Starting phenix.real_space_refine
on Wed Feb  4 09:01:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2026/7zka_14760.cif"
  }
  resolution = 2.9
  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=   0.001 sd=   0.018
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       6      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    6053      2.51       5
     N    1566      2.21       5
     O    1743      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9406
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9133
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1177, 9133
          Classifications: {'peptide': 1177}
          Link IDs: {'PTRANS': 29, 'TRANS': 1147}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 273
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 273
          Unusual residues: {' MG': 2, 'ATP': 2, 'JIZ': 1, 'LMN': 1, 'Y01': 3}
          Classifications: {'undetermined': 9, 'water': 4}
          Link IDs: {None: 12}
  Time building chain proxies: 1.84, per 1000 atoms: 0.20
  Number of scatterers: 9406
  At special positions: 0
  Unit cell: (71.625, 85.377, 150.699, 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      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1743      8.00
     N    1566      7.00
     C    6053      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 419.1 milliseconds
  

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2160

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 4 sheets defined
      71.4% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 40
    Processing helix  chain 'A' and resid 43 through 72
      removed outlier: 4.269A  pdb=" N   LEU A  64 " --> pdb=" O   HIS A  60 " (cutoff:3.500A)
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 94 through 154
      removed outlier: 3.565A  pdb=" N   TYR A 126 " --> pdb=" O   LEU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 162
    Processing helix  chain 'A' and resid 164 through 180
      removed outlier: 4.236A  pdb=" N   ASN A 168 " --> pdb=" O   VAL A 164 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   THR A 169 " --> pdb=" O   GLY A 165 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   VAL A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   SER A 176 " --> pdb=" O   THR A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 216
      removed outlier: 3.910A  pdb=" N   GLY A 187 " --> pdb=" O   GLY A 183 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   TRP A 208 " --> pdb=" O   PHE A 204 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   LYS A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   LEU A 210 " --> pdb=" O   ARG A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 256
      removed outlier: 3.707A  pdb=" N   LEU A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 264
    Processing helix  chain 'A' and resid 265 through 319
      removed outlier: 3.753A  pdb=" N   ASN A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 323 through 366
      removed outlier: 4.473A  pdb=" N   ILE A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   GLY A 337 " --> pdb=" O   SER A 333 " (cutoff:3.500A)
      Proline residue:  A 346  - end of helix
      removed outlier: 3.857A  pdb=" N   TYR A 359 " --> pdb=" O   ARG A 355 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   GLU A 360 " --> pdb=" O   GLY A 356 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   VAL A 361 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   PHE A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 428 through 437
    Processing helix  chain 'A' and resid 455 through 457
      No H-bonds generated for 'chain 'A' and resid 455 through 457'
    Processing helix  chain 'A' and resid 458 through 465
    Processing helix  chain 'A' and resid 479 through 486
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 514 through 518
    Processing helix  chain 'A' and resid 521 through 525
    Processing helix  chain 'A' and resid 528 through 542
    Processing helix  chain 'A' and resid 558 through 572
      removed outlier: 3.596A  pdb=" N   ALA A 572 " --> pdb=" O   ALA A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 590
      removed outlier: 3.739A  pdb=" N   VAL A 588 " --> pdb=" O   ARG A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 614
    Processing helix  chain 'A' and resid 616 through 624
    Processing helix  chain 'A' and resid 691 through 699
      removed outlier: 3.620A  pdb=" N   LEU A 699 " --> pdb=" O   ARG A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 702
      No H-bonds generated for 'chain 'A' and resid 700 through 702'
    Processing helix  chain 'A' and resid 703 through 737
      removed outlier: 3.753A  pdb=" N   PHE A 707 " --> pdb=" O   GLU A 703 " (cutoff:3.500A)
      Proline residue:  A 722  - end of helix
    Processing helix  chain 'A' and resid 742 through 747
    Processing helix  chain 'A' and resid 749 through 795
    Processing helix  chain 'A' and resid 796 through 802
      removed outlier: 3.562A  pdb=" N   PHE A 800 " --> pdb=" O   ASP A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 806 through 824
    Processing helix  chain 'A' and resid 828 through 850
    Processing helix  chain 'A' and resid 853 through 899
      removed outlier: 3.588A  pdb=" N   LEU A 857 " --> pdb=" O   LEU A 853 " (cutoff:3.500A)
      Proline residue:  A 862  - end of helix
      removed outlier: 3.777A  pdb=" N   LEU A 880 " --> pdb=" O   SER A 876 " (cutoff:3.500A)
      removed outlier: 4.952A  pdb=" N   LYS A 881 " --> pdb=" O   GLY A 877 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   ASN A 899 " --> pdb=" O   GLU A 895 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 907
