Starting phenix.real_space_refine
on Thu Jul 24 09:54:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7slq_25198/07_2025/7slq_25198.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7slq_25198/07_2025/7slq_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_25198/07_2025/7slq_25198.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2025/7slq_25198.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2025/7slq_25198.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7slq_25198/07_2025/7slq_25198.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP: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: {'GLN:plan1': 5, 'GLU:plan': 9, 'ARG:plan': 2, 'ASP:plan': 2}
          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: 4.07, per 1000 atoms: 0.75
  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: 1.47
  Conformation dependent library (CDL) restraints added in 708.5 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: 1.88
  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: 1.76

  Time building geometry restraints manager: 1.69 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:             0.560
  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:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.710
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  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:3.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.700
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.018   0.002   TRP A 620 
 HIS   0.005   0.002   HIS B 158 
 PHE   0.022   0.003   PHE B 168 
 TYR   0.022   0.003   TYR B  68 
 ARG   0.009   0.001   ARG A 484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13755 (  225)
  hydrogen bonds       : angle       5.95426 (  623)
  covalent geometry    : bond        0.01068 ( 5668)
  covalent geometry    : angle       1.16097 ( 7924)
  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  : 0.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  601 ARG cc_start: 0.7168 (ttm110) cc_final: 0.6914 (ttp-110)
  outliers start: 6
  outliers final: 2
  residues processed: 109
  average time/residue: 0.2341
  time to fit residues: 31.0180
Evaluate side-chains
  56 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 54
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
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 50 optimal weight:   20.0000
   chunk 45 optimal weight:    9.9990
   chunk 25 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:   20.0000
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:    0.8980
   chunk 18 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 528 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.167627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.125673 restraints weight = 9084.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.125886 restraints weight = 10332.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.127864 restraints weight = 8974.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.2169

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= 0.140
  Angle     :  0.616   8.791   7924  Z= 0.319
  Chirality :  0.041   0.196    934
  Planarity :  0.005   0.076    815
  Dihedral  : 21.448 161.864   1442
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  :  9.66 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.33), residues: 546
  helix: -0.51 (0.30), residues: 258
  sheet:  0.38 (0.74), residues: 52
  loop : -1.44 (0.36), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B 140 
 HIS   0.004   0.001   HIS B 528 
 PHE   0.023   0.002   PHE B  46 
 TYR   0.008   0.001   TYR B 483 
 ARG   0.006   0.001   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04262 (  225)
  hydrogen bonds       : angle       4.23378 (  623)
  covalent geometry    : bond        0.00308 ( 5668)
  covalent geometry    : angle       0.61560 ( 7924)
  Misc. bond           : bond        0.00145 (    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
  70 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 58
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  461 ILE cc_start: 0.8601 (mm) cc_final: 0.8395 (mm)
REVERT: A  601 ARG cc_start: 0.7264 (ttm110) cc_final: 0.7058 (ttp-170)
REVERT: A  625 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8112 (ptmm)
REVERT: A  636 ASN cc_start: 0.8979 (m-40) cc_final: 0.8755 (m-40)
  outliers start: 12
  outliers final: 7
  residues processed: 67
  average time/residue: 0.2094
  time to fit residues: 18.0239
Evaluate side-chains
  54 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain B residue  185 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 19 optimal weight:    5.9990
   chunk 10 optimal weight:    0.0060
   chunk 30 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 13 optimal weight:    0.5980
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:   10.0000
   chunk 22 optimal weight:    0.0060
   chunk 18 optimal weight:    0.0670
   overall best weight:    0.2550

-------------------------------------------------------------------------------
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 = 0.4433 r_free = 0.4433 target = 0.175076 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.136310 restraints weight = 9595.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.134985 restraints weight = 9899.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.137569 restraints weight = 8512.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7054
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   5669  Z= 0.101
  Angle     :  0.550   6.860   7924  Z= 0.285
  Chirality :  0.038   0.178    934
  Planarity :  0.005   0.078    815
  Dihedral  : 20.769 162.190   1436
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 10.34 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.35), residues: 546
  helix:  0.24 (0.32), residues: 263
  sheet:  0.16 (0.69), residues: 56
  loop : -1.09 (0.39), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B 533 
 HIS   0.003   0.001   HIS B  52 
 PHE   0.028   0.001   PHE B  56 
 TYR   0.011   0.001   TYR B 391 
 ARG   0.004   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03443 (  225)
  hydrogen bonds       : angle       3.90976 (  623)
  covalent geometry    : bond        0.00211 ( 5668)
  covalent geometry    : angle       0.54987 ( 7924)
  Misc. bond           : bond        0.00188 (    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
  75 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.7911 (ptmm)
REVERT: B   40 LYS cc_start: 0.7719 (OUTLIER) cc_final: 0.7374 (ptpp)
  outliers start: 13
  outliers final: 5
  residues processed: 70
  average time/residue: 0.1709
  time to fit residues: 15.8025
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    5.9990
   chunk 5 optimal weight:    1.9990
   chunk 22 optimal weight:   10.0000
   chunk 12 optimal weight:    0.5980
   chunk 57 optimal weight:    6.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
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 = 0.4424 r_free = 0.4424 target = 0.173817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.134752 restraints weight = 9768.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.134431 restraints weight = 9756.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.136547 restraints weight = 8318.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3164

