Starting phenix.real_space_refine
on Tue Aug  4 22:16:05 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8i3q_35154/08_2026/8i3q_35154.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      95      5.49       5
     S      12      5.16       5
     C    4057      2.51       5
     N    1312      2.21       5
     O    1521      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6998
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 2026
          Classifications: {'RNAv2': 95}
          Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 44, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 83}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4971
          Classifications: {'peptide': 595}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 38, 'TRANS': 556}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   6549  SG  CYS A 711      29.245  14.332  41.891  1.00 82.48           S
  ATOM   6569  SG  CYS A 714      27.687  10.896  43.793  1.00 85.07           S
  ATOM   6757  SG  CYS A 735      31.613  10.871  41.848  1.00 98.72           S
  ATOM   6776  SG  CYS A 738      28.630  10.360  40.525  1.00 97.60           S

  Time building chain proxies: 1.44, per 1000 atoms: 0.21
  Number of scatterers: 6998
  At special positions: 0
  Unit cell: (85.68, 91.56, 99.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      12     16.00
     P      95     15.00
     O    1521      8.00
     N    1312      7.00
     C    4057      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=0, symmetry=0
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 295.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 738 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 711 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 735 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 714 "
      Number of angles added : 6


  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1140

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 4 sheets defined
      50.6% alpha, 8.2% beta
      31 base pairs and 47 stacking pairs defined.
    Time for finding SS restraints: 0.68
  Creating SS restraints...
    Processing helix  chain 'A' and resid 35 through 65
    Processing helix  chain 'A' and resid 66 through 68
      No H-bonds generated for 'chain 'A' and resid 66 through 68'
    Processing helix  chain 'A' and resid 78 through 87
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.636A  pdb=" N   SER A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 113
    Processing helix  chain 'A' and resid 126 through 138
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 4.258A  pdb=" N   ASP A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 200
      removed outlier: 4.619A  pdb=" N   ARG A 177 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 5.630A  pdb=" N   ALA A 178 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 200 " --> pdb=" O   TRP A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 218
      removed outlier: 4.153A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   PHE A 211 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   ILE A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   PHE A 215 " --> pdb=" O   PHE A 211 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 367
      removed outlier: 3.526A  pdb=" N   GLU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.803A  pdb=" N   LEU A 470 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ARG A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 499
      removed outlier: 4.523A  pdb=" N   LYS A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 569 through 595
      removed outlier: 3.515A  pdb=" N   HIS A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   SER A 585 " --> pdb=" O   ARG A 581 " (cutoff:3.500A)
      removed outlier: 5.035A  pdb=" N   GLU A 586 " --> pdb=" O   ALA A 582 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 587 " --> pdb=" O   GLN A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 647
      removed outlier: 3.851A  pdb=" N   ASN A 647 " --> pdb=" O   LEU A 643 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 669
      removed outlier: 3.533A  pdb=" N   ASP A 669 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 678
      removed outlier: 3.604A  pdb=" N   ARG A 674 " --> pdb=" O   GLU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.521A  pdb=" N   ILE A 684 " --> pdb=" O   ALA A 680 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ARG A 695 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 710
    Processing helix  chain 'A' and resid 722 through 729
      removed outlier: 3.998A  pdb=" N   LYS A 726 " --> pdb=" O   LYS A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 757
      removed outlier: 3.723A  pdb=" N   TRP A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 389
      removed outlier: 6.819A  pdb=" N   ARG A 453 " --> pdb=" O   SER A 437 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   VAL A 439 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
      removed outlier: 6.116A  pdb=" N   GLY A 451 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   LEU A 441 " --> pdb=" O   ARG A 449 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ARG A 449 " --> pdb=" O   LEU A 441 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   PHE A 443 " --> pdb=" O   ARG A 447 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   ARG A 447 " --> pdb=" O   PHE A 443 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   VAL A 402 " --> pdb=" O   ASP A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 509 through 511
      removed outlier: 6.867A  pdb=" N   LEU A 510 " --> pdb=" O   VAL A 653 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   VAL A 700 " --> pdb=" O   ILE A 652 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 654 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 524
      removed outlier: 4.032A  pdb=" N   GLN A 531 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.505A  pdb=" N   VAL A 538 " --> pdb=" O   TYR A 544 " (cutoff:3.500A)

