Starting phenix.real_space_refine
on Fri Aug 22 23:15:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xmg_22258/08_2025/6xmg_22258.map"
  }
  resolution = 4.8
  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     154      5.49       5
     S      11      5.16       5
     C    4674      2.51       5
     N    1553      2.21       5
     O    1968      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8361
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5081
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 638, 5081
          Classifications: {'peptide': 638}
          Incomplete info: {'truncation_to_alanine': 53}
          Link IDs: {'PTRANS': 38, 'TRANS': 599}
          Chain breaks: 4
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 215
          Unresolved non-hydrogen angles: 266
          Unresolved non-hydrogen dihedrals: 187
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 8, 'ASN:plan1': 4, 'ASP:plan': 4, 'TYR:plan': 3, 'HIS:plan': 3, 'GLU:plan': 2, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 139
    Chain: "C"
      Number of atoms: 2772
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 130, 2772
          Classifications: {'RNA': 130}
          Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 5, 'rna3p_pur': 59, 'rna3p_pyr': 56}
          Link IDs: {'rna2p': 15, 'rna3p': 114}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 507
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 507
          Classifications: {'RNA': 24}
          Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 13}
          Link IDs: {'rna3p': 23}
    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   4654  SG  CYS A 714      51.688  83.830  49.919  1.00352.65           S

  Time building chain proxies: 1.97, per 1000 atoms: 0.24
  Number of scatterers: 8361
  At special positions: 0
  Unit cell: (106.05, 94.5, 132.3, 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      11     16.00
     P     154     15.00
     O    1968      8.00
     N    1553      7.00
     C    4674      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: 0.70
  Conformation dependent library (CDL) restraints added in 202.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 714 "


  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1218

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 4 sheets defined
      49.4% alpha, 5.8% beta
      43 base pairs and 104 stacking pairs defined.
    Time for finding SS restraints: 1.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 37 through 65
      removed outlier: 3.637A  pdb=" N   ALA A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   GLN A  52 " --> pdb=" O   LYS A  48 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLN A  62 " --> pdb=" O   SER A  58 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   TRP A  63 " --> pdb=" O   GLY A  59 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   ALA A  64 " --> pdb=" O   VAL A  60 " (cutoff:3.500A)
    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
      removed outlier: 3.754A  pdb=" N   TRP A  82 " --> pdb=" O   THR A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 92
      removed outlier: 3.970A  pdb=" N   SER A  91 " --> pdb=" O   GLU A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 112
      removed outlier: 3.622A  pdb=" N   ARG A 104 " --> pdb=" O   PRO A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 138
      removed outlier: 3.818A  pdb=" N   SER A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A 134 " --> pdb=" O   ARG A 130 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   SER A 138 " --> pdb=" O   LEU A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 153
    Processing helix  chain 'A' and resid 156 through 175
      removed outlier: 3.518A  pdb=" N   LYS A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   SER A 173 " --> pdb=" O   GLU A 169 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   ARG A 174 " --> pdb=" O   TRP A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 200
      removed outlier: 3.892A  pdb=" N   GLN A 198 " --> pdb=" O   GLN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 214
      removed outlier: 3.540A  pdb=" N   ALA A 210 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ASN A 212 " --> pdb=" O   ARG A 208 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A 214 " --> pdb=" O   ALA A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 237
    Processing helix  chain 'A' and resid 242 through 249
    Processing helix  chain 'A' and resid 336 through 347
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 4.565A  pdb=" N   LYS A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 366
      No H-bonds generated for 'chain 'A' and resid 364 through 366'
    Processing helix  chain 'A' and resid 430 through 434
      removed outlier: 3.669A  pdb=" N   THR A 434 " --> pdb=" O   PRO A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 476
      removed outlier: 3.741A  pdb=" N   LEU A 470 " --> pdb=" O   THR A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 482
      No H-bonds generated for 'chain 'A' and resid 480 through 482'
    Processing helix  chain 'A' and resid 483 through 499
      removed outlier: 3.723A  pdb=" N   PHE A 487 " --> pdb=" O   GLN A 483 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU A 488 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 489 " --> pdb=" O   GLN A 485 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   LEU A 495 " --> pdb=" O   ALA A 491 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   LEU A 496 " --> pdb=" O   ARG A 492 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLU A 497 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   THR A 498 " --> pdb=" O   ARG A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 507
    Processing helix  chain 'A' and resid 569 through 595
      removed outlier: 3.804A  pdb=" N   HIS A 576 " --> pdb=" O   HIS A 572 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LEU A 577 " --> pdb=" O   VAL A 573 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LYS A 579 " --> pdb=" O   ARG A 575 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ALA A 582 " --> pdb=" O   GLN A 578 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR A 595 " --> pdb=" O   ARG A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 644
      removed outlier: 3.593A  pdb=" N   ILE A 641 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.660A  pdb=" N   ARG A 685 " --> pdb=" O   HIS A 681 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ARG A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   VAL A 693 " --> pdb=" O   THR A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 722 through 731
      removed outlier: 4.009A  pdb=" N   ARG A 730 " --> pdb=" O   LYS A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 743 through 757
      removed outlier: 3.630A  pdb=" N   TRP A 757 " --> pdb=" O   GLY A 753 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 26
      removed outlier: 3.685A  pdb=" N   ARG A  26 " --> pdb=" O   ILE A 450 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ILE A 450 " --> pdb=" O   ARG A  26 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   SER A 438 " --> pdb=" O   ARG A 453 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LEU A 441 " --> pdb=" O   LYS A 387 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
    Processing sheet with id=AA3, first strand: chain 'A' and resid 509 through 511
      removed outlier: 3.564A  pdb=" N   VAL A 653 " --> pdb=" O   LEU A 510 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   ILE A 652 " --> pdb=" O   VAL A 700 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 524
      removed outlier: 6.725A  pdb=" N   ALA A 521 " --> pdb=" O   ALA A 532 " (cutoff:3.500A)
      removed outlier: 5.302A  pdb=" N   ALA A 532 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
      removed outlier: 7.350A  pdb=" N   PHE A 523 " --> pdb=" O   GLN A 530 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   GLN A 530 " --> pdb=" O   PHE A 523 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4

