Starting phenix.real_space_refine
on Fri Sep 11 00:55:06 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7to0_26025/09_2026/7to0_26025.cif"
  }
  resolution = 3.5
  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=   0.004
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      23      5.49       5
     S      33      5.16       5
     C    3727      2.51       5
     N    1027      2.21       5
     O    1178      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5989
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 682, 5479
          Classifications: {'peptide': 682}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 28, 'TRANS': 653}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "B"
      Number of atoms: 256
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 256
          Classifications: {'RNAv2': 12}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 5}
          Link IDs: {'rna3p': 11}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 253
          Classifications: {'RNAv2': 12}
          Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 11}
    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   4555  SG  CYS A 810      22.813  42.767  28.664  1.00 39.79           S
  ATOM   4994  SG  CYS A 864      21.545  40.805  25.017  1.00 55.33           S
  ATOM   5033  SG  CYS A 869      23.244  44.391  24.842  1.00 53.89           S

  Time building chain proxies: 1.18, per 1000 atoms: 0.20
  Number of scatterers: 5989
  At special positions: 0
  Unit cell: (97.188, 85.44, 77.964, 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      33     16.00
     P      23     15.00
     O    1178      8.00
     N    1027      7.00
     C    3727      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: 0.48
  Conformation dependent library (CDL) restraints added in 300.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "


  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1300

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 6 sheets defined
      47.5% alpha, 6.9% beta
      9 base pairs and 19 stacking pairs defined.
    Time for finding SS restraints: 0.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 252
      removed outlier: 3.693A  pdb=" N   LEU A 248 " --> pdb=" O   ARG A 244 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   GLU A 249 " --> pdb=" O   ASN A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 282
      removed outlier: 4.041A  pdb=" N   LYS A 270 " --> pdb=" O   THR A 266 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 315
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.603A  pdb=" N   GLY A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 434
      removed outlier: 3.697A  pdb=" N   ASP A 425 " --> pdb=" O   ASP A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 469 through 488
      removed outlier: 3.909A  pdb=" N   TYR A 473 " --> pdb=" O   ASP A 469 " (cutoff:3.500A)
      removed outlier: 4.143A  pdb=" N   ILE A 474 " --> pdb=" O   LYS A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 493 through 497
      removed outlier: 4.150A  pdb=" N   SER A 497 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
      removed outlier: 3.626A  pdb=" N   VAL A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 558
      removed outlier: 3.591A  pdb=" N   HIS A 557 " --> pdb=" O   ILE A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 576
    Processing helix  chain 'A' and resid 580 through 603
      removed outlier: 3.689A  pdb=" N   ASP A 585 " --> pdb=" O   GLU A 581 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU A 586 " --> pdb=" O   ILE A 582 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS A 593 " --> pdb=" O   ARG A 589 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ASP A 603 " --> pdb=" O   SER A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 649
      removed outlier: 3.783A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.631A  pdb=" N   ILE A 681 " --> pdb=" O   ALA A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 701
    Processing helix  chain 'A' and resid 720 through 729
    Processing helix  chain 'A' and resid 744 through 769
      removed outlier: 3.760A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
    Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296
    Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 322
    Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 460
      removed outlier: 6.842A  pdb=" N   GLN A 457 " --> pdb=" O   CYS A 738 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   PHE A 459 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819
      removed outlier: 7.293A  pdb=" N   LEU A 816 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   CYS A 810 " --> pdb=" O   LEU A 816 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 831 through 832
    Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846
      removed outlier: 6.652A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 7.143A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)

    243 hydrogen bonds defined for protein.