    221 hydrogen bonds defined for protein.
    633 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      80 hydrogen bonds
      144 hydrogen bond angles
      0 basepair planarities
      31 basepair parallelities
      47 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.68 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: 1385
        1.33 -     1.45: 2200
        1.45 -     1.57: 3566
        1.57 -     1.69: 188
        1.69 -     1.81: 17
  Bond restraints: 7356
  Sorted by residual:
  bond pdb=" N   LYS A  73 "
       pdb=" CA  LYS A  73 "
    ideal  model  delta    sigma   weight residual
    1.453  1.485 -0.032 8.30e-03 1.45e+04 1.51e+01
  bond pdb=" CA  GLU A 391 "
       pdb=" C   GLU A 391 "
    ideal  model  delta    sigma   weight residual
    1.525  1.485  0.040 1.32e-02 5.74e+03 9.11e+00
  bond pdb=" N   LEU A 705 "
       pdb=" CA  LEU A 705 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.06e-02 8.90e+03 9.11e+00
  bond pdb=" N   VAL A 710 "
       pdb=" CA  VAL A 710 "
    ideal  model  delta    sigma   weight residual
    1.461  1.495 -0.035 1.22e-02 6.72e+03 8.06e+00
  bond pdb=" N   ARG A 382 "
       pdb=" CA  ARG A 382 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.033 1.17e-02 7.31e+03 8.01e+00
  ... (remaining 7351 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.45: 9937
        2.45 -     4.91: 412
        4.91 -     7.36: 24
        7.36 -     9.81: 1
        9.81 -    12.27: 2
  Bond angle restraints: 10376
  Sorted by residual:
  angle pdb=" N   ALA A 482 "
        pdb=" CA  ALA A 482 "
        pdb=" C   ALA A 482 "
      ideal   model   delta    sigma   weight residual
     113.23  104.26    8.97 1.24e+00 6.50e-01 5.23e+01
  angle pdb=" N   LEU A 358 "
        pdb=" CA  LEU A 358 "
        pdb=" C   LEU A 358 "
      ideal   model   delta    sigma   weight residual
     111.36  104.29    7.07 1.09e+00 8.42e-01 4.20e+01
  angle pdb=" C3'   G C  74 "
        pdb=" O3'   G C  74 "
        pdb=" P     A C  75 "
      ideal   model   delta    sigma   weight residual
     119.70  126.09   -6.39 1.20e+00 6.94e-01 2.84e+01
  angle pdb=" CA  GLN A 483 "
        pdb=" CB  GLN A 483 "
        pdb=" CG  GLN A 483 "
      ideal   model   delta    sigma   weight residual
     114.10  123.92   -9.82 2.00e+00 2.50e-01 2.41e+01
  angle pdb=" C   PHE A 478 "
        pdb=" N   PRO A 479 "
        pdb=" CA  PRO A 479 "
      ideal   model   delta    sigma   weight residual
     119.84  114.25    5.59 1.25e+00 6.40e-01 2.00e+01
  ... (remaining 10371 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.71: 3912
       32.71 -    65.42: 332
       65.42 -    98.13: 26
       98.13 -   130.84: 0
      130.84 -   163.55: 4
  Dihedral angle restraints: 4274
    sinusoidal: 2530
      harmonic: 1744
  Sorted by residual:
  dihedral pdb=" C4'   U C 106 "
           pdb=" C3'   U C 106 "
           pdb=" C2'   U C 106 "
           pdb=" C1'   U C 106 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -40.15   76.50     1      3.10e+00 1.04e-01 7.66e+02
  dihedral pdb=" C4'   A C  14 "
           pdb=" C3'   A C  14 "
           pdb=" C2'   A C  14 "
           pdb=" C1'   A C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -36.22   72.56     1      3.10e+00 1.04e-01 7.00e+02
  dihedral pdb=" C4'   A C 113 "
           pdb=" C3'   A C 113 "
           pdb=" C2'   A C 113 "
           pdb=" C1'   A C 113 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -35.88   72.23     1      3.10e+00 1.04e-01 6.94e+02
  ... (remaining 4271 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 929
       0.071 -    0.143: 94
       0.143 -    0.214: 40
       0.214 -    0.285: 94
       0.285 -    0.357: 10
  Chirality restraints: 1167
  Sorted by residual:
  chirality pdb=" C2'   G C  74 "
            pdb=" C3'   G C  74 "
            pdb=" O2'   G C  74 "
            pdb=" C1'   G C  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.43   -0.36 2.00e-01 2.50e+01 3.18e+00
  chirality pdb=" P     A C  30 "
            pdb=" OP1   A C  30 "
            pdb=" OP2   A C  30 "
            pdb=" O5'   A C  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.52   -0.35 2.00e-01 2.50e+01 3.07e+00
  chirality pdb=" C3'   U C 106 "
            pdb=" C4'   U C 106 "
            pdb=" O3'   U C 106 "
            pdb=" C2'   U C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.85    0.35 2.00e-01 2.50e+01 3.05e+00
  ... (remaining 1164 not shown)