    195 hydrogen bonds defined for protein.
    573 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      99 hydrogen bonds
      194 hydrogen bond angles
      0 basepair planarities
      43 basepair parallelities
      104 stacking parallelities
  Total time for adding SS restraints: 1.55

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1025
        1.31 -     1.43: 3323
        1.43 -     1.56: 4192
        1.56 -     1.69: 305
        1.69 -     1.81: 16
  Bond restraints: 8861
  Sorted by residual:
  bond pdb=" C   ARG A 675 "
       pdb=" O   ARG A 675 "
    ideal  model  delta    sigma   weight residual
    1.233  1.180  0.052 1.09e-02 8.42e+03 2.31e+01
  bond pdb=" C   ARG A 675 "
       pdb=" N   VAL A 676 "
    ideal  model  delta    sigma   weight residual
    1.332  1.305  0.026 1.36e-02 5.41e+03 3.79e+00
  bond pdb=" CA  ILE A 766 "
       pdb=" CB  ILE A 766 "
    ideal  model  delta    sigma   weight residual
    1.539  1.530  0.009 5.40e-03 3.43e+04 2.68e+00
  bond pdb=" N   ARG A 675 "
       pdb=" CA  ARG A 675 "
    ideal  model  delta    sigma   weight residual
    1.463  1.482 -0.019 1.29e-02 6.01e+03 2.15e+00
  bond pdb=" N   LYS A 551 "
       pdb=" CA  LYS A 551 "
    ideal  model  delta    sigma   weight residual
    1.457  1.472 -0.015 1.29e-02 6.01e+03 1.27e+00
  ... (remaining 8856 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 12399
        1.49 -     2.98: 263
        2.98 -     4.47: 40
        4.47 -     5.95: 11
        5.95 -     7.44: 1
  Bond angle restraints: 12714
  Sorted by residual:
  angle pdb=" N   PRO A 229 "
        pdb=" CA  PRO A 229 "
        pdb=" CB  PRO A 229 "
      ideal   model   delta    sigma   weight residual
     103.00  110.44   -7.44 1.10e+00 8.26e-01 4.58e+01
  angle pdb=" C3'   A C 113 "
        pdb=" O3'   A C 113 "
        pdb=" P     A C 114 "
      ideal   model   delta    sigma   weight residual
     120.20  125.64   -5.44 1.50e+00 4.44e-01 1.32e+01
  angle pdb=" N   GLN A 552 "
        pdb=" CA  GLN A 552 "
        pdb=" C   GLN A 552 "
      ideal   model   delta    sigma   weight residual
     107.73  112.27   -4.54 1.34e+00 5.57e-01 1.15e+01
  angle pdb=" C   LEU A 203 "
        pdb=" N   THR A 204 "
        pdb=" CA  THR A 204 "
      ideal   model   delta    sigma   weight residual
     122.89  119.38    3.51 1.12e+00 7.97e-01 9.84e+00
  angle pdb=" C   LYS A 610 "
        pdb=" CA  LYS A 610 "
        pdb=" CB  LYS A 610 "
      ideal   model   delta    sigma   weight residual
     110.88  115.55   -4.67 1.57e+00 4.06e-01 8.86e+00
  ... (remaining 12709 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.70: 5085
       35.70 -    71.39: 409
       71.39 -   107.09: 54
      107.09 -   142.78: 4
      142.78 -   178.48: 5
  Dihedral angle restraints: 5557
    sinusoidal: 3693
      harmonic: 1864
  Sorted by residual:
  dihedral pdb=" O4'   U C  55 "
           pdb=" C1'   U C  55 "
           pdb=" N1    U C  55 "
           pdb=" C2    U C  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   44.85  155.15     1      1.50e+01 4.44e-03 8.14e+01
  dihedral pdb=" O4'   U C  45 "
           pdb=" C1'   U C  45 "
           pdb=" N1    U C  45 "
           pdb=" C2    U C  45 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   57.13  174.87     1      1.70e+01 3.46e-03 6.63e+01
  dihedral pdb=" CA  GLU A  21 "
           pdb=" C   GLU A  21 "