    708 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      23 hydrogen bonds
      46 hydrogen bond angles
      0 basepair planarities
      9 basepair parallelities
      19 stacking parallelities
  Total time for adding SS restraints: 1.04

  Time building geometry restraints manager: 0.66 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: 1640
        1.33 -     1.45: 1039
        1.45 -     1.58: 3388
        1.58 -     1.70: 45
        1.70 -     1.82: 46
  Bond restraints: 6158
  Sorted by residual:
  bond pdb=" N   VAL A 452 "
       pdb=" CA  VAL A 452 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 9.10e-03 1.21e+04 1.51e+01
  bond pdb=" CA  SER A 891 "
       pdb=" CB  SER A 891 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.037 1.31e-02 5.83e+03 8.09e+00
  bond pdb=" N   ILE A 489 "
       pdb=" CA  ILE A 489 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.22e-02 6.72e+03 8.02e+00
  bond pdb=" N   ILE A 262 "
       pdb=" CA  ILE A 262 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.95e+00
  bond pdb=" N   VAL A 414 "
       pdb=" CA  VAL A 414 "
    ideal  model  delta    sigma   weight residual
    1.452  1.485 -0.033 1.18e-02 7.18e+03 7.89e+00
  ... (remaining 6153 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 7026
        1.69 -     3.38: 1344
        3.38 -     5.07: 47
        5.07 -     6.77: 3
        6.77 -     8.46: 1
  Bond angle restraints: 8421
  Sorted by residual:
  angle pdb=" C   THR A 347 "
        pdb=" N   PRO A 348 "
        pdb=" CA  PRO A 348 "
      ideal   model   delta    sigma   weight residual
     119.47  127.93   -8.46 1.16e+00 7.43e-01 5.32e+01
  angle pdb=" N   VAL A 414 "
        pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     112.96  107.77    5.19 1.00e+00 1.00e+00 2.69e+01
  angle pdb=" N   ARG A 316 "
        pdb=" CA  ARG A 316 "
        pdb=" C   ARG A 316 "
      ideal   model   delta    sigma   weight residual
     114.75  109.47    5.28 1.26e+00 6.30e-01 1.75e+01
  angle pdb=" C   THR A 347 "
        pdb=" CA  THR A 347 "
        pdb=" CB  THR A 347 "
      ideal   model   delta    sigma   weight residual
     109.31  113.67   -4.36 1.23e+00 6.61e-01 1.26e+01
  angle pdb=" N   THR A 347 "
        pdb=" CA  THR A 347 "
        pdb=" C   THR A 347 "
      ideal   model   delta    sigma   weight residual
     109.62  104.76    4.86 1.45e+00 4.76e-01 1.13e+01
  ... (remaining 8416 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.65: 3290
       17.65 -    35.30: 307
       35.30 -    52.95: 88
       52.95 -    70.60: 13
       70.60 -    88.25: 7
  Dihedral angle restraints: 3705
    sinusoidal: 1703
      harmonic: 2002
  Sorted by residual:
  dihedral pdb=" C4'   G B  12 "
           pdb=" C3'   G B  12 "
           pdb=" C2'   G B  12 "
           pdb=" C1'   G B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.40   73.74     1      3.10e+00 1.04e-01 7.19e+02
  dihedral pdb=" O4'   G B  12 "
           pdb=" C4'   G B  12 "
           pdb=" C3'   G B  12 "
           pdb=" C2'   G B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.15   24.71  -59.85     1      4.00e+00 6.25e-02 2.99e+02
  dihedral pdb=" O4'   G B  12 "
           pdb=" C2'   G B  12 "
           pdb=" C1'   G B  12 "
           pdb=" C3'   G B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -94.41  -38.35  -56.06     3      3.80e+00 6.93e-02 1.46e+02
  ... (remaining 3702 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 524
       0.058 -    0.116: 308
       0.116 -    0.174: 97
       0.174 -    0.232: 23
       0.232 -    0.290: 4
  Chirality restraints: 956
  Sorted by residual:
  chirality pdb=" CB  VAL A 442 "
            pdb=" CA  VAL A 442 "
            pdb=" CG1 VAL A 442 "
            pdb=" CG2 VAL A 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.10e+00
  chirality pdb=" P     G B   2 "
            pdb=" OP1   G B   2 "
            pdb=" OP2   G B   2 "
            pdb=" O5'   G B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.42   -0.25 2.00e-01 2.50e+01 1.57e+00
  chirality pdb=" C2'   G B  12 "
            pdb=" C3'   G B  12 "
            pdb=" O2'   G B  12 "
            pdb=" C1'   G B  12 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.55   -0.24 2.00e-01 2.50e+01 1.48e+00
  ... (remaining 953 not shown)

  Planarity restraints: 994
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   9 "   -0.025 2.00e-02 2.50e+03   1.30e-02 5.09e+00
        pdb=" N9    G B   9 "    0.025 2.00e-02 2.50e+03
        pdb=" C8    G B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7    G B   9 "   -0.011 2.00e-02 2.50e+03
        pdb=" C5    G B   9 "    0.009 2.00e-02 2.50e+03
        pdb=" C6    G B   9 "   -0.001 2.00e-02 2.50e+03
        pdb=" O6    G B   9 "   -0.005 2.00e-02 2.50e+03
        pdb=" N1    G B   9 "   -0.004 2.00e-02 2.50e+03