  Planarity restraints: 1002
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 382 "    1.099 9.50e-02 1.11e+02   4.93e-01 1.46e+02
        pdb=" NE  ARG A 382 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 382 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 382 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 382 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 462 "   -0.328 9.50e-02 1.11e+02   1.47e-01 1.32e+01
        pdb=" NE  ARG A 462 "    0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 462 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 462 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 462 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 714 "   -0.014 2.00e-02 2.50e+03   2.86e-02 8.17e+00
        pdb=" C   CYS A 714 "    0.049 2.00e-02 2.50e+03
        pdb=" O   CYS A 714 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   ARG A 715 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 999 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 17
        2.39 -     3.02: 3754
        3.02 -     3.64: 11191
        3.64 -     4.27: 16937
        4.27 -     4.90: 25742
  Nonbonded interactions: 57641
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 723 "
            pdb=" NZ  LYS A 734 "
     model   vdw
     1.762 3.200
  nonbonded pdb=" O2'   G C  74 "
            pdb=" O5'   A C  75 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" NE2 GLN A  52 "
            pdb=" OH  TYR A 155 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" NH1 ARG A 754 "
            pdb=" OE1 GLU A 759 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O2'   A C  76 "
            pdb=" OP1   G C  77 "
     model   vdw
     2.279 3.040
  ... (remaining 57636 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.930
  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:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.670
  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:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
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      :  0.007   0.207   7360  Z= 0.356
  Angle     :  1.016  20.646  10382  Z= 0.532
  Chirality :  0.090   0.357   1167
  Planarity :  0.017   0.493   1002
  Dihedral  : 20.273 163.554   3134
  Min Nonbonded Distance : 1.762

