Starting phenix.real_space_refine
on Sat Aug 23 01:56:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.79
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5m_44217/08_2025/9b5m_44217.map"
  }
  resolution = 2.79
  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=   0.062
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
     P       3      5.49       5
     Mg      2      5.21       5
     S      41      5.16       5
     C    5703      2.51       5
     N    1470      2.21       5
     O    1716      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8935
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Classifications: {'peptide': 1}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.65, per 1000 atoms: 0.18
  Number of scatterers: 8935
  At special positions: 0
  Unit cell: (84.056, 100.016, 119.168, 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)
     S      41     16.00
     P       3     15.00
     Mg      2     11.99
     O    1716      8.00
     N    1470      7.00
     C    5703      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.91

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.70
  Conformation dependent library (CDL) restraints added in 319.5 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 9 sheets defined
      48.5% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.780A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.708A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.918A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.392A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 146
      removed outlier: 3.742A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   LYS A 145 " --> pdb=" O   ASP A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
      removed outlier: 3.562A  pdb=" N   ASP A 223 " --> pdb=" O   GLY A 220 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.290A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.619A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.335A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
      removed outlier: 3.525A  pdb=" N   SER A 427 " --> pdb=" O   GLU A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.654A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.847A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.824A  pdb=" N   LYS A 528 " --> pdb=" O   GLU A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 553
      removed outlier: 3.509A  pdb=" N   ARG A 542 " --> pdb=" O   ASN A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 582
      removed outlier: 3.565A  pdb=" N   SER A 581 " --> pdb=" O   SER A 578 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   SER A 582 " --> pdb=" O   TYR A 579 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 578 through 582'
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 630
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.669A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.538A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.554A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 737
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 4.008A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 3.883A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 796 through 800
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.633A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 883
      removed outlier: 3.565A  pdb=" N   GLU A 882 " --> pdb=" O   LYS A 879 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   TYR A 883 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 879 through 883'
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.880A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   ASN A  39 " --> pdb=" O   CYS A 125 " (cutoff:3.500A)
      removed outlier: 7.924A  pdb=" N   VAL A 127 " --> pdb=" O   ASN A  39 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   LEU A  41 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.239A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.166A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
      removed outlier: 4.166A  pdb=" N   PHE A 209 " --> pdb=" O   VAL A 257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.452A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.945A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.394A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   VAL A 990 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
      removed outlier: 5.128A  pdb=" N   SER A 947 " --> pdb=" O   VAL A 990 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   GLU A 992 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   LEU A 945 " --> pdb=" O   GLU A 992 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   CYS A 994 " --> pdb=" O   THR A 943 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.516A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.394A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 26
      removed outlier: 3.656A  pdb=" N   GLY C  24 " --> pdb=" O   GLN C  34 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)

    439 hydrogen bonds defined for protein.
    1209 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.16

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1512
        1.27 -     1.40: 2173
        1.40 -     1.54: 5272
        1.54 -     1.67: 121
        1.67 -     1.81: 62
  Bond restraints: 9140
  Sorted by residual:
  bond pdb=" C04 A1AIV D 201 "
       pdb=" C05 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.453  1.525 -0.072 2.00e-02 2.50e+03 1.29e+01
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.519  0.012 1.20e-02 6.94e+03 9.24e-01
  bond pdb=" C05 A1AIV D 201 "
       pdb=" N06 A1AIV D 201 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 8.68e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.404  0.012 1.30e-02 5.92e+03 8.24e-01
  bond pdb=" CA  ASP A 335 "
       pdb=" C   ASP A 335 "
    ideal  model  delta    sigma   weight residual
    1.531  1.523  0.008 1.12e-02 7.97e+03 5.54e-01
