+03
        pdb=" O6  G5J R   1 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 132 "   -0.037 5.00e-02 4.00e+02   5.69e-02 5.17e+00
        pdb=" N   PRO B 133 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 133 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 133 "   -0.032 5.00e-02 4.00e+02
  ... (remaining 812 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.69: 184
        2.69 -     3.25: 4857
        3.25 -     3.80: 8758
        3.80 -     4.35: 10821
        4.35 -     4.90: 17235
  Nonbonded interactions: 41855
  Sorted by model distance:
  nonbonded pdb=" O2'   A R 297 "
            pdb=" OP1   A R 298 "
     model   vdw
     2.144 3.040
  nonbonded pdb=" O   GLY A 532 "
            pdb=" OH  TYR B 391 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   SER B 461 "
            pdb=" OG1 THR B 491 "
     model   vdw
     2.331 3.040
  nonbonded pdb=" O   TYR A 650 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.337 3.040
  nonbonded pdb=" OD1 ASP A 474 "
            pdb=" O2' SAH A 701 "
     model   vdw
     2.341 3.040
  ... (remaining 41850 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:             0.600
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.240
  Find NCS groups from input model:        0.020
  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:    9.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
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      :  0.011   0.333   5669  Z= 0.560
  Angle     :  1.161  16.945   7924  Z= 0.628
  Chirality :  0.062   0.591    934
  Planarity :  0.007   0.069    815
  Dihedral  : 19.871 177.509   2430
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  4.94 %
    Favored  : 93.71 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -2.83 (0.30), residues: 546
  helix: -2.16 (0.25), residues: 252
  sheet: -0.52 (0.63), residues: 64
  loop : -1.76 (0.35), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 484 
 TYR   0.022   0.003   TYR B  68 
 PHE   0.022   0.003   PHE B 168 
 TRP   0.018   0.002   TRP A 620 
 HIS   0.005   0.002   HIS B 158 

Details of bonding type rmsd
  covalent geometry    : bond        0.01068 ( 5668)
  covalent geometry    : angle       1.16097 ( 7924)
  hydrogen bonds       : bond        0.13755 (  225)
  hydrogen bonds       : angle       5.95426 (  623)
  Misc. bond           : bond        0.03531 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 105
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  464 LYS cc_start: 0.7199 (OUTLIER) cc_final: 0.6972 (ptpt)
REVERT: A  601 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6913 (ttp-110)
  outliers start: 6
  outliers final: 1
  residues processed: 109
  average time/residue: 0.1026
  time to fit residues: 13.7401
Evaluate side-chains
  55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 LYS
Chi-restraints excluded: chain B residue  557 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0270
   chunk 31 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:   10.0000
   overall best weight:    1.1642