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= 0.126
  Angle     :  0.566   8.402   7924  Z= 0.290
  Chirality :  0.039   0.176    934
  Planarity :  0.005   0.078    815
  Dihedral  : 20.340 161.675   1436
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 13.93 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.35), residues: 546
  helix:  0.54 (0.33), residues: 258
  sheet:  0.40 (0.73), residues: 54
  loop : -1.22 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 465 
 HIS   0.004   0.001   HIS B  52 
 PHE   0.026   0.002   PHE B  56 
 TYR   0.013   0.001   TYR A 560 
 ARG   0.004   0.000   ARG A 484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  225)
  hydrogen bonds       : angle       3.92224 (  623)
  covalent geometry    : bond        0.00284 ( 5668)
  covalent geometry    : angle       0.56605 ( 7924)
  Misc. bond           : bond        0.00185 (    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
  61 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 44
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7982 (ptmm)
REVERT: B   40 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7505 (ptpp)
REVERT: B  545 ASN cc_start: 0.7945 (m110) cc_final: 0.7187 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 56
  average time/residue: 0.1419
  time to fit residues: 11.6321
Evaluate side-chains
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 39
  time to evaluate  : 0.851 
-------------------------------------------------------------------------------
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  603 ILE
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  159 TYR
Chi-restraints excluded: chain B residue  161 SER
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 36 optimal weight:    6.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:    7.9990
   chunk 54 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 35 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9990
   chunk 43 optimal weight:   20.0000
   chunk 24 optimal weight:    7.9990
   chunk 13 optimal weight:    0.4980
   chunk 4 optimal weight:    0.3980
   overall best weight:    0.6982

-------------------------------------------------------------------------------
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 = 0.4377 r_free = 0.4377 target = 0.170136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.129921 restraints weight = 9502.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.129298 restraints weight = 9874.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.132035 restraints weight = 8726.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.3887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7080
moved from start:          0.3469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5669  Z= 0.107
  Angle     :  0.536   7.449   7924  Z= 0.274
  Chirality :  0.038   0.171    934
  Planarity :  0.005   0.080    815
  Dihedral  : 20.210 161.772   1436
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.06 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.35), residues: 546
  helix:  0.70 (0.33), residues: 259
  sheet:  0.47 (0.72), residues: 56
  loop : -1.19 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 465 
 HIS   0.003   0.000   HIS B  52 
 PHE   0.024   0.001   PHE B  56 
 TYR   0.015   0.001   TYR A 560 
 ARG   0.003   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  225)
  hydrogen bonds       : angle       3.83102 (  623)
  covalent geometry    : bond        0.00237 ( 5668)
  covalent geometry    : angle       0.53610 ( 7924)
  Misc. bond           : bond        0.00183 (    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
  55 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 0.554 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.7989 (ptmm)
REVERT: B   40 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7493 (ptpp)
REVERT: B  545 ASN cc_start: 0.8065 (m110) cc_final: 0.7334 (t0)
  outliers start: 14
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1825
  time to fit residues: 12.8830
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  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  603 ILE
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  159 TYR
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 36 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 21 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    9.9990
   chunk 24 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 28 optimal weight:   10.0000
   chunk 39 optimal weight:    4.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    1.8184