  ... (remaining 9135 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 12247
        1.37 -     2.74: 71
        2.74 -     4.10: 64
        4.10 -     5.47: 4
        5.47 -     6.84: 4
  Bond angle restraints: 12390
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  128.54   -6.84 1.80e+00 3.09e-01 1.44e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.17    3.36 1.18e+00 7.24e-01 8.19e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.70    4.49 1.76e+00 3.23e-01 6.52e+00
  angle pdb=" C2' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.83  105.60    6.23 2.67e+00 1.40e-01 5.44e+00
  angle pdb=" C1' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     110.58  104.55    6.03 2.79e+00 1.28e-01 4.66e+00
  ... (remaining 12385 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.78: 5339
       17.78 -    35.57: 166
       35.57 -    53.35: 36
       53.35 -    71.13: 8
       71.13 -    88.92: 3
  Dihedral angle restraints: 5552
    sinusoidal: 2262
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -141.25   55.25     1      1.00e+01 1.00e-02 4.13e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.75   16.25     0      5.00e+00 4.00e-02 1.06e+01
  dihedral pdb=" CA  LEU A 870 "
           pdb=" CB  LEU A 870 "
           pdb=" CG  LEU A 870 "
           pdb=" CD1 LEU A 870 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.39  -59.39     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 5549 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1210
       0.056 -    0.112: 131
       0.112 -    0.167: 30
       0.167 -    0.223: 0
       0.223 -    0.279: 3
  Chirality restraints: 1374
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.95e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.90    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.72    0.23 2.00e-01 2.50e+01 1.27e+00
  ... (remaining 1371 not shown)

  Planarity restraints: 1604
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C  94 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO C  95 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO C  95 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C  95 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C  17 "    0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO C  18 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO C  18 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO C  18 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  90 "    0.016 5.00e-02 4.00e+02   2.40e-02 9.20e-01
        pdb=" N   PRO A  91 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "    0.013 5.00e-02 4.00e+02
  ... (remaining 1601 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 64
        2.61 -     3.18: 7688
        3.18 -     3.75: 13075
        3.75 -     4.33: 19674
        4.33 -     4.90: 32681
  Nonbonded interactions: 73182
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2B ATP A1103 "
     model   vdw
     2.034 2.170
  nonbonded pdb=" OD2 ASP A 465 "
            pdb="MG    MG A1102 "
     model   vdw
     2.035 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.085 2.170
  nonbonded pdb=" OD2 ASP A 537 "
            pdb="MG    MG A1101 "
     model   vdw
     2.108 2.170
  nonbonded pdb=" OE1 GLU A 518 "
            pdb=" NH1 ARG A 986 "
     model   vdw
     2.253 3.120
  ... (remaining 73177 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.180
  Find NCS groups from input model:        0.040
  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:6.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
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      :  0.010   0.876   9143  Z= 0.485
  Angle     :  0.622  45.741  12392  Z= 0.305
  Chirality :  0.042   0.279   1374
  Planarity :  0.003   0.031   1604
  Dihedral  :  9.700  88.918   3425
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 1.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  2.22 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.26), residues: 1126
  helix:  1.67 (0.25), residues: 486
  sheet:  0.13 (0.38), residues: 182
  loop :  0.12 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 919 
 TYR   0.007   0.001   TYR A 736 
 PHE   0.009   0.001   PHE A 842 
 TRP   0.004   0.001   TRP A 608 
 HIS   0.001   0.000   HIS C  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9140)
  covalent geometry    : angle       0.44591 (12390)
  SS BOND              : bond        0.87617 (    1)
  SS BOND              : angle      34.11469 (    2)
  hydrogen bonds       : bond        0.14513 (  426)
  hydrogen bonds       : angle       5.67783 ( 1209)
  Misc. bond           : bond        0.07801 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.8076 (pt0) cc_final: 0.7809 (pp20)
REVERT: A  182 THR cc_start: 0.8035 (t) cc_final: 0.7766 (m)
REVERT: A  184 MET cc_start: 0.7588 (mtp) cc_final: 0.7341 (mtt)
REVERT: A  196 MET cc_start: 0.7689 (mmp) cc_final: 0.7015 (mmp)
REVERT: A  273 LYS cc_start: 0.7224 (mttt) cc_final: 0.6854 (mtmp)
REVERT: A  274 ASP cc_start: 0.7601 (t70) cc_final: 0.6922 (p0)
REVERT: A  341 LYS cc_start: 0.7206 (mmmt) cc_final: 0.6947 (mmpt)
REVERT: A  423 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6371 (tp30)
REVERT: A  442 MET cc_start: 0.7959 (tpp) cc_final: 0.7320 (mmm)
REVERT: A  596 LYS cc_start: 0.7997 (tmtt) cc_final: 0.7388 (tttt)
REVERT: A  601 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7290 (mtp180)
REVERT: A  611 ASP cc_start: 0.6783 (m-30) cc_final: 0.6470 (m-30)
REVERT: A  668 MET cc_start: 0.7483 (mmm) cc_final: 0.7221 (mmm)
REVERT: A  754 TYR cc_start: 0.7024 (t80) cc_final: 0.6594 (t80)
REVERT: A  755 ASN cc_start: 0.8345 (m-40) cc_final: 0.7659 (p0)
REVERT: A  878 LYS cc_start: 0.8063 (mmtp) cc_final: 0.7766 (mmtm)
REVERT: A  879 LYS cc_start: 0.7919 (mmmm) cc_final: 0.7347 (mttp)
REVERT: A  935 GLN cc_start: 0.7513 (tp40) cc_final: 0.6921 (tt0)
REVERT: A  937 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.6773 (mp0)
REVERT: A  979 LYS cc_start: 0.7626 (mmtp) cc_final: 0.7358 (mmmt)