Molprobity Statistics.
  All-atom Clashscore : 14.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  :  4.43 %
    Favored  : 90.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.34), residues: 585
  helix:  1.56 (0.31), residues: 267
  sheet: -0.12 (0.62), residues: 70
  loop : -1.64 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  40 
 TYR   0.013   0.002   TYR A  18 
 PHE   0.016   0.002   PHE A 398 
 TRP   0.028   0.002   TRP A 632 
 HIS   0.004   0.001   HIS A 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.32 ( 7356)
  covalent geometry    : angle       0.95910 /  0.53 (10376)
  hydrogen bonds       : bond        0.16786 /  8.90 (  301)
  hydrogen bonds       : angle       5.90318 /  2.34 (  777)
  metal coordination   : bond        0.19495 /  9.75 (    4)
  metal coordination   : angle      13.92871 /  4.64 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 82
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A  570 ARG cc_start: 0.6936 (OUTLIER) cc_final: 0.6653 (mtp-110)
  outliers start: 28
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1535
  time to fit residues: 18.7744
Evaluate side-chains
  42 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 31
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  483 GLN
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  517 ASP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain A residue  577 LEU
Chi-restraints excluded: chain A residue  738 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    0.2980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    6.9990
   chunk 27 optimal weight:    7.9990
   overall best weight:    3.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 383 HIS
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 578 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.135709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.102725 restraints weight = 12145.976|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 1.94
r_work: 0.3343 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8069
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.054   7360  Z= 0.316
  Angle     :  1.147  19.350  10382  Z= 0.487
  Chirality :  0.085   0.965   1167
  Planarity :  0.007   0.070   1002
  Dihedral  : 17.564 168.241   1833
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 10.79 %
    Favored  : 85.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.00 (0.34), residues: 585
  helix:  1.48 (0.29), residues: 269
  sheet: -0.94 (0.57), residues: 75
  loop : -1.41 (0.40), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 480 
 TYR   0.015   0.002   TYR A 665 
 PHE   0.022   0.003   PHE A 678 
 TRP   0.017   0.003   TRP A 632 
 HIS   0.007   0.002   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00710 /  0.32 ( 7356)
  covalent geometry    : angle       1.14207 /  0.49 (10376)
  hydrogen bonds       : bond        0.07785 /  4.05 (  301)
  hydrogen bonds       : angle       4.23555 /  1.70 (  777)
  metal coordination   : bond        0.00437 /  0.22 (    4)
  metal coordination   : angle       4.56856 /  1.52 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 36
  time to evaluate  : 0.132 
Fit side-chains
REVERT: A  144 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7230 (mt-10)
REVERT: A  721 ASN cc_start: 0.5197 (t0) cc_final: 0.4915 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 51
  average time/residue: 0.1102
  time to fit residues: 6.8479
Evaluate side-chains
  36 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 25
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  144 GLU
Chi-restraints excluded: chain A residue  380 VAL
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  631 ASP
Chi-restraints excluded: chain A residue  642 GLN
Chi-restraints excluded: chain A residue  707 SER
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 17 optimal weight:    5.9990
   chunk 62 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.1184

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.139043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.106692 restraints weight = 12070.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3587 rms_B_bonded: 1.93
r_work: 0.3419 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7360  Z= 0.142
  Angle     :  0.887  12.808  10382  Z= 0.376
  Chirality :  0.067   0.517   1167
  Planarity :  0.005   0.052   1002
  Dihedral  : 17.273 179.691   1816
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 12.52 %
    Favored  : 85.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.35), residues: 585
  helix:  2.15 (0.30), residues: 266
  sheet: -0.58 (0.59), residues: 71
  loop : -1.23 (0.40), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 627 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.013   0.002   PHE A  81 
 TRP   0.016   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.14 ( 7356)
  covalent geometry    : angle       0.88500 /  0.38 (10376)
  hydrogen bonds       : bond        0.05851 /  3.03 (  301)
  hydrogen bonds       : angle       3.79223 /  1.54 (  777)
  metal coordination   : bond        0.00355 /  0.18 (    4)
  metal coordination   : angle       2.50653 /  0.84 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  37 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 26
  time to evaluate  : 0.141 
Fit side-chains
  outliers start: 11
  outliers final: 7
  residues processed: 36
  average time/residue: 0.1283
  time to fit residues: 5.7432
Evaluate side-chains
  31 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 24
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  122 ASP
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  391 GLU
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 12 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 0 optimal weight:   20.0000
   chunk 1 optimal weight:    4.9990
   chunk 37 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 58 optimal weight:    0.0370
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   overall best weight:    0.8860