        pdb=" C2    G B   9 "    0.003 2.00e-02 2.50e+03
        pdb=" N2    G B   9 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3    G B   9 "    0.011 2.00e-02 2.50e+03
        pdb=" C4    G B   9 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 566 "    0.026 2.00e-02 2.50e+03   1.45e-02 4.18e+00
        pdb=" CG  TYR A 566 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 566 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 566 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 566 "    0.005 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 566 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 566 "    0.014 2.00e-02 2.50e+03
        pdb=" OH  TYR A 566 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B   7 "   -0.024 2.00e-02 2.50e+03   1.03e-02 2.92e+00
        pdb=" N9    A B   7 "    0.018 2.00e-02 2.50e+03
        pdb=" C8    A B   7 "    0.003 2.00e-02 2.50e+03
        pdb=" N7    A B   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5    A B   7 "    0.005 2.00e-02 2.50e+03
        pdb=" C6    A B   7 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B   7 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1    A B   7 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2    A B   7 "    0.001 2.00e-02 2.50e+03
        pdb=" N3    A B   7 "    0.006 2.00e-02 2.50e+03
        pdb=" C4    A B   7 "    0.006 2.00e-02 2.50e+03
  ... (remaining 991 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 1243
        2.81 -     3.33: 5567
        3.33 -     3.86: 9870
        3.86 -     4.38: 11248
        4.38 -     4.90: 19078
  Nonbonded interactions: 47006
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 723 "
            pdb=" OG1 THR A 727 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   GLU A 503 "
            pdb=" OG1 THR A 506 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" O   PHE A 789 "
            pdb=" OG  SER A 793 "
     model   vdw
     2.365 3.040
  nonbonded pdb=" OD1 ASP A 392 "
            pdb=" NH2 ARG A 791 "
     model   vdw
     2.414 3.120
  ... (remaining 47001 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:             1.050
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.360
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
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      :  0.014   0.418   6161  Z= 0.864
  Angle     :  1.188   8.457   8421  Z= 0.843
  Chirality :  0.078   0.290    956
  Planarity :  0.004   0.024    994
  Dihedral  : 14.869  88.252   2405
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 12.66 %
    Favored  : 86.51 %
  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: -3.00 (0.27), residues: 680
  helix: -0.59 (0.25), residues: 300
  sheet: -3.23 (0.48), residues: 90
  loop : -3.09 (0.27), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.026   0.004   TYR A 566 
 PHE   0.016   0.004   PHE A 388 
 TRP   0.016   0.004   TRP A 873 
 HIS   0.010   0.003   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01096 /  0.81 ( 6158)
  covalent geometry    : angle       1.18782 /  0.84 ( 8421)
  hydrogen bonds       : bond        0.12240 /  7.78 (  266)
  hydrogen bonds       : angle       5.04160 /  3.50 (  754)
  metal coordination   : bond        0.40450 / 20.30 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 138
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  272 PHE cc_start: 0.8675 (t80) cc_final: 0.8435 (t80)
REVERT: A  279 GLU cc_start: 0.8652 (tp30) cc_final: 0.8441 (tp30)
REVERT: A  283 LYS cc_start: 0.8818 (mtpm) cc_final: 0.8608 (mtpp)
REVERT: A  435 ASP cc_start: 0.8367 (t70) cc_final: 0.7873 (t70)
REVERT: A  613 ASP cc_start: 0.7796 (t70) cc_final: 0.7566 (t0)
REVERT: A  679 LYS cc_start: 0.7585 (tppt) cc_final: 0.7367 (tttt)
REVERT: A  732 ARG cc_start: 0.6464 (ptt90) cc_final: 0.5340 (ptm160)
REVERT: A  758 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  889 ILE cc_start: 0.8863 (tp) cc_final: 0.8458 (tp)
REVERT: A  895 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7778 (tm-30)
  outliers start: 5
  outliers final: 2
  residues processed: 142
  average time/residue: 0.0860
  time to fit residues: 15.5554
Evaluate side-chains
  81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 79
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  324 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 289 GLN
A 299 GLN
A 305 GLN
A 336 GLN
A 354 ASN
A 381 HIS
A 384 ASN
A 501 ASN
A 517 GLN
A 608 ASN
A 619 GLN
A 623 HIS
A 769 GLN

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.126080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.104458 restraints weight = 8258.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.107761 restraints weight = 4812.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.109814 restraints weight = 3385.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.111431 restraints weight = 2707.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.112468 restraints weight = 2291.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6161  Z= 0.142