REVERT: A  987 LYS cc_start: 0.8506 (mtpt) cc_final: 0.7992 (mttm)
REVERT: C   59 ASP cc_start: 0.8182 (m-30) cc_final: 0.7858 (t0)
REVERT: C   72 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7737 (mtp85)
  outliers start: 9
  outliers final: 3
  residues processed: 133
  average time/residue: 0.6673
  time to fit residues: 93.4142
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain C residue   85 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.130129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.088169 restraints weight = 11211.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3026 rms_B_bonded: 2.33
r_work: 0.2894 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7440
moved from start:          0.1021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9143  Z= 0.175
  Angle     :  0.517   7.450  12392  Z= 0.268
  Chirality :  0.043   0.146   1374
  Planarity :  0.004   0.041   1604
  Dihedral  :  6.209  65.431   1254
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  :  6.85 %
    Favored  : 91.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.25), residues: 1126
  helix:  1.67 (0.25), residues: 484
  sheet:  0.61 (0.38), residues: 174
  loop :  0.07 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   5 
 TYR   0.011   0.001   TYR C  74 
 PHE   0.012   0.001   PHE A 321 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9140)
  covalent geometry    : angle       0.51526 (12390)
  SS BOND              : bond        0.01300 (    1)
  SS BOND              : angle       3.12198 (    2)
  hydrogen bonds       : bond        0.04771 (  426)
  hydrogen bonds       : angle       4.61689 ( 1209)
  Misc. bond           : bond        0.00450 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8422 (pt0) cc_final: 0.8080 (pp20)
REVERT: A  182 THR cc_start: 0.8232 (t) cc_final: 0.7935 (m)
REVERT: A  184 MET cc_start: 0.7657 (mtp) cc_final: 0.7351 (mtt)
REVERT: A  196 MET cc_start: 0.7925 (mmp) cc_final: 0.7362 (mmp)
REVERT: A  273 LYS cc_start: 0.7457 (mttt) cc_final: 0.7115 (mtmp)
REVERT: A  274 ASP cc_start: 0.7781 (t70) cc_final: 0.7057 (p0)
REVERT: A  423 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6654 (tp30)
REVERT: A  596 LYS cc_start: 0.7926 (tmtt) cc_final: 0.7370 (tttt)
REVERT: A  601 ARG cc_start: 0.7236 (mtm-85) cc_final: 0.6956 (mtp85)
REVERT: A  611 ASP cc_start: 0.7238 (m-30) cc_final: 0.6829 (m-30)
REVERT: A  652 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6767 (ttt-90)
REVERT: A  699 GLN cc_start: 0.8113 (mp10) cc_final: 0.7523 (mp10)
REVERT: A  755 ASN cc_start: 0.8165 (m-40) cc_final: 0.7344 (p0)
REVERT: A  762 LYS cc_start: 0.8237 (pttm) cc_final: 0.7803 (mmtt)
REVERT: A  879 LYS cc_start: 0.8063 (mmmm) cc_final: 0.7549 (mttp)
REVERT: A  935 GLN cc_start: 0.7689 (tp40) cc_final: 0.7076 (tt0)
REVERT: A  937 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7640 (mp0)
REVERT: A  979 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7425 (mmmt)
REVERT: A  987 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8075 (mttp)
REVERT: A 1011 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7393 (tttp)
REVERT: C   38 MET cc_start: 0.8073 (tpt) cc_final: 0.7865 (tpp)
REVERT: C   59 ASP cc_start: 0.8522 (m-30) cc_final: 0.7925 (t0)
REVERT: C   72 ARG cc_start: 0.8088 (mmm-85) cc_final: 0.7422 (mtp85)
  outliers start: 16
  outliers final: 5
  residues processed: 114
  average time/residue: 0.6853
  time to fit residues: 81.9976
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  510 GLN
Chi-restraints excluded: chain A residue  652 ARG
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 108 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 75 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 66 optimal weight:    0.4980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.088954 restraints weight = 11192.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 2.55
r_work: 0.2891 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2753 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7438
moved from start:          0.1181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9143  Z= 0.138
  Angle     :  0.502  12.611  12392  Z= 0.260
  Chirality :  0.042   0.184   1374
  Planarity :  0.004   0.044   1604
  Dihedral  :  6.034  62.439   1253
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.17 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.25), residues: 1126
  helix:  1.65 (0.24), residues: 486
  sheet:  0.57 (0.38), residues: 174
  loop :  0.07 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C   5 
 TYR   0.012   0.001   TYR C  74 
 PHE   0.009   0.001   PHE A 321 
 TRP   0.005   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 9140)
  covalent geometry    : angle       0.50095 (12390)
  SS BOND              : bond        0.02069 (    1)
  SS BOND              : angle       3.10755 (    2)
  hydrogen bonds       : bond        0.04191 (  426)
  hydrogen bonds       : angle       4.41444 ( 1209)
  Misc. bond           : bond        0.00124 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8435 (pt0) cc_final: 0.8094 (pp20)
REVERT: A  182 THR cc_start: 0.8338 (t) cc_final: 0.8089 (m)
REVERT: A  184 MET cc_start: 0.7523 (mtp) cc_final: 0.7008 (mtt)
REVERT: A  196 MET cc_start: 0.7928 (mmp) cc_final: 0.7648 (mmm)
REVERT: A  273 LYS cc_start: 0.7561 (mttt) cc_final: 0.7236 (mtmp)
REVERT: A  274 ASP cc_start: 0.7782 (t70) cc_final: 0.7033 (p0)
REVERT: A  341 LYS cc_start: 0.7367 (mmmt) cc_final: 0.7100 (mmpt)
REVERT: A  423 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6636 (tp30)
REVERT: A  596 LYS cc_start: 0.7904 (tmtt) cc_final: 0.7476 (tttt)
REVERT: A  601 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6936 (mtp85)
REVERT: A  611 ASP cc_start: 0.7237 (m-30) cc_final: 0.6819 (m-30)
REVERT: A  699 GLN cc_start: 0.8140 (mp10) cc_final: 0.7764 (mp10)
REVERT: A  755 ASN cc_start: 0.8225 (m-40) cc_final: 0.7457 (p0)
REVERT: A  878 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7524 (mmtm)