           pdb=" N   ARG A  22 "
           pdb=" CA  ARG A  22 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.04  -19.96     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 5554 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1346
       0.046 -    0.093: 128
       0.093 -    0.139: 19
       0.139 -    0.185: 3
       0.185 -    0.232: 2
  Chirality restraints: 1498
  Sorted by residual:
  chirality pdb=" CA  PRO A 229 "
            pdb=" N   PRO A 229 "
            pdb=" C   PRO A 229 "
            pdb=" CB  PRO A 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.49    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" C3'   A C 113 "
            pdb=" C4'   A C 113 "
            pdb=" O3'   A C 113 "
            pdb=" C2'   A C 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.54   -0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" C3'   A C  76 "
            pdb=" C4'   A C  76 "
            pdb=" O3'   A C  76 "
            pdb=" C2'   A C  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 6.88e-01
  ... (remaining 1495 not shown)

  Planarity restraints: 1088
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 675 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.28e+00
        pdb=" C   ARG A 675 "    0.050 2.00e-02 2.50e+03
        pdb=" O   ARG A 675 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   VAL A 676 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 427 "   -0.014 2.00e-02 2.50e+03   1.38e-02 3.83e+00
        pdb=" CG  TYR A 427 "    0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 427 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 427 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 427 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 427 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 427 "   -0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 427 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 156 "   -0.027 5.00e-02 4.00e+02   4.09e-02 2.68e+00
        pdb=" N   PRO A 157 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 157 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 157 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1085 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 658
        2.73 -     3.27: 8128
        3.27 -     3.81: 15463
        3.81 -     4.36: 19635
        4.36 -     4.90: 27945
  Nonbonded interactions: 71829
  Sorted by model distance:
  nonbonded pdb=" O   CYS A 714 "
            pdb="ZN    ZN A 801 "
     model   vdw
     2.187 2.230
  nonbonded pdb=" O   ARG A 685 "
            pdb=" OG1 THR A 689 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O2'   U C  13 "
            pdb=" OP2   G C  22 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OG1 THR A 466 "
            pdb=" OE1 GLU A 468 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" NH2 ARG A  26 "
            pdb=" O2'   C C 111 "
     model   vdw
     2.299 3.120
  ... (remaining 71824 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:             0.540
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.130
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:0.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052   8862  Z= 0.128
  Angle     :  0.526   7.443  12714  Z= 0.329
  Chirality :  0.029   0.232   1498
  Planarity :  0.004   0.041   1088
  Dihedral  : 21.640 178.481   4339
  Min Nonbonded Distance : 2.187