  Angle     :  0.570   7.451   8421  Z= 0.271
  Chirality :  0.043   0.188    956
  Planarity :  0.003   0.030    994
  Dihedral  :  8.854  71.711   1014
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.98 %
    Favored  : 82.89 %
  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: -1.55 (0.31), residues: 680
  helix:  0.99 (0.29), residues: 307
  sheet: -2.86 (0.49), residues: 95
  loop : -2.74 (0.30), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 811 
 TYR   0.011   0.001   TYR A 383 
 PHE   0.025   0.001   PHE A 685 
 TRP   0.006   0.001   TRP A 646 
 HIS   0.007   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00322 /  0.14 ( 6158)
  covalent geometry    : angle       0.56989 /  0.27 ( 8421)
  hydrogen bonds       : bond        0.03575 /  2.37 (  266)
  hydrogen bonds       : angle       3.58004 /  2.46 (  754)
  metal coordination   : bond        0.01557 /  0.79 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.8609 (tp30) cc_final: 0.8314 (tp30)
REVERT: A  283 LYS cc_start: 0.8666 (mtpm) cc_final: 0.8414 (mtpp)
REVERT: A  435 ASP cc_start: 0.8442 (t70) cc_final: 0.7862 (t70)
REVERT: A  454 TYR cc_start: 0.7016 (OUTLIER) cc_final: 0.6613 (m-10)
REVERT: A  613 ASP cc_start: 0.7686 (t70) cc_final: 0.7474 (t70)
REVERT: A  732 ARG cc_start: 0.6582 (ptt90) cc_final: 0.5853 (ptm160)
REVERT: A  754 ASN cc_start: 0.7847 (m-40) cc_final: 0.7598 (m-40)
REVERT: A  758 GLU cc_start: 0.8444 (tm-30) cc_final: 0.7960 (tm-30)
REVERT: A  805 ASN cc_start: 0.7422 (t0) cc_final: 0.7118 (t0)
REVERT: A  889 ILE cc_start: 0.9232 (tp) cc_final: 0.8925 (tp)
REVERT: A  895 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7333 (tm-30)
REVERT: A  907 LYS cc_start: 0.8947 (mttt) cc_final: 0.8730 (mttm)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0638
  time to fit residues: 8.2716
Evaluate side-chains
  81 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 32 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 16 optimal weight:    0.0370
   chunk 49 optimal weight:    3.9990
   chunk 61 optimal weight:    0.1980
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   overall best weight:    0.5660

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 678 GLN
A 708 GLN
A 794 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.125987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103978 restraints weight = 8276.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.107314 restraints weight = 4796.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.109532 restraints weight = 3374.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.110982 restraints weight = 2680.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.112119 restraints weight = 2291.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.2577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6161  Z= 0.107
  Angle     :  0.520   6.733   8421  Z= 0.245
  Chirality :  0.041   0.156    956
  Planarity :  0.003   0.031    994
  Dihedral  :  8.526  68.810   1011
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.82 %
    Favored  : 82.89 %
  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: -0.92 (0.32), residues: 680
  helix:  1.67 (0.30), residues: 307
  sheet: -2.96 (0.50), residues: 88
  loop : -2.49 (0.31), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 811 
 TYR   0.011   0.001   TYR A 622 
 PHE   0.019   0.001   PHE A 685 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 6158)
  covalent geometry    : angle       0.51954 /  0.25 ( 8421)
  hydrogen bonds       : bond        0.03135 /  2.05 (  266)
  hydrogen bonds       : angle       3.44014 /  2.37 (  754)
  metal coordination   : bond        0.00116 /  0.06 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  277 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8851 (mp)
REVERT: A  283 LYS cc_start: 0.8725 (mtpm) cc_final: 0.8282 (mttp)
REVERT: A  454 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6607 (m-10)
REVERT: A  613 ASP cc_start: 0.7706 (t70) cc_final: 0.7428 (t70)
REVERT: A  754 ASN cc_start: 0.7991 (m-40) cc_final: 0.7765 (m-40)
REVERT: A  758 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: A  889 ILE cc_start: 0.9236 (tp) cc_final: 0.8945 (tp)
REVERT: A  895 GLU cc_start: 0.8024 (tm-30) cc_final: 0.7469 (tm-30)
REVERT: A  907 LYS cc_start: 0.8947 (mttt) cc_final: 0.8708 (mttm)
  outliers start: 20
  outliers final: 11
  residues processed: 91
  average time/residue: 0.0597
  time to fit residues: 7.6009
Evaluate side-chains
  79 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  277 ILE
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 45 optimal weight:    0.0870