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 572 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.140744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.108902 restraints weight = 12230.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 1.95
r_work: 0.3457 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7360  Z= 0.130
  Angle     :  0.819  11.696  10382  Z= 0.346
  Chirality :  0.062   0.458   1167
  Planarity :  0.005   0.050   1002
  Dihedral  : 17.116 179.111   1815
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 14.07 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.16 (0.35), residues: 585
  helix:  2.60 (0.30), residues: 259
  sheet: -0.28 (0.62), residues: 69
  loop : -0.90 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  17 
 TYR   0.012   0.001   TYR A 359 
 PHE   0.011   0.001   PHE A  50 
 TRP   0.016   0.002   TRP A 632 
 HIS   0.002   0.001   HIS A 681 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.13 ( 7356)
  covalent geometry    : angle       0.81823 /  0.35 (10376)
  hydrogen bonds       : bond        0.05278 /  2.73 (  301)
  hydrogen bonds       : angle       3.56243 /  1.46 (  777)
  metal coordination   : bond        0.00230 /  0.11 (    4)
  metal coordination   : angle       1.78973 /  0.60 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.196 
Fit side-chains
  outliers start: 6
  outliers final: 3
  residues processed: 33
  average time/residue: 0.1445
  time to fit residues: 5.8788
Evaluate side-chains
  24 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 21
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 33 optimal weight:    4.9990
   chunk 7 optimal weight:    9.9990
   chunk 24 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 36 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 57 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.142488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.111030 restraints weight = 12085.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3642 rms_B_bonded: 1.93
r_work: 0.3472 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7360  Z= 0.117
  Angle     :  0.783  11.222  10382  Z= 0.329
  Chirality :  0.060   0.426   1167
  Planarity :  0.004   0.045   1002
  Dihedral  : 17.017 178.217   1812
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.30 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 16.38 %
    Favored  : 82.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.36), residues: 585
  helix:  2.75 (0.30), residues: 259
  sheet: -0.26 (0.63), residues: 70
  loop : -0.74 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.011   0.001   PHE A  50 
 TRP   0.019   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.12 ( 7356)
  covalent geometry    : angle       0.78195 /  0.33 (10376)
  hydrogen bonds       : bond        0.05005 /  2.60 (  301)
  hydrogen bonds       : angle       3.46878 /  1.43 (  777)
  metal coordination   : bond        0.00197 /  0.10 (    4)
  metal coordination   : angle       1.69168 /  0.56 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 28
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
  outliers start: 5
  outliers final: 5
  residues processed: 32
  average time/residue: 0.1413
  time to fit residues: 5.5554
Evaluate side-chains
  30 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 25
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 26 optimal weight:    0.9990
   chunk 61 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0770
   chunk 5 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 18 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    1.1544