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole: -2.01 (0.33), residues: 628
  helix: -0.24 (0.31), residues: 275
  sheet: -3.40 (0.70), residues: 40
  loop : -2.07 (0.34), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 638 
 TYR   0.033   0.002   TYR A 427 
 PHE   0.010   0.001   PHE A 398 
 TRP   0.010   0.001   TRP A  82 
 HIS   0.002   0.001   HIS A 159 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 8861)
  covalent geometry    : angle       0.52635 (12714)
  hydrogen bonds       : bond        0.29104 (  294)
  hydrogen bonds       : angle      10.14900 (  767)
  metal coordination   : bond        0.00034 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8048 (t-100) cc_final: 0.7491 (t-100)
REVERT: A  177 ARG cc_start: 0.8976 (mpt180) cc_final: 0.8533 (mmt180)
REVERT: A  371 ARG cc_start: 0.9227 (tpm170) cc_final: 0.8842 (tpm170)
REVERT: A  631 ASP cc_start: 0.8883 (m-30) cc_final: 0.8400 (p0)
REVERT: A  683 ARG cc_start: 0.9657 (mmp80) cc_final: 0.9224 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1468
  time to fit residues: 5.9710
Evaluate side-chains
  27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    7.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    8.9990
   chunk 74 optimal weight:   20.0000
   overall best weight:    6.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 115 ASN
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 467 GLN
A 572 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.048991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.039628 restraints weight = 134511.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.040368 restraints weight = 107847.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.040845 restraints weight = 91548.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.041245 restraints weight = 81439.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.041556 restraints weight = 74298.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.2603

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8862  Z= 0.230
  Angle     :  0.773   7.378  12714  Z= 0.385
  Chirality :  0.040   0.197   1498
  Planarity :  0.006   0.045   1088
  Dihedral  : 23.715 178.932   3081
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 26.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.82 %
    Favored  : 95.98 %
  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 aren not related in a simple way.
  whole: -1.76 (0.32), residues: 628
  helix: -0.09 (0.29), residues: 280
  sheet: -2.97 (0.85), residues: 30
  loop : -2.01 (0.34), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 675 
 TYR   0.016   0.002   TYR A 427 
 PHE   0.022   0.002   PHE A 756 
 TRP   0.022   0.002   TRP A 724 
 HIS   0.005   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 8861)
  covalent geometry    : angle       0.77283 (12714)
  hydrogen bonds       : bond        0.10259 (  294)
  hydrogen bonds       : angle       5.57556 (  767)
  metal coordination   : bond        0.00345 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  31 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 30
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8319 (t-100) cc_final: 0.7850 (t-100)
REVERT: A  371 ARG cc_start: 0.9246 (tpm170) cc_final: 0.8850 (tpm170)
REVERT: A  377 TYR cc_start: 0.3575 (m-10) cc_final: 0.3005 (m-10)
REVERT: A  580 MET cc_start: 0.7377 (mtt) cc_final: 0.6934 (mtt)
REVERT: A  631 ASP cc_start: 0.9034 (m-30) cc_final: 0.8547 (p0)
REVERT: A  683 ARG cc_start: 0.9631 (mmp80) cc_final: 0.9338 (mmp80)
  outliers start: 1
  outliers final: 0
  residues processed: 31
  average time/residue: 0.1777
  time to fit residues: 6.9505
Evaluate side-chains
  27 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 27
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 28 optimal weight:   30.0000
   chunk 63 optimal weight:   20.0000
   chunk 68 optimal weight:   10.0000
   chunk 23 optimal weight:   40.0000
   chunk 7 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 67 optimal weight:   20.0000
   chunk 61 optimal weight:    7.9990
   chunk 16 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    5.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  52 GLN
A  54 ASN
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 530 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.047514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.038316 restraints weight = 130987.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.039035 restraints weight = 104390.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.039556 restraints weight = 88638.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.039924 restraints weight = 78303.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.040224 restraints weight = 71546.530|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.3520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8862  Z= 0.184
  Angle     :  0.668   5.801  12714  Z= 0.344
  Chirality :  0.038   0.223   1498
  Planarity :  0.005   0.039   1088
  Dihedral  : 24.019 174.914   3081
  Min Nonbonded Distance : 2.081