-------------------------------------------------------------------------------
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 = 0.4345 r_free = 0.4345 target = 0.166773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.125178 restraints weight = 9471.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.125472 restraints weight = 9192.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.127178 restraints weight = 8478.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7202
moved from start:          0.3636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5669  Z= 0.171
  Angle     :  0.609   9.469   7924  Z= 0.307
  Chirality :  0.040   0.186    934
  Planarity :  0.005   0.083    815
  Dihedral  : 20.077 161.844   1436
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 16.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.35), residues: 546
  helix:  0.77 (0.33), residues: 253
  sheet:  0.73 (0.70), residues: 61
  loop : -1.37 (0.37), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 465 
 HIS   0.004   0.001   HIS B  52 
 PHE   0.020   0.001   PHE B  56 
 TYR   0.021   0.002   TYR A 560 
 ARG   0.006   0.001   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04259 (  225)
  hydrogen bonds       : angle       4.02915 (  623)
  covalent geometry    : bond        0.00388 ( 5668)
  covalent geometry    : angle       0.60887 ( 7924)
  Misc. bond           : bond        0.00158 (    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
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 36
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  625 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8101 (ptmm)
REVERT: B   40 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7565 (ptpp)
REVERT: B  545 ASN cc_start: 0.8223 (m110) cc_final: 0.7444 (t0)
  outliers start: 17
  outliers final: 11
  residues processed: 51
  average time/residue: 0.1546
  time to fit residues: 11.0243
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  : 0.516 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  476 ASP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  603 ILE
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
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 57 optimal weight:    7.9990
   chunk 18 optimal weight:    0.0050
   chunk 46 optimal weight:   20.0000
   chunk 26 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 47 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.7796

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.168774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.127354 restraints weight = 9296.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.127565 restraints weight = 9289.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.129648 restraints weight = 8211.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7117
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5669  Z= 0.107
  Angle     :  0.527   7.579   7924  Z= 0.269
  Chirality :  0.038   0.175    934
  Planarity :  0.005   0.084    815
  Dihedral  : 19.946 162.149   1436
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 17.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.14 (0.36), residues: 546
  helix:  0.87 (0.33), residues: 260
  sheet:  0.43 (0.71), residues: 58
  loop : -1.36 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 465 
 HIS   0.002   0.000   HIS B  52 
 PHE   0.021   0.001   PHE B  56 
 TYR   0.013   0.001   TYR A 560 
 ARG   0.003   0.000   ARG B 108 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03639 (  225)
  hydrogen bonds       : angle       3.86428 (  623)
  covalent geometry    : bond        0.00234 ( 5668)
  covalent geometry    : angle       0.52684 ( 7924)
  Misc. bond           : bond        0.00181 (    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
  53 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 39
  time to evaluate  : 0.512 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   40 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7516 (ptpp)
  outliers start: 14
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1393
  time to fit residues: 10.0827
Evaluate side-chains
  46 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  476 ASP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  603 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    7.9990
   chunk 35 optimal weight:    2.9990
   chunk 15 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 36 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 25 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 52 optimal weight:    0.0470
   chunk 58 optimal weight:   10.0000
   overall best weight:    2.5684

-------------------------------------------------------------------------------
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 = 0.4372 r_free = 0.4372 target = 0.168356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.131390 restraints weight = 9759.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.129559 restraints weight = 12443.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.131244 restraints weight = 10848.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.4005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041   5669  Z= 0.223
  Angle     :  0.680  10.518   7924  Z= 0.343
  Chirality :  0.042   0.202    934
  Planarity :  0.006   0.090    815
  Dihedral  : 19.970 161.825   1436
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 17.98 %
    Favored  : 78.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.35), residues: 546
  helix:  0.47 (0.32), residues: 261
  sheet:  0.42 (0.69), residues: 61
  loop : -1.58 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.054   0.003   TRP A 465 
 HIS   0.005   0.001   HIS B  52 
 PHE   0.022   0.002   PHE B  56 
 TYR   0.021   0.002   TYR A 560 
 ARG   0.005   0.001   ARG A 484 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04935 (  225)
  hydrogen bonds       : angle       4.28115 (  623)
  covalent geometry    : bond        0.00506 ( 5668)
  covalent geometry    : angle       0.67971 ( 7924)
  Misc. bond           : bond        0.00150 (    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
  57 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 40
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
REVERT: A  576 ASP cc_start: 0.7594 (t0) cc_final: 0.7288 (t0)
REVERT: B   79 LYS cc_start: 0.7269 (mtpt) cc_final: 0.6979 (mtpp)
REVERT: B  545 ASN cc_start: 0.7655 (p0) cc_final: 0.7023 (p0)
  outliers start: 17
  outliers final: 11
  residues processed: 55
  average time/residue: 0.1420
  time to fit residues: 11.0575
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  476 ASP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  603 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 9 optimal weight:    0.4980
   chunk 0 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9980
   chunk 6 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 34 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 35 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.4409 r_free = 0.4409 target = 0.172111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.133446 restraints weight = 9758.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.134258 restraints weight = 8796.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.136194 restraints weight = 8172.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.4111