-------------------------------------------------------------------------------
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 = 0.4329 r_free = 0.4329 target = 0.167327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.124971 restraints weight = 9154.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.124169 restraints weight = 10207.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.126515 restraints weight = 8571.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.126811 restraints weight = 5719.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.127230 restraints weight = 5979.677|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5669  Z= 0.143
  Angle     :  0.627   8.393   7924  Z= 0.325
  Chirality :  0.042   0.230    934
  Planarity :  0.005   0.076    815
  Dihedral  : 21.445 161.862   1442
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  :  9.44 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -1.35 (0.33), residues: 546
  helix: -0.59 (0.30), residues: 259
  sheet:  0.33 (0.75), residues: 52
  loop : -1.43 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 488 
 TYR   0.008   0.001   TYR B 391 
 PHE   0.025   0.002   PHE B  46 
 TRP   0.019   0.002   TRP B 140 
 HIS   0.003   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 5668)
  covalent geometry    : angle       0.62663 ( 7924)
  hydrogen bonds       : bond        0.04344 (  225)
  hydrogen bonds       : angle       4.28452 (  623)
  Misc. bond           : bond        0.00314 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 ILE cc_start: 0.8615 (mm) cc_final: 0.8409 (mm)
REVERT: A  601 ARG cc_start: 0.7278 (ttm110) cc_final: 0.7068 (ttp-170)
REVERT: A  625 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8158 (ptmm)
REVERT: A  636 ASN cc_start: 0.8970 (m-40) cc_final: 0.8741 (m-40)
  outliers start: 11
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0932
  time to fit residues: 8.3345
Evaluate side-chains
  57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  625 LYS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  161 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 46 optimal weight:   10.0000
   chunk 50 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 44 optimal weight:   10.0000
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B 530 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.172383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.133572 restraints weight = 9585.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.133249 restraints weight = 11018.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135700 restraints weight = 9421.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.136147 restraints weight = 6778.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.136836 restraints weight = 7135.941|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5669  Z= 0.139
  Angle     :  0.589   8.744   7924  Z= 0.304
  Chirality :  0.040   0.184    934
  Planarity :  0.005   0.075    815
  Dihedral  : 20.717 162.748   1436
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 10.34 %
    Favored  : 85.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.70 (0.34), residues: 546
  helix:  0.12 (0.32), residues: 259
  sheet:  0.11 (0.79), residues: 47
  loop : -1.16 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 488 
 TYR   0.012   0.001   TYR A 560 
 PHE   0.029   0.001   PHE B  56 
 TRP   0.023   0.002   TRP A 465 
 HIS   0.005   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 5668)
  covalent geometry    : angle       0.58935 ( 7924)
  hydrogen bonds       : bond        0.03988 (  225)
  hydrogen bonds       : angle       4.02746 (  623)
  Misc. bond           : bond        0.00178 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 56
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8096 (ptmm)
REVERT: B   40 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7424 (ptpp)
REVERT: B  545 ASN cc_start: 0.7768 (m110) cc_final: 0.7117 (t0)
  outliers start: 18
  outliers final: 7
  residues processed: 69
  average time/residue: 0.0619
  time to fit residues: 5.8787
Evaluate side-chains
  54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  625 LYS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue  109 ILE
Chi-restraints excluded: chain B residue  159 TYR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 35 optimal weight:    0.2980
   chunk 48 optimal weight:    2.9990
   chunk 11 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 25 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN
B 530 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.174000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.134335 restraints weight = 9548.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.133640 restraints weight = 9611.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135791 restraints weight = 8450.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.136350 restraints weight = 5917.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.136583 restraints weight = 5669.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.3182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   5669  Z= 0.109
  Angle     :  0.559   8.748   7924  Z= 0.284
  Chirality :  0.038   0.172    934
  Planarity :  0.005   0.077    815
  Dihedral  : 20.366 161.990   1436
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 14.83 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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 (0.35), residues: 546
  helix:  0.52 (0.33), residues: 259
  sheet:  0.34 (0.80), residues: 49
  loop : -1.28 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 488 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.027   0.001   PHE B  56 
 TRP   0.027   0.002   TRP A 465 
 HIS   0.003   0.001   HIS B  52 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5668)
  covalent geometry    : angle       0.55861 ( 7924)
  hydrogen bonds       : bond        0.03604 (  225)
  hydrogen bonds       : angle       3.83143 (  623)
  Misc. bond           : bond        0.00179 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 48
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7522 (ptpp)
REVERT: B  186 LEU cc_start: 0.6282 (tp) cc_final: 0.6052 (mp)
REVERT: B  545 ASN cc_start: 0.8140 (m110) cc_final: 0.7362 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 57
  average time/residue: 0.0609
  time to fit residues: 4.7990
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 28 optimal weight:    9.9990
   chunk 10 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9980
   chunk 16 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0060
   chunk 25 optimal weight:    0.0980
   chunk 1 optimal weight:    1.9990
   chunk 36 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 44 optimal weight:    7.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.4200