Molprobity Statistics.
  All-atom Clashscore : 24.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.32), residues: 628
  helix: -0.06 (0.30), residues: 285
  sheet: -2.89 (0.85), residues: 29
  loop : -2.15 (0.34), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 674 
 TYR   0.015   0.002   TYR A 175 
 PHE   0.017   0.002   PHE A 533 
 TRP   0.016   0.002   TRP A 724 
 HIS   0.007   0.002   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 8861)
  covalent geometry    : angle       0.66829 (12714)
  hydrogen bonds       : bond        0.07751 (  294)
  hydrogen bonds       : angle       5.28788 (  767)
  metal coordination   : bond        0.00178 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8310 (t-100) cc_final: 0.8033 (t-100)
REVERT: A  377 TYR cc_start: 0.3469 (m-10) cc_final: 0.3010 (m-80)
REVERT: A  631 ASP cc_start: 0.9013 (m-30) cc_final: 0.8407 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1897
  time to fit residues: 6.5895
Evaluate side-chains
  23 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 23
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 19 optimal weight:   30.0000
   chunk 38 optimal weight:    7.9990
   chunk 7 optimal weight:    0.9990
   chunk 31 optimal weight:    5.9990
   chunk 66 optimal weight:   20.0000
   chunk 76 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 15 optimal weight:    2.9990
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   overall best weight:    4.7990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.047087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.037804 restraints weight = 133455.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.038550 restraints weight = 106758.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.039047 restraints weight = 90134.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.039491 restraints weight = 79801.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.039779 restraints weight = 72233.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3230
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.3920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8862  Z= 0.179
  Angle     :  0.674   8.998  12714  Z= 0.343
  Chirality :  0.039   0.287   1498
  Planarity :  0.005   0.042   1088
  Dihedral  : 24.038 176.138   3081
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 24.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  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 aren not related in a simple way.
  whole: -1.64 (0.33), residues: 628
  helix:  0.35 (0.31), residues: 275
  sheet: -2.87 (0.85), residues: 29
  loop : -2.29 (0.33), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 674 
 TYR   0.017   0.002   TYR A 427 
 PHE   0.017   0.002   PHE A 756 
 TRP   0.018   0.002   TRP A  82 
 HIS   0.005   0.001   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 ( 8861)
  covalent geometry    : angle       0.67432 (12714)
  hydrogen bonds       : bond        0.07641 (  294)
  hydrogen bonds       : angle       5.25369 (  767)
  metal coordination   : bond        0.00073 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  28 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 28
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8326 (t-100) cc_final: 0.8044 (t-100)
REVERT: A  377 TYR cc_start: 0.3113 (m-10) cc_final: 0.2641 (m-10)
REVERT: A  631 ASP cc_start: 0.9014 (m-30) cc_final: 0.8410 (p0)
REVERT: A  683 ARG cc_start: 0.9670 (mmp80) cc_final: 0.9453 (mmp80)
  outliers start: 0
  outliers final: 0
  residues processed: 28
  average time/residue: 0.1890
  time to fit residues: 6.6019
Evaluate side-chains
  22 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 22
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 24 optimal weight:   20.0000
   chunk 31 optimal weight:    0.0770
   chunk 66 optimal weight:   20.0000
   chunk 25 optimal weight:   20.0000
   chunk 44 optimal weight:   30.0000
   chunk 16 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 56 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 75 optimal weight:   30.0000
   overall best weight:    9.8150

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.041655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.032511 restraints weight = 141708.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.033244 restraints weight = 111309.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.033815 restraints weight = 93057.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.034245 restraints weight = 80968.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.034436 restraints weight = 72706.328|
|-----------------------------------------------------------------------------|
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.5822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068   8862  Z= 0.324
  Angle     :  0.938   9.799  12714  Z= 0.473
  Chirality :  0.047   0.271   1498
  Planarity :  0.008   0.071   1088
  Dihedral  : 24.868 176.372   3081
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 45.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.19 %
    Favored  : 89.81 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  5.43 %
    Favored  : 94.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.37 (0.31), residues: 628
  helix: -0.33 (0.30), residues: 274
  sheet: -3.33 (0.83), residues: 30
  loop : -2.58 (0.32), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 685 
 TYR   0.019   0.002   TYR A 175 
 PHE   0.025   0.004   PHE A 452 
 TRP   0.027   0.003   TRP A  82 
 HIS   0.005   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00635 ( 8861)
  covalent geometry    : angle       0.93783 (12714)
  hydrogen bonds       : bond        0.11764 (  294)
  hydrogen bonds       : angle       5.98670 (  767)
  metal coordination   : bond        0.00241 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8652 (t-100) cc_final: 0.8248 (t-100)
REVERT: A  177 ARG cc_start: 0.8492 (mpt180) cc_final: 0.8267 (mmt180)
REVERT: A  579 LYS cc_start: 0.6526 (mttt) cc_final: 0.6081 (mttt)
REVERT: A  631 ASP cc_start: 0.8821 (m-30) cc_final: 0.8206 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1761
  time to fit residues: 5.6718
Evaluate side-chains
  19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 5 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 9 optimal weight:   20.0000
   chunk 26 optimal weight:   20.0000
   chunk 77 optimal weight:   20.0000
   chunk 49 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 42 optimal weight:    2.9990
   chunk 62 optimal weight:    7.9990
   overall best weight:    5.1788