REVERT: A  879 LYS cc_start: 0.8044 (mmmm) cc_final: 0.7534 (mttp)
REVERT: A  935 GLN cc_start: 0.7711 (tp40) cc_final: 0.7101 (tt0)
REVERT: A  937 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7692 (mp0)
REVERT: A  979 LYS cc_start: 0.7706 (mmtp) cc_final: 0.7380 (mmmt)
REVERT: A  987 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8033 (mttm)
REVERT: A 1011 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7390 (tttp)
REVERT: C   38 MET cc_start: 0.8135 (tpt) cc_final: 0.7913 (tpp)
REVERT: C   59 ASP cc_start: 0.8448 (m-30) cc_final: 0.7791 (t0)
REVERT: C   72 ARG cc_start: 0.8095 (mmm-85) cc_final: 0.7540 (mtp85)
  outliers start: 11
  outliers final: 6
  residues processed: 111
  average time/residue: 0.6550
  time to fit residues: 76.7414
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 99
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  878 LYS
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 80 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 104 optimal weight:    0.4980
   chunk 53 optimal weight:    0.5980
   chunk 100 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.129811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.087987 restraints weight = 11415.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3008 rms_B_bonded: 2.57
r_work: 0.2874 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.1288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9143  Z= 0.170
  Angle     :  0.515  11.549  12392  Z= 0.266
  Chirality :  0.043   0.155   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  6.072  62.604   1253
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 2.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  :  9.07 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.25), residues: 1126
  helix:  1.55 (0.24), residues: 486
  sheet:  0.47 (0.37), residues: 174
  loop :  0.06 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C   5 
 TYR   0.013   0.001   TYR C  74 
 PHE   0.011   0.001   PHE A 321 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 9140)
  covalent geometry    : angle       0.51438 (12390)
  SS BOND              : bond        0.01853 (    1)
  SS BOND              : angle       1.24350 (    2)
  hydrogen bonds       : bond        0.04357 (  426)
  hydrogen bonds       : angle       4.41293 ( 1209)
  Misc. bond           : bond        0.00024 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.360 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8442 (pt0) cc_final: 0.8093 (pp20)
REVERT: A  182 THR cc_start: 0.8366 (t) cc_final: 0.8121 (m)
REVERT: A  184 MET cc_start: 0.7578 (mtp) cc_final: 0.7093 (mtt)
REVERT: A  196 MET cc_start: 0.7936 (mmp) cc_final: 0.7664 (mmm)
REVERT: A  273 LYS cc_start: 0.7559 (mttt) cc_final: 0.7345 (mttp)
REVERT: A  274 ASP cc_start: 0.7783 (t70) cc_final: 0.7031 (p0)
REVERT: A  333 GLN cc_start: 0.7505 (mp10) cc_final: 0.7246 (mp10)
REVERT: A  341 LYS cc_start: 0.7374 (mmmt) cc_final: 0.7107 (mmpt)
REVERT: A  423 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6782 (tp30)
REVERT: A  465 ASP cc_start: 0.8497 (t0) cc_final: 0.8211 (t0)
REVERT: A  596 LYS cc_start: 0.7852 (tmtt) cc_final: 0.7429 (tttt)
REVERT: A  601 ARG cc_start: 0.7247 (mtm-85) cc_final: 0.6967 (mtp85)
REVERT: A  611 ASP cc_start: 0.7264 (m-30) cc_final: 0.6865 (m-30)
REVERT: A  699 GLN cc_start: 0.8169 (mp10) cc_final: 0.7847 (mp10)
REVERT: A  755 ASN cc_start: 0.8228 (m-40) cc_final: 0.7494 (p0)
REVERT: A  878 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7503 (mmtm)
REVERT: A  879 LYS cc_start: 0.8038 (mmmm) cc_final: 0.7530 (mttp)
REVERT: A  935 GLN cc_start: 0.7737 (tp40) cc_final: 0.7123 (tt0)
REVERT: A  937 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7674 (mp0)
REVERT: A  979 LYS cc_start: 0.7733 (mmtp) cc_final: 0.7388 (mmmt)
REVERT: A  987 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8036 (mttm)
REVERT: A 1011 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7376 (tttp)
REVERT: C   32 HIS cc_start: 0.7339 (t-170) cc_final: 0.7015 (t70)
REVERT: C   38 MET cc_start: 0.8095 (tpt) cc_final: 0.7862 (tpp)
REVERT: C   59 ASP cc_start: 0.8460 (m-30) cc_final: 0.7790 (t0)
REVERT: C   72 ARG cc_start: 0.8094 (mmm-85) cc_final: 0.7537 (mtp85)
  outliers start: 17
  outliers final: 8
  residues processed: 113
  average time/residue: 0.6267
  time to fit residues: 74.7626
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  878 LYS
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 110 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 80 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0470
   chunk 40 optimal weight:    0.5980
   chunk 24 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 48 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.4078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.131008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.090601 restraints weight = 11260.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.44
r_work: 0.2911 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.1353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9143  Z= 0.117
  Angle     :  0.477  10.365  12392  Z= 0.246
  Chirality :  0.041   0.151   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  5.919  57.728   1253
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 2.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 10.28 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.25), residues: 1126
  helix:  1.67 (0.24), residues: 485
  sheet:  0.50 (0.37), residues: 181
  loop :  0.05 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C   8 
 TYR   0.012   0.001   TYR C  74 
 PHE   0.009   0.001   PHE A 321 
 TRP   0.005   0.001   TRP A 669 
 HIS   0.001   0.000   HIS A 604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9140)
  covalent geometry    : angle       0.47683 (12390)
  SS BOND              : bond        0.02156 (    1)
  SS BOND              : angle       0.56669 (    2)