   chunk 54 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 8 optimal weight:    0.1980
   chunk 44 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.4358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.104529 restraints weight = 8229.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.107898 restraints weight = 4745.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.110095 restraints weight = 3346.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.111714 restraints weight = 2658.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.112737 restraints weight = 2252.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   6161  Z= 0.095
  Angle     :  0.507   5.688   8421  Z= 0.241
  Chirality :  0.041   0.213    956
  Planarity :  0.003   0.030    994
  Dihedral  :  8.549  70.078   1011
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 14.97 %
    Favored  : 81.91 %
  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: -0.63 (0.33), residues: 680
  helix:  1.99 (0.30), residues: 307
  sheet: -2.80 (0.49), residues: 93
  loop : -2.43 (0.33), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 488 
 TYR   0.008   0.001   TYR A 383 
 PHE   0.017   0.001   PHE A 685 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.007   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00215 /  0.10 ( 6158)
  covalent geometry    : angle       0.50713 /  0.24 ( 8421)
  hydrogen bonds       : bond        0.03028 /  1.98 (  266)
  hydrogen bonds       : angle       3.38173 /  2.34 (  754)
  metal coordination   : bond        0.00093 /  0.05 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 72
  time to evaluate  : 0.229 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.6610 (m-10)
REVERT: A  613 ASP cc_start: 0.7716 (t70) cc_final: 0.7436 (t70)
REVERT: A  732 ARG cc_start: 0.6332 (ptt90) cc_final: 0.6123 (ptm160)
REVERT: A  754 ASN cc_start: 0.8013 (m-40) cc_final: 0.7759 (m-40)
REVERT: A  758 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A  889 ILE cc_start: 0.9201 (tp) cc_final: 0.8918 (tp)
REVERT: A  895 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7402 (tm-30)
REVERT: A  907 LYS cc_start: 0.8937 (mttt) cc_final: 0.8687 (mttm)
  outliers start: 19
  outliers final: 14
  residues processed: 82
  average time/residue: 0.0609
  time to fit residues: 7.1962
Evaluate side-chains
  77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 THR
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 557 HIS
A 623 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.123443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.101183 restraints weight = 8438.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.104535 restraints weight = 4893.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.106708 restraints weight = 3465.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 19)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.107839 restraints weight = 2785.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.109119 restraints weight = 2444.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3320
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.3175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6161  Z= 0.134
  Angle     :  0.548   8.539   8421  Z= 0.259
  Chirality :  0.043   0.258    956
  Planarity :  0.003   0.032    994
  Dihedral  :  8.446  67.359   1011
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 14.97 %
    Favored  : 81.58 %
  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: -0.48 (0.33), residues: 680
  helix:  2.12 (0.30), residues: 306
  sheet: -2.88 (0.49), residues: 93
  loop : -2.27 (0.33), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 488 
 TYR   0.009   0.001   TYR A 383 
 PHE   0.017   0.001   PHE A 685 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.13 ( 6158)
  covalent geometry    : angle       0.54842 /  0.26 ( 8421)
  hydrogen bonds       : bond        0.03303 /  2.17 (  266)
  hydrogen bonds       : angle       3.49598 /  2.40 (  754)
  metal coordination   : bond        0.00220 /  0.11 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 68
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.8631 (tp30) cc_final: 0.8271 (tp30)
REVERT: A  454 TYR cc_start: 0.7140 (OUTLIER) cc_final: 0.6768 (m-80)
REVERT: A  732 ARG cc_start: 0.6575 (ptt90) cc_final: 0.6366 (ptm160)
REVERT: A  754 ASN cc_start: 0.8021 (m-40) cc_final: 0.7764 (m-40)
REVERT: A  758 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8023 (tm-30)
REVERT: A  889 ILE cc_start: 0.9289 (tp) cc_final: 0.9006 (tp)
REVERT: A  895 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7477 (tm-30)
  outliers start: 21
  outliers final: 14
  residues processed: 80
  average time/residue: 0.0566
  time to fit residues: 6.5772
Evaluate side-chains
  73 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 58