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 HIS
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 681 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.044053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.035078 restraints weight = 136514.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.035823 restraints weight = 106988.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.036347 restraints weight = 89374.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.036788 restraints weight = 78636.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.037042 restraints weight = 70610.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7772
moved from start:          0.5537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8862  Z= 0.196
  Angle     :  0.739   9.081  12714  Z= 0.383
  Chirality :  0.041   0.278   1498
  Planarity :  0.006   0.082   1088
  Dihedral  : 24.718 174.459   3081
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 31.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  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 aren not related in a simple way.
  whole: -2.14 (0.32), residues: 628
  helix: -0.21 (0.30), residues: 273
  sheet: -2.97 (0.68), residues: 44
  loop : -2.35 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 619 
 TYR   0.014   0.002   TYR A 175 
 PHE   0.025   0.003   PHE A 733 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.008   0.002   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8861)
  covalent geometry    : angle       0.73933 (12714)
  hydrogen bonds       : bond        0.07821 (  294)
  hydrogen bonds       : angle       5.51333 (  767)
  metal coordination   : bond        0.00089 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  26 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 MET cc_start: 0.9413 (tmm) cc_final: 0.9170 (tmm)
REVERT: A  170 TRP cc_start: 0.8200 (t-100) cc_final: 0.7823 (t-100)
REVERT: A  177 ARG cc_start: 0.8730 (mpt180) cc_final: 0.8362 (mmt180)
REVERT: A  377 TYR cc_start: 0.4360 (m-80) cc_final: 0.3968 (m-80)
REVERT: A  579 LYS cc_start: 0.6425 (mttt) cc_final: 0.5905 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 26
  average time/residue: 0.1437
  time to fit residues: 4.9957
Evaluate side-chains
  19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 32 optimal weight:   20.0000
   chunk 18 optimal weight:    6.9990
   chunk 17 optimal weight:    8.9990
   chunk 31 optimal weight:    0.1980
   chunk 70 optimal weight:   10.0000
   chunk 43 optimal weight:   30.0000
   chunk 11 optimal weight:   30.0000
   chunk 30 optimal weight:    6.9990
   chunk 40 optimal weight:    9.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    6.2388

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  54 ASN
** A 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 563 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.043100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.034157 restraints weight = 139255.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.034899 restraints weight = 108750.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.035444 restraints weight = 90814.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.035857 restraints weight = 79490.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.036174 restraints weight = 71701.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.5959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8862  Z= 0.223
  Angle     :  0.758   8.887  12714  Z= 0.389
  Chirality :  0.040   0.274   1498
  Planarity :  0.006   0.066   1088
  Dihedral  : 24.704 175.147   3081
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 36.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.02 %
    Favored  : 96.78 %
  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 aren not related in a simple way.
  whole: -2.18 (0.32), residues: 628
  helix: -0.20 (0.31), residues: 273
  sheet: -3.18 (0.67), residues: 44
  loop : -2.38 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 619 
 TYR   0.019   0.002   TYR A 377 
 PHE   0.016   0.003   PHE A 533 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.006   0.002   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 8861)
  covalent geometry    : angle       0.75791 (12714)
  hydrogen bonds       : bond        0.08707 (  294)
  hydrogen bonds       : angle       5.55729 (  767)
  metal coordination   : bond        0.00007 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  25 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 24
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8168 (t-100) cc_final: 0.7803 (t-100)
REVERT: A  177 ARG cc_start: 0.8702 (mpt180) cc_final: 0.8410 (mmt180)
REVERT: A  377 TYR cc_start: 0.5098 (m-80) cc_final: 0.4495 (m-80)
REVERT: A  579 LYS cc_start: 0.6436 (mttt) cc_final: 0.5913 (mttt)
REVERT: A  685 ARG cc_start: 0.8943 (mtt90) cc_final: 0.8606 (mtt180)
  outliers start: 1
  outliers final: 0
  residues processed: 25
  average time/residue: 0.1701
  time to fit residues: 5.4886
Evaluate side-chains
  19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 8 optimal weight:    6.9990
   chunk 31 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 39 optimal weight:    9.9990
   chunk 68 optimal weight:   20.0000
   chunk 25 optimal weight:    8.9990
   chunk 73 optimal weight:   30.0000
   chunk 18 optimal weight:    9.9990
   overall best weight:    6.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.043178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.034310 restraints weight = 137359.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.035040 restraints weight = 107492.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.035595 restraints weight = 89821.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.035960 restraints weight = 78239.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.036294 restraints weight = 70960.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.6156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8862  Z= 0.216
  Angle     :  0.751   8.733  12714  Z= 0.387
  Chirality :  0.040   0.276   1498
  Planarity :  0.006   0.055   1088
  Dihedral  : 24.753 174.715   3081
  Min Nonbonded Distance : 1.996