  hydrogen bonds       : bond        0.03788 (  426)
  hydrogen bonds       : angle       4.26259 ( 1209)
  Misc. bond           : bond        0.00059 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.231 
Fit side-chains
REVERT: A  114 GLU cc_start: 0.8442 (pt0) cc_final: 0.8121 (pp20)
REVERT: A  182 THR cc_start: 0.8420 (t) cc_final: 0.8194 (m)
REVERT: A  184 MET cc_start: 0.7456 (mtp) cc_final: 0.6909 (mtt)
REVERT: A  196 MET cc_start: 0.7963 (mmp) cc_final: 0.7696 (mmm)
REVERT: A  273 LYS cc_start: 0.7598 (mttt) cc_final: 0.7393 (mttp)
REVERT: A  274 ASP cc_start: 0.7809 (t70) cc_final: 0.7060 (p0)
REVERT: A  306 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8190 (mp0)
REVERT: A  333 GLN cc_start: 0.7553 (mp10) cc_final: 0.7328 (mp10)
REVERT: A  341 LYS cc_start: 0.7401 (mmmt) cc_final: 0.7129 (mmpt)
REVERT: A  423 GLU cc_start: 0.7074 (mt-10) cc_final: 0.6717 (tp30)
REVERT: A  465 ASP cc_start: 0.8577 (t0) cc_final: 0.8305 (t0)
REVERT: A  596 LYS cc_start: 0.7853 (tmtt) cc_final: 0.7464 (tttt)
REVERT: A  601 ARG cc_start: 0.7279 (mtm-85) cc_final: 0.7002 (mtp85)
REVERT: A  611 ASP cc_start: 0.7298 (m-30) cc_final: 0.6889 (m-30)
REVERT: A  699 GLN cc_start: 0.8230 (mp10) cc_final: 0.7880 (mp10)
REVERT: A  755 ASN cc_start: 0.8258 (m-40) cc_final: 0.7551 (p0)
REVERT: A  879 LYS cc_start: 0.8071 (mmmm) cc_final: 0.7563 (mttp)
REVERT: A  935 GLN cc_start: 0.7784 (tp40) cc_final: 0.7162 (tt0)
REVERT: A  937 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7606 (mp0)
REVERT: A  979 LYS cc_start: 0.7779 (mmtp) cc_final: 0.7435 (mmmt)
REVERT: A  987 LYS cc_start: 0.8537 (mtpt) cc_final: 0.8099 (mttm)
REVERT: A 1011 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (tttp)
REVERT: C   32 HIS cc_start: 0.7408 (t-170) cc_final: 0.7094 (t70)
REVERT: C   38 MET cc_start: 0.8066 (tpt) cc_final: 0.7796 (tpp)
REVERT: C   59 ASP cc_start: 0.8441 (m-30) cc_final: 0.7791 (t0)
REVERT: C   72 ARG cc_start: 0.8081 (mmm-85) cc_final: 0.7553 (mtp85)
  outliers start: 12
  outliers final: 5
  residues processed: 106
  average time/residue: 0.6696
  time to fit residues: 74.8522
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  306 GLU
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0770
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 93 optimal weight:    0.0470
   chunk 88 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   chunk 109 optimal weight:    0.0970
   chunk 40 optimal weight:    0.5980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.2834

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.132158 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.090144 restraints weight = 11315.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.61
r_work: 0.2919 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7435
moved from start:          0.1460

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9143  Z= 0.100
  Angle     :  0.462   9.736  12392  Z= 0.238
  Chirality :  0.041   0.156   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  5.743  57.715   1253
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 2.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 10.28 %
    Favored  : 88.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.26), residues: 1126
  helix:  1.80 (0.24), residues: 485
  sheet:  0.29 (0.37), residues: 189
  loop :  0.15 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C   5 
 TYR   0.011   0.001   TYR C  74 
 PHE   0.008   0.001   PHE A 321 
 TRP   0.005   0.001   TRP A 669 
 HIS   0.001   0.000   HIS A 604 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9140)
  covalent geometry    : angle       0.46201 (12390)
  SS BOND              : bond        0.01214 (    1)
  SS BOND              : angle       0.74727 (    2)
  hydrogen bonds       : bond        0.03375 (  426)
  hydrogen bonds       : angle       4.12191 ( 1209)
  Misc. bond           : bond        0.00034 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   32 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7652 (mmm)
REVERT: A  114 GLU cc_start: 0.8438 (pt0) cc_final: 0.8105 (pp20)
REVERT: A  182 THR cc_start: 0.8347 (t) cc_final: 0.8138 (m)
REVERT: A  184 MET cc_start: 0.7424 (mtp) cc_final: 0.6956 (mtt)
REVERT: A  196 MET cc_start: 0.7893 (mmp) cc_final: 0.7231 (mmp)
REVERT: A  229 VAL cc_start: 0.7024 (t) cc_final: 0.6675 (p)
REVERT: A  273 LYS cc_start: 0.7566 (mttt) cc_final: 0.7362 (mttp)
REVERT: A  274 ASP cc_start: 0.7793 (t70) cc_final: 0.7004 (p0)
REVERT: A  423 GLU cc_start: 0.6999 (mt-10) cc_final: 0.6649 (tp30)
REVERT: A  465 ASP cc_start: 0.8544 (t0) cc_final: 0.8249 (t0)
REVERT: A  596 LYS cc_start: 0.7757 (tmtt) cc_final: 0.7360 (tttt)
REVERT: A  611 ASP cc_start: 0.7242 (m-30) cc_final: 0.6845 (m-30)
REVERT: A  699 GLN cc_start: 0.8180 (mp10) cc_final: 0.7825 (mp10)
REVERT: A  755 ASN cc_start: 0.8253 (m-40) cc_final: 0.7526 (p0)
REVERT: A  879 LYS cc_start: 0.8015 (mmmm) cc_final: 0.7506 (mttp)
REVERT: A  935 GLN cc_start: 0.7725 (tp40) cc_final: 0.7100 (tt0)
REVERT: A  937 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7586 (mp0)
REVERT: A  979 LYS cc_start: 0.7735 (mmtp) cc_final: 0.7350 (mmmt)
REVERT: A  987 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8050 (mttm)
REVERT: A 1011 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7394 (tttp)
REVERT: C   32 HIS cc_start: 0.7297 (t-170) cc_final: 0.6947 (t70)
REVERT: C   38 MET cc_start: 0.8103 (tpt) cc_final: 0.7847 (tpp)
REVERT: C   59 ASP cc_start: 0.8409 (m-30) cc_final: 0.7745 (t0)
REVERT: C   72 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7518 (mtp85)
  outliers start: 15
  outliers final: 6
  residues processed: 113
  average time/residue: 0.6322
  time to fit residues: 75.3313
Evaluate side-chains
  110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.0020
   chunk 72 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 111 optimal weight:    4.9990
   chunk 11 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0470
   overall best weight:    0.5286