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.098774 restraints weight = 8448.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.102047 restraints weight = 4902.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.104256 restraints weight = 3487.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.105586 restraints weight = 2789.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.106708 restraints weight = 2418.952|
|-----------------------------------------------------------------------------|
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
moved from start:          0.3475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6161  Z= 0.163
  Angle     :  0.578   7.359   8421  Z= 0.275
  Chirality :  0.044   0.244    956
  Planarity :  0.003   0.034    994
  Dihedral  :  8.493  67.096   1011
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 16.45 %
    Favored  : 80.10 %
  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: -0.48 (0.33), residues: 680
  helix:  2.10 (0.30), residues: 306
  sheet: -2.99 (0.50), residues: 88
  loop : -2.21 (0.33), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 811 
 TYR   0.018   0.002   TYR A 622 
 PHE   0.016   0.002   PHE A 853 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.008   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00387 /  0.16 ( 6158)
  covalent geometry    : angle       0.57817 /  0.27 ( 8421)
  hydrogen bonds       : bond        0.03481 /  2.28 (  266)
  hydrogen bonds       : angle       3.61814 /  2.48 (  754)
  metal coordination   : bond        0.00227 /  0.11 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 62
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.8622 (tp30) cc_final: 0.8058 (tp30)
REVERT: A  454 TYR cc_start: 0.7247 (OUTLIER) cc_final: 0.6830 (m-80)
REVERT: A  479 MET cc_start: 0.8280 (mtm) cc_final: 0.7928 (mtm)
REVERT: A  620 GLU cc_start: 0.8198 (tp30) cc_final: 0.7662 (tp30)
REVERT: A  758 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8027 (tm-30)
REVERT: A  889 ILE cc_start: 0.9271 (tp) cc_final: 0.9007 (tp)
  outliers start: 21
  outliers final: 16
  residues processed: 75
  average time/residue: 0.0468
  time to fit residues: 5.1941
Evaluate side-chains
  74 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 57
  time to evaluate  : 0.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  674 THR
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9990
   chunk 64 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.121432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.099276 restraints weight = 8403.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.102513 restraints weight = 4884.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.104760 restraints weight = 3491.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.106021 restraints weight = 2782.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.107134 restraints weight = 2425.821|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6161  Z= 0.140
  Angle     :  0.559   7.986   8421  Z= 0.264
  Chirality :  0.044   0.260    956
  Planarity :  0.003   0.034    994
  Dihedral  :  8.519  69.107   1011
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.94 %
    Favored  : 92.06 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 16.78 %
    Favored  : 79.28 %
  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: -0.33 (0.34), residues: 680
  helix:  2.18 (0.30), residues: 306
  sheet: -2.73 (0.50), residues: 93
  loop : -2.14 (0.34), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 811 
 TYR   0.026   0.001   TYR A 622 
 PHE   0.013   0.001   PHE A 853 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.009   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.14 ( 6158)
  covalent geometry    : angle       0.55860 /  0.26 ( 8421)
  hydrogen bonds       : bond        0.03340 /  2.19 (  266)
  hydrogen bonds       : angle       3.55770 /  2.44 (  754)
  metal coordination   : bond        0.00189 /  0.09 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 62
  time to evaluate  : 0.230 
Fit side-chains
REVERT: A  279 GLU cc_start: 0.8625 (tp30) cc_final: 0.8059 (tp30)
REVERT: A  454 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6840 (m-80)
REVERT: A  620 GLU cc_start: 0.8177 (tp30) cc_final: 0.7650 (tp30)
REVERT: A  754 ASN cc_start: 0.7737 (m-40) cc_final: 0.7482 (m-40)
REVERT: A  758 GLU cc_start: 0.8567 (tm-30) cc_final: 0.7987 (tm-30)
REVERT: A  889 ILE cc_start: 0.9273 (tp) cc_final: 0.9010 (tp)
REVERT: A  895 GLU cc_start: 0.8058 (tm-30) cc_final: 0.7517 (tm-30)
  outliers start: 24
  outliers final: 17
  residues processed: 78
  average time/residue: 0.0502
  time to fit residues: 5.7222
Evaluate side-chains
  77 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 59