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.140035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.108241 restraints weight = 12152.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.94
r_work: 0.3424 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.4384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7360  Z= 0.136
  Angle     :  0.802  11.103  10382  Z= 0.338
  Chirality :  0.062   0.459   1167
  Planarity :  0.005   0.078   1002
  Dihedral  : 16.949 179.668   1812
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.41 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.36), residues: 585
  helix:  2.75 (0.30), residues: 258
  sheet: -0.19 (0.62), residues: 71
  loop : -0.80 (0.41), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.014   0.002   PHE A  50 
 TRP   0.016   0.001   TRP A 632 
 HIS   0.003   0.001   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 ( 7356)
  covalent geometry    : angle       0.80082 /  0.34 (10376)
  hydrogen bonds       : bond        0.05526 /  2.86 (  301)
  hydrogen bonds       : angle       3.57103 /  1.47 (  777)
  metal coordination   : bond        0.00230 /  0.11 (    4)
  metal coordination   : angle       1.93265 /  0.64 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 28
  time to evaluate  : 0.131 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7722 (t)
REVERT: A   40 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.7396 (mmm-85)
REVERT: A  163 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7306 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 38
  average time/residue: 0.1108
  time to fit residues: 5.1821
Evaluate side-chains
  33 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 25
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 2 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 58 optimal weight:    0.8980
   chunk 53 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 61 optimal weight:    0.6980
   chunk 7 optimal weight:   10.0000
   chunk 14 optimal weight:    0.6980
   chunk 10 optimal weight:    0.9990
   chunk 3 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.141556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.109998 restraints weight = 12047.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 1.93
r_work: 0.3454 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7360  Z= 0.119
  Angle     :  0.779  10.606  10382  Z= 0.328
  Chirality :  0.060   0.429   1167
  Planarity :  0.005   0.079   1002
  Dihedral  : 16.937 178.220   1812
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 15.41 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.42 (0.36), residues: 585
  helix:  2.81 (0.30), residues: 260
  sheet: -0.22 (0.61), residues: 77
  loop : -0.74 (0.42), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 226 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.011   0.001   PHE A  50 
 TRP   0.019   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.12 ( 7356)
  covalent geometry    : angle       0.77844 /  0.33 (10376)
  hydrogen bonds       : bond        0.05150 /  2.66 (  301)
  hydrogen bonds       : angle       3.47172 /  1.44 (  777)
  metal coordination   : bond        0.00195 /  0.10 (    4)
  metal coordination   : angle       1.64110 /  0.55 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  40 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 28
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
REVERT: A   25 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7615 (t)
REVERT: A   40 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7353 (mmm-85)
REVERT: A  645 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6394 (tt0)
  outliers start: 12
  outliers final: 5
  residues processed: 39
  average time/residue: 0.1239
  time to fit residues: 6.0399
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 26
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 37 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.136727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.104442 restraints weight = 12098.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 1.94
r_work: 0.3354 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.4650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7360  Z= 0.179
  Angle     :  0.860  11.528  10382  Z= 0.365
  Chirality :  0.065   0.535   1167
  Planarity :  0.005   0.086   1002
  Dihedral  : 16.943 178.750   1812
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 16.57 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.36), residues: 585
  helix:  2.55 (0.30), residues: 258
  sheet: -0.22 (0.61), residues: 76
  loop : -0.87 (0.41), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 627 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.017   0.002   PHE A  50 
 TRP   0.019   0.002   TRP A 632 
 HIS   0.004   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.18 ( 7356)
  covalent geometry    : angle       0.85789 /  0.36 (10376)
  hydrogen bonds       : bond        0.06246 /  3.23 (  301)
  hydrogen bonds       : angle       3.75033 /  1.54 (  777)
  metal coordination   : bond        0.00241 /  0.12 (    4)
  metal coordination   : angle       2.45166 /  0.82 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 28
  time to evaluate  : 0.128 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7757 (t)
REVERT: A   40 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7424 (mmm-85)
  outliers start: 10
  outliers final: 5
  residues processed: 37
  average time/residue: 0.0979
  time to fit residues: 4.5909
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 27
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   34 GLN
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 7 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 3 optimal weight:    4.9990
   chunk 40 optimal weight:    0.0070
   chunk 20 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0370
   chunk 29 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0470
   overall best weight:    0.2974