Molprobity Statistics.
  All-atom Clashscore : 34.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.39 %
    Favored  : 90.61 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.81 %
    Favored  : 97.99 %
  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 aren not related in a simple way.
  whole: -2.21 (0.32), residues: 628
  helix: -0.23 (0.31), residues: 272
  sheet: -3.27 (0.66), residues: 44
  loop : -2.36 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 619 
 TYR   0.019   0.002   TYR A 377 
 PHE   0.017   0.003   PHE A 533 
 TRP   0.023   0.002   TRP A  82 
 HIS   0.007   0.002   HIS A 681 

Details of bonding type rmsd
  covalent geometry    : bond        0.00418 ( 8861)
  covalent geometry    : angle       0.75071 (12714)
  hydrogen bonds       : bond        0.08361 (  294)
  hydrogen bonds       : angle       5.52118 (  767)
  metal coordination   : bond        0.00052 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8161 (t-100) cc_final: 0.7774 (t-100)
REVERT: A  177 ARG cc_start: 0.8657 (mpt180) cc_final: 0.8431 (mmt180)
REVERT: A  563 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.8031 (pp30)
REVERT: A  579 LYS cc_start: 0.6450 (mttt) cc_final: 0.5928 (mttt)
REVERT: A  685 ARG cc_start: 0.8905 (mtt90) cc_final: 0.8502 (mtt180)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1787
  time to fit residues: 5.5268
Evaluate side-chains
  20 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 19
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:   30.0000
   chunk 42 optimal weight:    0.0570
   chunk 34 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 73 optimal weight:    7.9990
   chunk 64 optimal weight:   20.0000
   chunk 10 optimal weight:   40.0000
   chunk 63 optimal weight:   20.0000
   chunk 7 optimal weight:   20.0000
   chunk 23 optimal weight:   40.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    7.4108

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
A  54 ASN
A 563 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.042081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.033460 restraints weight = 140004.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.034144 restraints weight = 109531.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.034648 restraints weight = 91711.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.035045 restraints weight = 80610.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.035324 restraints weight = 72558.912|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.6592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8862  Z= 0.249
  Angle     :  0.806   8.643  12714  Z= 0.413
  Chirality :  0.042   0.272   1498
  Planarity :  0.006   0.051   1088
  Dihedral  : 24.891 174.919   3081
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 40.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.15 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.01 %
    Favored  : 98.79 %
  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 aren not related in a simple way.
  whole: -2.36 (0.32), residues: 628
  helix: -0.30 (0.31), residues: 271
  sheet: -3.62 (0.66), residues: 45
  loop : -2.45 (0.34), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 447 
 TYR   0.014   0.002   TYR A 175 
 PHE   0.023   0.003   PHE A 533 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.005   0.002   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00483 ( 8861)
  covalent geometry    : angle       0.80597 (12714)
  hydrogen bonds       : bond        0.09327 (  294)
  hydrogen bonds       : angle       5.62988 (  767)
  metal coordination   : bond        0.00069 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  24 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 23
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.8049 (t-100) cc_final: 0.7645 (t-100)
REVERT: A  177 ARG cc_start: 0.8596 (mpt180) cc_final: 0.8372 (mmt180)
REVERT: A  377 TYR cc_start: 0.4372 (m-10) cc_final: 0.3842 (m-10)
REVERT: A  579 LYS cc_start: 0.6606 (mttt) cc_final: 0.6091 (mttt)
  outliers start: 1
  outliers final: 0
  residues processed: 24
  average time/residue: 0.1719
  time to fit residues: 5.3337
Evaluate side-chains
  19 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 19
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 26 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   chunk 25 optimal weight:    9.9990
   chunk 53 optimal weight:    0.0970
   chunk 51 optimal weight:    6.9990
   chunk 50 optimal weight:   30.0000
   chunk 9 optimal weight:   20.0000
   chunk 11 optimal weight:   20.0000
   chunk 70 optimal weight:   10.0000
   chunk 64 optimal weight:   20.0000
   overall best weight:    5.5986