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.171715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.132661 restraints weight = 9785.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.132855 restraints weight = 10954.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.134695 restraints weight = 9521.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.135236 restraints weight = 6577.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.135443 restraints weight = 6551.950|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5669  Z= 0.145
  Angle     :  0.574   8.407   7924  Z= 0.293
  Chirality :  0.039   0.181    934
  Planarity :  0.005   0.080    815
  Dihedral  : 20.228 161.934   1436
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 15.28 %
    Favored  : 81.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.36 (0.35), residues: 546
  helix:  0.59 (0.33), residues: 260
  sheet:  0.75 (0.71), residues: 61
  loop : -1.50 (0.37), residues: 225

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 484 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.024   0.001   PHE B  56 
 TRP   0.032   0.002   TRP A 465 
 HIS   0.006   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 5668)
  covalent geometry    : angle       0.57383 ( 7924)
  hydrogen bonds       : bond        0.03971 (  225)
  hydrogen bonds       : angle       3.92876 (  623)
  Misc. bond           : bond        0.00169 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8167 (ptmm)
REVERT: B   40 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7531 (ptpp)
  outliers start: 15
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0684
  time to fit residues: 5.0156
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  625 LYS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   40 LYS
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 56 optimal weight:   10.0000
   chunk 29 optimal weight:   20.0000
   chunk 49 optimal weight:    0.0980
   chunk 18 optimal weight:    8.9990
   chunk 47 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.170181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.130768 restraints weight = 9728.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.130311 restraints weight = 11227.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.133057 restraints weight = 9184.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.132609 restraints weight = 6464.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.133531 restraints weight = 6786.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.3657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5669  Z= 0.167
  Angle     :  0.610   9.503   7924  Z= 0.305
  Chirality :  0.040   0.186    934
  Planarity :  0.005   0.081    815
  Dihedral  : 20.127 162.245   1436
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 16.18 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.35 (0.35), residues: 546
  helix:  0.62 (0.33), residues: 254
  sheet:  0.49 (0.75), residues: 56
  loop : -1.35 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 484 
 TYR   0.011   0.001   TYR B 391 
 PHE   0.020   0.001   PHE B  56 
 TRP   0.037   0.002   TRP A 465 
 HIS   0.007   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 5668)
  covalent geometry    : angle       0.61043 ( 7924)
  hydrogen bonds       : bond        0.04287 (  225)
  hydrogen bonds       : angle       4.06749 (  623)
  Misc. bond           : bond        0.00163 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 43
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  576 ASP cc_start: 0.7814 (t0) cc_final: 0.7456 (t0)
REVERT: B  100 VAL cc_start: 0.7384 (OUTLIER) cc_final: 0.7138 (p)
REVERT: B  532 TYR cc_start: 0.7180 (t80) cc_final: 0.6870 (t80)
REVERT: B  545 ASN cc_start: 0.7796 (p0) cc_final: 0.7152 (p0)
  outliers start: 19
  outliers final: 10
  residues processed: 58
  average time/residue: 0.0588
  time to fit residues: 4.9189
Evaluate side-chains
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  100 VAL
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  554 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 7 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 26 optimal weight:    8.9990
   chunk 0 optimal weight:    7.9990
   chunk 20 optimal weight:    5.9990
   chunk 9 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.166580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.123654 restraints weight = 9470.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.122824 restraints weight = 8571.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.125289 restraints weight = 7982.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.125354 restraints weight = 5910.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.125831 restraints weight = 6363.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.3825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.3826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5669  Z= 0.124
  Angle     :  0.552   8.001   7924  Z= 0.283
  Chirality :  0.039   0.179    934
  Planarity :  0.005   0.084    815
  Dihedral  : 20.019 162.226   1436
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.08 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.35 (0.35), residues: 546
  helix:  0.70 (0.33), residues: 260
  sheet:  0.04 (0.79), residues: 51
  loop : -1.35 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 488 
 TYR   0.012   0.001   TYR B 391 
 PHE   0.020   0.001   PHE B  56 
 TRP   0.034   0.002   TRP A 465 
 HIS   0.007   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5668)
  covalent geometry    : angle       0.55161 ( 7924)
  hydrogen bonds       : bond        0.03886 (  225)
  hydrogen bonds       : angle       4.04298 (  623)
  Misc. bond           : bond        0.00174 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: B  545 ASN cc_start: 0.7927 (p0) cc_final: 0.7293 (p0)
  outliers start: 15
  outliers final: 10
  residues processed: 54
  average time/residue: 0.0673
  time to fit residues: 4.9385
Evaluate side-chains
  47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 37
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  554 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 58 optimal weight:   10.0000
   chunk 55 optimal weight:    9.9990
   chunk 26 optimal weight:    9.9990
   chunk 13 optimal weight:    5.9990
   chunk 40 optimal weight:    0.4980
   chunk 8 optimal weight:    0.2980
   chunk 59 optimal weight:    4.9990
   chunk 50 optimal weight:   20.0000
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   overall best weight:    2.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 682 HIS
B  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.169099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.130191 restraints weight = 9815.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.129385 restraints weight = 10238.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.131567 restraints weight = 9531.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.131941 restraints weight = 6551.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.132797 restraints weight = 6378.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7220
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   5669  Z= 0.192
  Angle     :  0.631  10.155   7924  Z= 0.319
  Chirality :  0.041   0.193    934
  Planarity :  0.005   0.087    815
  Dihedral  : 19.929 161.894   1436
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 16.40 %
    Favored  : 79.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.34 (0.36), residues: 546
  helix:  0.68 (0.33), residues: 254
  sheet:  0.36 (0.79), residues: 54
  loop : -1.36 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 531 
 TYR   0.012   0.002   TYR B 391 
 PHE   0.021   0.002   PHE B  46 
 TRP   0.050   0.002   TRP A 465 
 HIS   0.007   0.002   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 5668)
  covalent geometry    : angle       0.63126 ( 7924)
  hydrogen bonds       : bond        0.04547 (  225)
  hydrogen bonds       : angle       4.23474 (  623)
  Misc. bond           : bond        0.00161 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 ASP cc_start: 0.7814 (t0) cc_final: 0.7470 (t0)
REVERT: A  625 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8354 (ptmm)
REVERT: B  545 ASN cc_start: 0.7768 (p0) cc_final: 0.7148 (p0)
  outliers start: 18
  outliers final: 12
  residues processed: 55
  average time/residue: 0.0665
  time to fit residues: 5.0428
Evaluate side-chains
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 40
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  538 GLN
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  625 LYS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  554 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0370
   chunk 38 optimal weight:    4.9990
   chunk 55 optimal weight:    9.9990
   chunk 6 optimal weight:    0.7980
   chunk 9 optimal weight:    0.5980
   chunk 16 optimal weight:    2.9990
   chunk 28 optimal weight:    9.9990
   chunk 51 optimal weight:    5.9990
   overall best weight:    0.8460