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.131489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.089656 restraints weight = 11345.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.58
r_work: 0.2901 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1485

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9143  Z= 0.133
  Angle     :  0.480   9.912  12392  Z= 0.247
  Chirality :  0.042   0.164   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  5.780  57.945   1253
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.09 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.26), residues: 1126
  helix:  1.74 (0.24), residues: 485
  sheet:  0.59 (0.37), residues: 181
  loop :  0.10 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   5 
 TYR   0.012   0.001   TYR C  74 
 PHE   0.010   0.001   PHE A 321 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9140)
  covalent geometry    : angle       0.48029 (12390)
  SS BOND              : bond        0.01328 (    1)
  SS BOND              : angle       0.90913 (    2)
  hydrogen bonds       : bond        0.03706 (  426)
  hydrogen bonds       : angle       4.17315 ( 1209)
  Misc. bond           : bond        0.00016 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.375 
Fit side-chains
REVERT: A   32 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7660 (mmm)
REVERT: A  114 GLU cc_start: 0.8411 (pt0) cc_final: 0.8088 (pp20)
REVERT: A  182 THR cc_start: 0.8367 (t) cc_final: 0.8152 (m)
REVERT: A  184 MET cc_start: 0.7484 (mtp) cc_final: 0.6985 (mtt)
REVERT: A  196 MET cc_start: 0.7932 (mmp) cc_final: 0.7279 (mmp)
REVERT: A  229 VAL cc_start: 0.7022 (t) cc_final: 0.6692 (p)
REVERT: A  273 LYS cc_start: 0.7558 (mttt) cc_final: 0.7354 (mttp)
REVERT: A  274 ASP cc_start: 0.7812 (t70) cc_final: 0.7009 (p0)
REVERT: A  333 GLN cc_start: 0.7474 (mp10) cc_final: 0.7166 (mp10)
REVERT: A  341 LYS cc_start: 0.7349 (mmmt) cc_final: 0.7078 (mmpt)
REVERT: A  423 GLU cc_start: 0.7107 (mt-10) cc_final: 0.6788 (tp30)
REVERT: A  465 ASP cc_start: 0.8526 (t0) cc_final: 0.8229 (t0)
REVERT: A  596 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7392 (tttt)
REVERT: A  611 ASP cc_start: 0.7235 (m-30) cc_final: 0.6820 (m-30)
REVERT: A  699 GLN cc_start: 0.8153 (mp10) cc_final: 0.7804 (mp10)
REVERT: A  755 ASN cc_start: 0.8234 (m-40) cc_final: 0.7519 (p0)
REVERT: A  879 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7514 (mttp)
REVERT: A  935 GLN cc_start: 0.7717 (tp40) cc_final: 0.7096 (tt0)
REVERT: A  937 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7605 (mp0)
REVERT: A  979 LYS cc_start: 0.7738 (mmtp) cc_final: 0.7345 (mmmt)
REVERT: A  987 LYS cc_start: 0.8488 (mtpt) cc_final: 0.8041 (mttm)
REVERT: A 1011 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7360 (tttp)
REVERT: C   32 HIS cc_start: 0.7289 (t-170) cc_final: 0.6930 (t70)
REVERT: C   38 MET cc_start: 0.8092 (tpt) cc_final: 0.7831 (tpp)
REVERT: C   59 ASP cc_start: 0.8398 (m-30) cc_final: 0.7740 (t0)
REVERT: C   72 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7533 (mtp85)
  outliers start: 12
  outliers final: 8
  residues processed: 108
  average time/residue: 0.6333
  time to fit residues: 72.1683
Evaluate side-chains
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 98
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  626 MET
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.5980
   chunk 104 optimal weight:    0.4980
   chunk 44 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 47 optimal weight:    0.5980
   chunk 55 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    0.5780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.131058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.089105 restraints weight = 11339.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3027 rms_B_bonded: 2.59
r_work: 0.2895 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9143  Z= 0.141
  Angle     :  0.488   9.869  12392  Z= 0.251
  Chirality :  0.042   0.148   1374
  Planarity :  0.004   0.047   1604
  Dihedral  :  5.823  58.193   1253
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.29 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1126
  helix:  1.72 (0.24), residues: 485
  sheet:  0.59 (0.37), residues: 181
  loop :  0.09 (0.30), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   5 
 TYR   0.013   0.001   TYR C  74 
 PHE   0.010   0.001   PHE A 321 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.001   HIS C 125 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 9140)
  covalent geometry    : angle       0.48819 (12390)
  SS BOND              : bond        0.01328 (    1)
  SS BOND              : angle       0.98751 (    2)
  hydrogen bonds       : bond        0.03834 (  426)
  hydrogen bonds       : angle       4.20448 ( 1209)
  Misc. bond           : bond        0.00034 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.221 
Fit side-chains
REVERT: A   32 MET cc_start: 0.7973 (OUTLIER) cc_final: 0.7630 (mmm)
REVERT: A  114 GLU cc_start: 0.8425 (pt0) cc_final: 0.8069 (pp20)
REVERT: A  182 THR cc_start: 0.8387 (t) cc_final: 0.8175 (m)
REVERT: A  184 MET cc_start: 0.7627 (mtp) cc_final: 0.7196 (mtt)
REVERT: A  196 MET cc_start: 0.7933 (mmp) cc_final: 0.7281 (mmp)
REVERT: A  229 VAL cc_start: 0.7011 (t) cc_final: 0.6675 (p)
REVERT: A  273 LYS cc_start: 0.7546 (mttt) cc_final: 0.7330 (mttp)
REVERT: A  274 ASP cc_start: 0.7818 (t70) cc_final: 0.7014 (p0)
REVERT: A  333 GLN cc_start: 0.7678 (mp10) cc_final: 0.7411 (mp10)
REVERT: A  423 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6788 (tp30)
REVERT: A  465 ASP cc_start: 0.8543 (t0) cc_final: 0.8251 (t0)
REVERT: A  596 LYS cc_start: 0.7836 (tmtt) cc_final: 0.7415 (tttt)
REVERT: A  611 ASP cc_start: 0.7247 (m-30) cc_final: 0.6834 (m-30)
REVERT: A  699 GLN cc_start: 0.8164 (mp10) cc_final: 0.7809 (mp10)
REVERT: A  755 ASN cc_start: 0.8283 (m-40) cc_final: 0.7640 (p0)
REVERT: A  879 LYS cc_start: 0.8018 (mmmm) cc_final: 0.7508 (mttp)
REVERT: A  935 GLN cc_start: 0.7723 (tp40) cc_final: 0.7108 (tt0)