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.043107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.033786 restraints weight = 138536.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.034597 restraints weight = 108154.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.035201 restraints weight = 89939.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.035645 restraints weight = 78179.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.035921 restraints weight = 70301.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.6599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8862  Z= 0.202
  Angle     :  0.738   8.522  12714  Z= 0.381
  Chirality :  0.040   0.272   1498
  Planarity :  0.006   0.046   1088
  Dihedral  : 24.771 174.355   3081
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 36.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.71 %
    Favored  : 90.29 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.40 %
    Favored  : 99.40 %
  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 aren not related in a simple way.
  whole: -2.28 (0.32), residues: 628
  helix: -0.28 (0.31), residues: 273
  sheet: -3.61 (0.63), residues: 45
  loop : -2.35 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 674 
 TYR   0.012   0.002   TYR A 175 
 PHE   0.024   0.002   PHE A 533 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.005   0.002   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8861)
  covalent geometry    : angle       0.73795 (12714)
  hydrogen bonds       : bond        0.07990 (  294)
  hydrogen bonds       : angle       5.48671 (  767)
  metal coordination   : bond        0.00011 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  22 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 21
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 TRP cc_start: 0.7973 (t-100) cc_final: 0.7565 (t-100)
REVERT: A  377 TYR cc_start: 0.4317 (m-10) cc_final: 0.3780 (m-80)
REVERT: A  579 LYS cc_start: 0.6716 (mttt) cc_final: 0.6202 (mttt)
  outliers start: 1
  outliers final: 0
  residues processed: 22
  average time/residue: 0.1575
  time to fit residues: 4.6579
Evaluate side-chains
  17 residues out of total 550 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 17
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 0 optimal weight:   40.0000
   chunk 19 optimal weight:    7.9990
   chunk 63 optimal weight:   20.0000
   chunk 54 optimal weight:    9.9990
   chunk 44 optimal weight:   30.0000
   chunk 15 optimal weight:    0.9990
   chunk 25 optimal weight:   30.0000
   chunk 72 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 32 optimal weight:    8.9990
   chunk 33 optimal weight:    9.9990
   overall best weight:    7.5990

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

Flipped N/Q/H residues before XYZ refinement:
A  54 ASN
A 563 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.042021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.032890 restraints weight = 140805.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.033675 restraints weight = 110092.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.034228 restraints weight = 91508.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.034679 restraints weight = 80089.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.034959 restraints weight = 71857.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.6892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8862  Z= 0.244
  Angle     :  0.780   8.747  12714  Z= 0.402
  Chirality :  0.041   0.271   1498
  Planarity :  0.006   0.047   1088
  Dihedral  : 24.855 174.704   3081
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 41.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.51 %
    Favored  : 89.49 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.21 %
    Favored  : 98.59 %
  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 aren not related in a simple way.
  whole: -2.37 (0.32), residues: 628
  helix: -0.31 (0.31), residues: 272
  sheet: -3.62 (0.63), residues: 45
  loop : -2.45 (0.34), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 698 
 TYR   0.017   0.002   TYR A 175 
 PHE   0.025   0.003   PHE A 533 
 TRP   0.024   0.002   TRP A  82 
 HIS   0.005   0.002   HIS A 572 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 8861)
  covalent geometry    : angle       0.78047 (12714)
  hydrogen bonds       : bond        0.09020 (  294)
  hydrogen bonds       : angle       5.61399 (  767)
  metal coordination   : bond        0.00087 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1368.80 seconds
wall clock time: 24 minutes 43.15 seconds (1483.15 seconds total)