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 576 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.142051 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.110466 restraints weight = 12181.259|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 1.96
r_work: 0.3468 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7360  Z= 0.111
  Angle     :  0.788  16.508  10382  Z= 0.328
  Chirality :  0.059   0.390   1167
  Planarity :  0.005   0.080   1002
  Dihedral  : 16.907 176.495   1812
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 16.96 %
    Favored  : 81.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.36), residues: 585
  helix:  2.71 (0.30), residues: 266
  sheet: -0.15 (0.62), residues: 77
  loop : -0.80 (0.42), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 674 
 TYR   0.012   0.001   TYR A 665 
 PHE   0.008   0.001   PHE A 756 
 TRP   0.021   0.001   TRP A 632 
 HIS   0.002   0.000   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 ( 7356)
  covalent geometry    : angle       0.78725 /  0.33 (10376)
  hydrogen bonds       : bond        0.04809 /  2.50 (  301)
  hydrogen bonds       : angle       3.38639 /  1.40 (  777)
  metal coordination   : bond        0.00195 /  0.10 (    4)
  metal coordination   : angle       1.45676 /  0.49 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 31
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.7865 (OUTLIER) cc_final: 0.7608 (t)
REVERT: A   40 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7251 (mmm-85)
  outliers start: 7
  outliers final: 4
  residues processed: 37
  average time/residue: 0.1108
  time to fit residues: 5.1678
Evaluate side-chains
  32 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 26
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:   20.0000
   chunk 38 optimal weight:    0.7980
   chunk 19 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 55 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 64 optimal weight:    0.4980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.140245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.108382 restraints weight = 12136.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.3595 rms_B_bonded: 1.96
r_work: 0.3430 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.4877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7360  Z= 0.120
  Angle     :  0.799  17.575  10382  Z= 0.332
  Chirality :  0.059   0.405   1167
  Planarity :  0.005   0.078   1002
  Dihedral  : 16.807 177.894   1812
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 17.34 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.36), residues: 585
  helix:  2.92 (0.30), residues: 258
  sheet:  0.03 (0.62), residues: 76
  loop : -0.65 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.012   0.001   PHE A  50 
 TRP   0.020   0.001   TRP A 632 
 HIS   0.002   0.001   HIS A 572 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 7356)
  covalent geometry    : angle       0.79799 /  0.33 (10376)
  hydrogen bonds       : bond        0.05280 /  2.72 (  301)
  hydrogen bonds       : angle       3.44623 /  1.43 (  777)
  metal coordination   : bond        0.00199 /  0.10 (    4)
  metal coordination   : angle       1.75419 /  0.58 (    6)

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

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

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1170 Ramachandran restraints generated.
    585 Oldfield, 0 Emsley, 585 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A   25 VAL cc_start: 0.7882 (OUTLIER) cc_final: 0.7609 (t)
REVERT: A   40 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7331 (mmm-85)
  outliers start: 6
  outliers final: 4
  residues processed: 33
  average time/residue: 0.1105
  time to fit residues: 4.6228
Evaluate side-chains
  34 residues out of total 519 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 28
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 VAL
Chi-restraints excluded: chain A residue   40 ARG
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  361 LYS
Chi-restraints excluded: chain A residue  594 LEU
Chi-restraints excluded: chain A residue  732 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 29 optimal weight:    9.9990
   chunk 9 optimal weight:    8.9990
   chunk 17 optimal weight:    0.7980
   chunk 57 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0010
   chunk 61 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   overall best weight:    1.2788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.138084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.105983 restraints weight = 12041.425|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.95
r_work: 0.3387 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.4984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7360  Z= 0.142
  Angle     :  0.830  17.462  10382  Z= 0.348
  Chirality :  0.062   0.484   1167
  Planarity :  0.005   0.083   1002
  Dihedral  : 16.846 179.521   1812
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.15 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.34 %
    Favored  : 81.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.36), residues: 585
  helix:  2.78 (0.30), residues: 258
  sheet: -0.02 (0.61), residues: 76
  loop : -0.72 (0.42), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.011   0.001   TYR A 359 
 PHE   0.014   0.001   PHE A  50 
 TRP   0.019   0.002   TRP A 632 
 HIS   0.003   0.001   HIS A 159 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.14 ( 7356)
  covalent geometry    : angle       0.82868 /  0.35 (10376)
  hydrogen bonds       : bond        0.05750 /  2.97 (  301)
  hydrogen bonds       : angle       3.59795 /  1.48 (  777)
  metal coordination   : bond        0.00224 /  0.11 (    4)
  metal coordination   : angle       2.17996 /  0.73 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1356.70 seconds
wall clock time: 23 minutes 47.84 seconds (1427.84 seconds total)