REVERT: A  937 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7634 (mp0)
REVERT: A  969 LYS cc_start: 0.7271 (mtmt) cc_final: 0.6994 (mtpp)
REVERT: A  979 LYS cc_start: 0.7745 (mmtp) cc_final: 0.7347 (mmmt)
REVERT: A  987 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8038 (mttm)
REVERT: A 1011 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7362 (tttp)
REVERT: C   32 HIS cc_start: 0.7252 (t-170) cc_final: 0.6891 (t70)
REVERT: C   38 MET cc_start: 0.8125 (tpt) cc_final: 0.7867 (tpp)
REVERT: C   59 ASP cc_start: 0.8397 (m-30) cc_final: 0.7737 (t0)
REVERT: C   72 ARG cc_start: 0.8069 (mmm-85) cc_final: 0.7540 (mtp85)
  outliers start: 12
  outliers final: 7
  residues processed: 107
  average time/residue: 0.6201
  time to fit residues: 69.9182
Evaluate side-chains
  107 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 84 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 100 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 95 optimal weight:    1.9990
   chunk 107 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   overall best weight:    0.5738

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.088970 restraints weight = 11313.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.57
r_work: 0.2893 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7447
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9143  Z= 0.142
  Angle     :  0.493   9.825  12392  Z= 0.254
  Chirality :  0.042   0.153   1374
  Planarity :  0.004   0.047   1604
  Dihedral  :  5.831  58.282   1253
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 11.29 %
    Favored  : 87.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.26), residues: 1126
  helix:  1.70 (0.24), residues: 485
  sheet:  0.62 (0.37), residues: 180
  loop :  0.10 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   5 
 TYR   0.013   0.001   TYR C  74 
 PHE   0.010   0.001   PHE A 321 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9140)
  covalent geometry    : angle       0.49262 (12390)
  SS BOND              : bond        0.01201 (    1)
  SS BOND              : angle       1.01817 (    2)
  hydrogen bonds       : bond        0.03841 (  426)
  hydrogen bonds       : angle       4.21661 ( 1209)
  Misc. bond           : bond        0.00011 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A   32 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7637 (mmm)
REVERT: A  114 GLU cc_start: 0.8424 (pt0) cc_final: 0.8069 (pp20)
REVERT: A  182 THR cc_start: 0.8392 (t) cc_final: 0.8182 (m)
REVERT: A  184 MET cc_start: 0.7637 (mtp) cc_final: 0.7210 (mtt)
REVERT: A  196 MET cc_start: 0.7944 (mmp) cc_final: 0.7294 (mmp)
REVERT: A  229 VAL cc_start: 0.7024 (t) cc_final: 0.6696 (p)
REVERT: A  273 LYS cc_start: 0.7552 (mttt) cc_final: 0.7336 (mttp)
REVERT: A  274 ASP cc_start: 0.7823 (t70) cc_final: 0.7017 (p0)
REVERT: A  333 GLN cc_start: 0.7713 (mp10) cc_final: 0.7418 (mp10)
REVERT: A  423 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6796 (tp30)
REVERT: A  465 ASP cc_start: 0.8546 (t0) cc_final: 0.8219 (t0)
REVERT: A  596 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7428 (tttt)
REVERT: A  611 ASP cc_start: 0.7255 (m-30) cc_final: 0.6843 (m-30)
REVERT: A  699 GLN cc_start: 0.8173 (mp10) cc_final: 0.7822 (mp10)
REVERT: A  755 ASN cc_start: 0.8281 (m-40) cc_final: 0.7654 (p0)
REVERT: A  879 LYS cc_start: 0.8020 (mmmm) cc_final: 0.7511 (mttp)
REVERT: A  935 GLN cc_start: 0.7726 (tp40) cc_final: 0.7111 (tt0)
REVERT: A  937 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7636 (mp0)
REVERT: A  969 LYS cc_start: 0.7281 (mtmt) cc_final: 0.7004 (mtpp)
REVERT: A  979 LYS cc_start: 0.7751 (mmtp) cc_final: 0.7353 (mmmt)
REVERT: A  987 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8049 (mttm)
REVERT: A 1011 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7371 (tttp)
REVERT: C   32 HIS cc_start: 0.7206 (t-170) cc_final: 0.6841 (t70)
REVERT: C   38 MET cc_start: 0.8138 (tpt) cc_final: 0.7878 (tpp)
REVERT: C   59 ASP cc_start: 0.8396 (m-30) cc_final: 0.7738 (t0)
REVERT: C   72 ARG cc_start: 0.8075 (mmm-85) cc_final: 0.7544 (mtp85)
  outliers start: 12
  outliers final: 7
  residues processed: 109
  average time/residue: 0.6318
  time to fit residues: 72.9161
Evaluate side-chains
  109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 110 optimal weight:    0.6980
   chunk 109 optimal weight:    0.7980
   chunk 86 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 102 optimal weight:    0.5980
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.130584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.088849 restraints weight = 11228.697|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.55
r_work: 0.2889 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2752 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9143  Z= 0.156
  Angle     :  0.510   9.468  12392  Z= 0.261
  Chirality :  0.043   0.156   1374
  Planarity :  0.004   0.046   1604
  Dihedral  :  5.891  58.381   1253
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 2.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  : 11.39 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.21 (0.25), residues: 1126
  helix:  1.64 (0.24), residues: 485
  sheet:  0.60 (0.37), residues: 180
  loop :  0.08 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C   5 
 TYR   0.014   0.001   TYR C  74 
 PHE   0.011   0.001   PHE A 321 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 9140)
  covalent geometry    : angle       0.51005 (12390)
  SS BOND              : bond        0.02257 (    1)
  SS BOND              : angle       0.57358 (    2)
  hydrogen bonds       : bond        0.04014 (  426)
  hydrogen bonds       : angle       4.26972 ( 1209)
  Misc. bond           : bond        0.00075 (    2)

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

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

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2252 Ramachandran restraints generated.