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.167289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.125028 restraints weight = 9588.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.124182 restraints weight = 8455.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.126403 restraints weight = 8046.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.126761 restraints weight = 5832.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.126993 restraints weight = 5794.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7197
moved from start:          0.4162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5669  Z= 0.115
  Angle     :  0.545   7.479   7924  Z= 0.280
  Chirality :  0.038   0.179    934
  Planarity :  0.005   0.089    815
  Dihedral  : 19.888 162.068   1436
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.08 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.22 (0.36), residues: 546
  helix:  0.84 (0.34), residues: 260
  sheet:  0.04 (0.80), residues: 51
  loop : -1.30 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.013   0.001   TYR B 391 
 PHE   0.019   0.001   PHE B  56 
 TRP   0.026   0.002   TRP A 465 
 HIS   0.008   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 5668)
  covalent geometry    : angle       0.54498 ( 7924)
  hydrogen bonds       : bond        0.03773 (  225)
  hydrogen bonds       : angle       4.12492 (  623)
  Misc. bond           : bond        0.00161 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  576 ASP cc_start: 0.7788 (t0) cc_final: 0.7414 (t0)
REVERT: B  545 ASN cc_start: 0.8011 (p0) cc_final: 0.7400 (p0)
  outliers start: 13
  outliers final: 11
  residues processed: 54
  average time/residue: 0.0546
  time to fit residues: 4.2756
Evaluate side-chains
  50 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 39
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  409 ILE
Chi-restraints excluded: chain B residue  554 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0370
   chunk 15 optimal weight:    5.9990
   chunk 56 optimal weight:    9.9990
   chunk 58 optimal weight:   10.0000
   chunk 40 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   overall best weight:    1.1462