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 61 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 41 optimal weight:    0.3980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.4586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.117683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.095871 restraints weight = 8522.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.099010 restraints weight = 4913.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.101096 restraints weight = 3497.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.102067 restraints weight = 2812.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.103268 restraints weight = 2498.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   6161  Z= 0.206
  Angle     :  0.620   8.146   8421  Z= 0.294
  Chirality :  0.046   0.267    956
  Planarity :  0.004   0.037    994
  Dihedral  :  8.505  65.562   1011
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 17.11 %
    Favored  : 78.95 %
  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: -0.54 (0.33), residues: 680
  helix:  1.97 (0.30), residues: 307
  sheet: -2.94 (0.47), residues: 98
  loop : -2.14 (0.35), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 811 
 TYR   0.028   0.002   TYR A 622 
 PHE   0.020   0.002   PHE A 853 
 TRP   0.005   0.001   TRP A 771 
 HIS   0.009   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00491 /  0.21 ( 6158)
  covalent geometry    : angle       0.62041 /  0.29 ( 8421)
  hydrogen bonds       : bond        0.03751 /  2.44 (  266)
  hydrogen bonds       : angle       3.76889 /  2.58 (  754)
  metal coordination   : bond        0.00279 /  0.14 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 59
  time to evaluate  : 0.160 
Fit side-chains
REVERT: A  425 ASP cc_start: 0.7534 (t0) cc_final: 0.7326 (t0)
REVERT: A  454 TYR cc_start: 0.7259 (OUTLIER) cc_final: 0.6754 (m-80)
REVERT: A  620 GLU cc_start: 0.8317 (tp30) cc_final: 0.7888 (tp30)
REVERT: A  754 ASN cc_start: 0.7865 (m-40) cc_final: 0.7578 (m-40)
REVERT: A  758 GLU cc_start: 0.8621 (tm-30) cc_final: 0.8036 (tm-30)
REVERT: A  889 ILE cc_start: 0.9280 (tp) cc_final: 0.9028 (tp)
  outliers start: 24
  outliers final: 14
  residues processed: 74
  average time/residue: 0.0688
  time to fit residues: 7.0905
Evaluate side-chains
  70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 17 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0970
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 6 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 37 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 289 GLN
A 623 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.120267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.097891 restraints weight = 8540.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.101171 restraints weight = 4969.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.103370 restraints weight = 3530.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.104648 restraints weight = 2829.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.105740 restraints weight = 2463.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6161  Z= 0.142
  Angle     :  0.577   8.557   8421  Z= 0.272
  Chirality :  0.044   0.281    956
  Planarity :  0.003   0.035    994
  Dihedral  :  8.524  70.023   1011
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.38 %
    Favored  : 91.62 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.93 %
    Favored  : 78.78 %
  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: -0.37 (0.34), residues: 680
  helix:  2.14 (0.30), residues: 306
  sheet: -2.72 (0.46), residues: 103
  loop : -2.09 (0.36), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 488 
 TYR   0.025   0.001   TYR A 622 
 PHE   0.014   0.001   PHE A 853 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.009   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00336 /  0.14 ( 6158)
  covalent geometry    : angle       0.57672 /  0.27 ( 8421)
  hydrogen bonds       : bond        0.03405 /  2.22 (  266)
  hydrogen bonds       : angle       3.64524 /  2.50 (  754)
  metal coordination   : bond        0.00184 /  0.09 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 62
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6719 (m-80)
REVERT: A  620 GLU cc_start: 0.8281 (tp30) cc_final: 0.7830 (tp30)
REVERT: A  754 ASN cc_start: 0.7749 (m-40) cc_final: 0.7489 (m-40)
REVERT: A  758 GLU cc_start: 0.8581 (tm-30) cc_final: 0.7982 (tm-30)
REVERT: A  889 ILE cc_start: 0.9277 (tp) cc_final: 0.9020 (tp)
REVERT: A  895 GLU cc_start: 0.8096 (tm-30) cc_final: 0.7603 (tm-30)
  outliers start: 20
  outliers final: 17
  residues processed: 73
  average time/residue: 0.0515
  time to fit residues: 5.6363
Evaluate side-chains
  76 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 58
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  289 GLN