    1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A   32 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7619 (mmm)
REVERT: A  114 GLU cc_start: 0.8424 (pt0) cc_final: 0.8065 (pp20)
REVERT: A  182 THR cc_start: 0.8398 (t) cc_final: 0.8174 (m)
REVERT: A  184 MET cc_start: 0.7626 (mtp) cc_final: 0.7185 (mtt)
REVERT: A  196 MET cc_start: 0.7947 (mmp) cc_final: 0.7296 (mmp)
REVERT: A  229 VAL cc_start: 0.7012 (t) cc_final: 0.6695 (p)
REVERT: A  273 LYS cc_start: 0.7543 (mttt) cc_final: 0.7321 (mttp)
REVERT: A  274 ASP cc_start: 0.7830 (t70) cc_final: 0.7013 (p0)
REVERT: A  333 GLN cc_start: 0.7768 (mp10) cc_final: 0.7475 (mp10)
REVERT: A  423 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6791 (tp30)
REVERT: A  465 ASP cc_start: 0.8555 (t0) cc_final: 0.8236 (t0)
REVERT: A  596 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7480 (tttt)
REVERT: A  611 ASP cc_start: 0.7206 (m-30) cc_final: 0.6796 (m-30)
REVERT: A  699 GLN cc_start: 0.8176 (mp10) cc_final: 0.7815 (mp10)
REVERT: A  755 ASN cc_start: 0.8289 (m-40) cc_final: 0.7661 (p0)
REVERT: A  879 LYS cc_start: 0.8051 (mmmm) cc_final: 0.7549 (mttp)
REVERT: A  935 GLN cc_start: 0.7728 (tp40) cc_final: 0.7112 (tt0)
REVERT: A  937 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7636 (mp0)
REVERT: A  969 LYS cc_start: 0.7269 (mtmt) cc_final: 0.6994 (mtpp)
REVERT: A  979 LYS cc_start: 0.7758 (mmtp) cc_final: 0.7358 (mmmt)
REVERT: A  987 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8037 (mttm)
REVERT: A 1011 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7400 (tttp)
REVERT: C   32 HIS cc_start: 0.7205 (t-170) cc_final: 0.6811 (t70)
REVERT: C   38 MET cc_start: 0.8222 (tpt) cc_final: 0.7959 (tpp)
REVERT: C   59 ASP cc_start: 0.8395 (m-30) cc_final: 0.7736 (t0)
REVERT: C   72 ARG cc_start: 0.8072 (mmm-85) cc_final: 0.7480 (mtp85)
  outliers start: 10
  outliers final: 7
  residues processed: 106
  average time/residue: 0.6687
  time to fit residues: 74.5300
Evaluate side-chains
  105 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   32 MET
Chi-restraints excluded: chain A residue   80 GLN
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  568 THR
Chi-restraints excluded: chain A residue  937 GLU
Chi-restraints excluded: chain A residue 1003 VAL
Chi-restraints excluded: chain A residue 1011 LYS
Chi-restraints excluded: chain C residue   85 CYS
Chi-restraints excluded: chain C residue  104 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 101 optimal weight:    0.5980
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    0.0980
   chunk 30 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.5180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131044 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.090221 restraints weight = 11156.422|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.25
r_work: 0.2913 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7514
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9143  Z= 0.135
  Angle     :  0.496   9.373  12392  Z= 0.256
  Chirality :  0.042   0.148   1374
  Planarity :  0.004   0.047   1604
  Dihedral  :  5.869  58.400   1253
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 11.19 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.22 (0.25), residues: 1126
  helix:  1.67 (0.24), residues: 485
  sheet:  0.60 (0.38), residues: 175
  loop :  0.07 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C   5 
 TYR   0.013   0.001   TYR C  74 
 PHE   0.010   0.001   PHE A 321 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.002   0.000   HIS A 818 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9140)
  covalent geometry    : angle       0.49567 (12390)
  SS BOND              : bond        0.02031 (    1)
  SS BOND              : angle       0.32267 (    2)
  hydrogen bonds       : bond        0.03894 (  426)
  hydrogen bonds       : angle       4.23720 ( 1209)
  Misc. bond           : bond        0.00003 (    2)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 3061.17 seconds
wall clock time: 52 minutes 27.69 seconds (3147.69 seconds total)