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

Flipped N/Q/H residues before XYZ refinement:
B  33 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4407 r_free = 0.4407 target = 0.171530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.133139 restraints weight = 9658.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.133212 restraints weight = 10402.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.135367 restraints weight = 8903.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.135656 restraints weight = 6462.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.135892 restraints weight = 6432.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.4278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5669  Z= 0.130
  Angle     :  0.563   8.895   7924  Z= 0.287
  Chirality :  0.038   0.180    934
  Planarity :  0.005   0.092    815
  Dihedral  : 19.873 161.462   1436
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.30 %
    Favored  : 79.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.26 (0.36), residues: 546
  helix:  0.82 (0.34), residues: 260
  sheet: -0.08 (0.79), residues: 51
  loop : -1.31 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  58 
 TYR   0.013   0.001   TYR B 391 
 PHE   0.031   0.002   PHE B  56 
 TRP   0.036   0.002   TRP A 465 
 HIS   0.008   0.001   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 5668)
  covalent geometry    : angle       0.56335 ( 7924)
  hydrogen bonds       : bond        0.03888 (  225)
  hydrogen bonds       : angle       4.12166 (  623)
  Misc. bond           : bond        0.00151 (    1)

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

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

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1092 Ramachandran restraints generated.
    546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  576 ASP cc_start: 0.7747 (t0) cc_final: 0.7432 (t0)
REVERT: B  545 ASN cc_start: 0.7907 (p0) cc_final: 0.7283 (p0)
  outliers start: 13
  outliers final: 13
  residues processed: 53
  average time/residue: 0.0594
  time to fit residues: 4.5303
Evaluate side-chains
  49 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  450 LEU
Chi-restraints excluded: chain A residue  476 ASP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  554 VAL
Chi-restraints excluded: chain A residue  606 HIS
Chi-restraints excluded: chain A residue  661 TYR
Chi-restraints excluded: chain B residue   33 GLN
Chi-restraints excluded: chain B residue   85 THR
Chi-restraints excluded: chain B residue  161 SER
Chi-restraints excluded: chain B residue  379 LEU
Chi-restraints excluded: chain B residue  409 ILE
Chi-restraints excluded: chain B residue  554 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 22 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 48 optimal weight:   40.0000
   chunk 56 optimal weight:   10.0000
   chunk 41 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 10 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    3.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 489 HIS
B  33 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.165965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.126425 restraints weight = 9915.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.125281 restraints weight = 11280.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.127928 restraints weight = 9952.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.127823 restraints weight = 6940.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.128372 restraints weight = 7157.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7313
moved from start:          0.4530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.053   5669  Z= 0.289
  Angle     :  0.743  10.766   7924  Z= 0.379
  Chirality :  0.045   0.212    934
  Planarity :  0.006   0.088    815
  Dihedral  : 20.024 161.411   1436
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  3.37 %
    Allowed  : 17.30 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    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: -0.87 (0.35), residues: 546
  helix:  0.19 (0.32), residues: 262
  sheet: -0.36 (0.80), residues: 54
  loop : -1.48 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B  58 
 TYR   0.018   0.002   TYR B 532 
 PHE   0.019   0.002   PHE B  56 
 TRP   0.072   0.003   TRP A 465 
 HIS   0.008   0.002   HIS B 528 

Details of bonding type rmsd
  covalent geometry    : bond        0.00659 ( 5668)
  covalent geometry    : angle       0.74313 ( 7924)
  hydrogen bonds       : bond        0.05587 (  225)
  hydrogen bonds       : angle       4.71676 (  623)
  Misc. bond           : bond        0.00149 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 897.59 seconds
wall clock time: 16 minutes 6.19 seconds (966.19 seconds total)