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  653 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  711 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 57 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 15 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    1.4786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.117751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.095735 restraints weight = 8586.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.098802 restraints weight = 4968.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.100841 restraints weight = 3571.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.102360 restraints weight = 2884.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.103188 restraints weight = 2472.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050   6161  Z= 0.207
  Angle     :  0.633   8.564   8421  Z= 0.301
  Chirality :  0.046   0.291    956
  Planarity :  0.004   0.037    994
  Dihedral  :  8.463  66.667   1011
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.68 %
    Favored  : 91.32 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 17.43 %
    Favored  : 78.95 %
  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: -0.67 (0.33), residues: 680
  helix:  1.88 (0.30), residues: 311
  sheet: -2.84 (0.44), residues: 109
  loop : -2.32 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 488 
 TYR   0.027   0.002   TYR A 622 
 PHE   0.020   0.002   PHE A 853 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.010   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00492 /  0.21 ( 6158)
  covalent geometry    : angle       0.63258 /  0.30 ( 8421)
  hydrogen bonds       : bond        0.03776 /  2.47 (  266)
  hydrogen bonds       : angle       3.82238 /  2.61 (  754)
  metal coordination   : bond        0.00290 /  0.14 (    3)

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

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

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1360 Ramachandran restraints generated.
    680 Oldfield, 0 Emsley, 680 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 58
  time to evaluate  : 0.225 
Fit side-chains
REVERT: A  454 TYR cc_start: 0.7241 (OUTLIER) cc_final: 0.6731 (m-80)
REVERT: A  620 GLU cc_start: 0.8345 (tp30) cc_final: 0.7996 (tp30)
REVERT: A  754 ASN cc_start: 0.7871 (m-40) cc_final: 0.7587 (m-40)
REVERT: A  758 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8038 (tm-30)
REVERT: A  889 ILE cc_start: 0.9283 (tp) cc_final: 0.9030 (tp)
  outliers start: 22
  outliers final: 14
  residues processed: 71
  average time/residue: 0.0685
  time to fit residues: 6.8513
Evaluate side-chains
  70 residues out of total 610 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 55
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  454 TYR
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  629 ILE
Chi-restraints excluded: chain A residue  643 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  673 MET
Chi-restraints excluded: chain A residue  709 CYS
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  742 THR
Chi-restraints excluded: chain A residue  766 LEU
Chi-restraints excluded: chain A residue  853 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 70
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 623 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.119907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.097828 restraints weight = 8445.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.100990 restraints weight = 4894.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.103139 restraints weight = 3505.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.104614 restraints weight = 2809.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.105205 restraints weight = 2411.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6161  Z= 0.147
  Angle     :  0.581   7.132   8421  Z= 0.277
  Chirality :  0.044   0.289    956
  Planarity :  0.004   0.035    994
  Dihedral  :  8.523  70.127   1011
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.09 %
    Favored  : 79.11 %
  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: -0.38 (0.34), residues: 680
  helix:  2.15 (0.30), residues: 305
  sheet: -2.77 (0.45), residues: 103
  loop : -2.09 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 488 
 TYR   0.027   0.001   TYR A 622 
 PHE   0.015   0.001   PHE A 853 
 TRP   0.005   0.001   TRP A 512 
 HIS   0.010   0.001   HIS A 623 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.15 ( 6158)
  covalent geometry    : angle       0.58057 /  0.28 ( 8421)
  hydrogen bonds       : bond        0.03461 /  2.26 (  266)
  hydrogen bonds       : angle       3.69460 /  2.53 (  754)
  metal coordination   : bond        0.00196 /  0.10 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 970.91 seconds
wall clock time: 17 minutes 31.50 seconds (1051.50 seconds total)