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= 0.117
  Angle     :  0.566  10.242   7924  Z= 0.286
  Chirality :  0.039   0.181    934
  Planarity :  0.005   0.090    815
  Dihedral  : 19.920 162.294   1436
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.55 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.36), residues: 546
  helix:  0.84 (0.34), residues: 260
  sheet:  0.36 (0.71), residues: 58
  loop : -1.39 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 465 
 HIS   0.003   0.001   HIS B  52 
 PHE   0.021   0.001   PHE B  56 
 TYR   0.014   0.001   TYR A 560 
 ARG   0.003   0.000   ARG B  58 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03882 (  225)
  hydrogen bonds       : angle       4.05592 (  623)
  covalent geometry    : bond        0.00258 ( 5668)
  covalent geometry    : angle       0.56606 ( 7924)
  Misc. bond           : bond        0.00157 (    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
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 37
  time to evaluate  : 0.584 
Fit side-chains
   revert: symmetry clash
REVERT: B  545 ASN cc_start: 0.7799 (p0) cc_final: 0.7145 (p0)
  outliers start: 11
  outliers final: 11
  residues processed: 47
  average time/residue: 0.2099
  time to fit residues: 13.9618
Evaluate side-chains
  47 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 36
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  441 TRP
Chi-restraints excluded: chain A residue  461 ILE
Chi-restraints excluded: chain A residue  476 ASP
Chi-restraints excluded: chain A residue  548 VAL
Chi-restraints excluded: chain A residue  603 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 43 optimal weight:   20.0000
   chunk 42 optimal weight:    0.0370
   chunk 34 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0470
   chunk 27 optimal weight:    4.9990
   chunk 3 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.5756

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.168888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.128523 restraints weight = 9421.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.127922 restraints weight = 9054.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.129859 restraints weight = 8990.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.4276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5669  Z= 0.102
  Angle     :  0.545  10.193   7924  Z= 0.275
  Chirality :  0.038   0.171    934
  Planarity :  0.005   0.091    815
  Dihedral  : 19.837 161.463   1436
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 19.78 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.36), residues: 546
  helix:  0.98 (0.34), residues: 260
  sheet:  0.56 (0.71), residues: 58
  loop : -1.36 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 465 
 HIS   0.002   0.001   HIS B  52 
 PHE   0.007   0.001   PHE B  56 
 TYR   0.011   0.001   TYR B 391 
 ARG   0.002   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03546 (  225)
  hydrogen bonds       : angle       4.01956 (  623)
  covalent geometry    : bond        0.00222 ( 5668)
  covalent geometry    : angle       0.54496 ( 7924)
  Misc. bond           : bond        0.00150 (    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
  51 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
REVERT: B   45 TRP cc_start: 0.8188 (m-10) cc_final: 0.7837 (m-90)
REVERT: B  545 ASN cc_start: 0.7931 (p0) cc_final: 0.7265 (p0)
  outliers start: 11
  outliers final: 10
  residues processed: 50
  average time/residue: 0.1491
  time to fit residues: 10.5167
Evaluate side-chains
  48 residues out of total 494 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
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  603 ILE
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  129 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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 20 optimal weight:    0.0060
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 9 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 49 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 43 optimal weight:   20.0000
   overall best weight:    0.8400

-------------------------------------------------------------------------------
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 = 0.4366 r_free = 0.4366 target = 0.168429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.127657 restraints weight = 9425.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.127605 restraints weight = 8934.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.130150 restraints weight = 8214.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3876
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7114
moved from start:          0.4374

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5669  Z= 0.110
  Angle     :  0.549   7.997   7924  Z= 0.277
  Chirality :  0.038   0.174    934
  Planarity :  0.005   0.086    815
  Dihedral  : 19.766 161.199   1436
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.55 %
    Favored  : 77.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.36), residues: 546
  helix:  1.00 (0.34), residues: 259
  sheet:  0.62 (0.71), residues: 58
  loop : -1.33 (0.38), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 465 
 HIS   0.002   0.001   HIS B  52 
 PHE   0.005   0.001   PHE B 497 
 TYR   0.012   0.001   TYR A 560 
 ARG   0.002   0.000   ARG A 488 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03588 (  225)
  hydrogen bonds       : angle       3.96175 (  623)
  covalent geometry    : bond        0.00244 ( 5668)
  covalent geometry    : angle       0.54893 ( 7924)
  Misc. bond           : bond        0.00148 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1913.35 seconds
wall clock time: 34 minutes 8.99 seconds (2048.99 seconds total)