    Processing helix  chain 'A' and resid 908 through 962
      removed outlier: 4.537A  pdb=" N   ILE A 922 " --> pdb=" O   GLN A 918 " (cutoff:3.500A)
      Proline residue:  A 923  - end of helix
    Processing helix  chain 'A' and resid 969 through 1010
      Proline residue:  A 992  - end of helix
      removed outlier: 3.956A  pdb=" N   VAL A 999 " --> pdb=" O   ALA A 995 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   SER A1000 " --> pdb=" O   LYS A 996 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1071 through 1080
      removed outlier: 3.617A  pdb=" N   VAL A1076 " --> pdb=" O   LYS A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1100
      No H-bonds generated for 'chain 'A' and resid 1098 through 1100'
    Processing helix  chain 'A' and resid 1101 through 1108
    Processing helix  chain 'A' and resid 1122 through 1129
    Processing helix  chain 'A' and resid 1137 through 1148
    Processing helix  chain 'A' and resid 1150 through 1157
    Processing helix  chain 'A' and resid 1159 through 1163
    Processing helix  chain 'A' and resid 1166 through 1170
    Processing helix  chain 'A' and resid 1173 through 1188
      removed outlier: 4.099A  pdb=" N   ARG A1188 " --> pdb=" O   ARG A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1203 through 1217
      removed outlier: 3.587A  pdb=" N   ALA A1217 " --> pdb=" O   ALA A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1229 through 1236
    Processing helix  chain 'A' and resid 1252 through 1259
      removed outlier: 3.505A  pdb=" N   GLN A1259 " --> pdb=" O   GLN A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1261 through 1271
    Processing sheet with id=AA1, first strand: chain 'A' and resid 406 through 412
      removed outlier: 6.789A  pdb=" N   LYS A 407 " --> pdb=" O   HIS A 394 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   HIS A 394 " --> pdb=" O   LYS A 407 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   LEU A 409 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
      removed outlier: 5.469A  pdb=" N   PHE A 390 " --> pdb=" O   SER A 448 " (cutoff:3.500A)
      removed outlier: 7.525A  pdb=" N   SER A 448 " --> pdb=" O   PHE A 390 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   ASN A 392 " --> pdb=" O   MET A 446 " (cutoff:3.500A)
      removed outlier: 5.033A  pdb=" N   MET A 446 " --> pdb=" O   ASN A 392 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 466 through 469
      removed outlier: 6.444A  pdb=" N   GLY A 467 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   ASP A 551 " --> pdb=" O   GLY A 467 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   VAL A 469 " --> pdb=" O   ASP A 551 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   LEU A 548 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 8.121A  pdb=" N   ILE A 581 " --> pdb=" O   LEU A 548 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   LEU A 550 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ILE A 594 " --> pdb=" O   GLN A 605 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   GLN A 605 " --> pdb=" O   ILE A 594 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLY A 596 " --> pdb=" O   VAL A 603 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1050 through 1056
      removed outlier: 6.881A  pdb=" N   GLN A1050 " --> pdb=" O   VAL A1037 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   VAL A1037 " --> pdb=" O   GLN A1050 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   LEU A1052 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
      removed outlier: 5.459A  pdb=" N   PHE A1033 " --> pdb=" O   PHE A1091 " (cutoff:3.500A)
      removed outlier: 6.979A  pdb=" N   PHE A1091 " --> pdb=" O   PHE A1033 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   GLY A1035 " --> pdb=" O   SER A1089 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   SER A1089 " --> pdb=" O   GLY A1035 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1112
      removed outlier: 6.379A  pdb=" N   GLY A1110 " --> pdb=" O   LEU A1194 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   ASP A1196 " --> pdb=" O   GLY A1110 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   VAL A1112 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   LEU A1062 " --> pdb=" O   VAL A1225 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   THR A1061 " --> pdb=" O   LEU A1238 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   VAL A1240 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 6.202A  pdb=" N   ALA A1063 " --> pdb=" O   VAL A1240 " (cutoff:3.500A)
      removed outlier: 7.285A  pdb=" N   ILE A1242 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   VAL A1065 " --> pdb=" O   ILE A1242 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   ILE A1239 " --> pdb=" O   HIS A1250 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   HIS A1250 " --> pdb=" O   ILE A1239 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL A1241 " --> pdb=" O   LYS A1248 " (cutoff:3.500A)

    635 hydrogen bonds defined for protein.
    1845 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: 1.70

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1514
        1.31 -     1.44: 2466
        1.44 -     1.56: 5509
        1.56 -     1.69: 34
        1.69 -     1.82: 64
  Bond restraints: 9587
  Sorted by residual:
  bond pdb=" C03 JIZ A1401 "
       pdb=" N02 JIZ A1401 "
    ideal  model  delta    sigma   weight residual
    1.367  1.639 -0.272 2.00e-02 2.50e+03 1.86e+02
  bond pdb=" C08 JIZ A1401 "
       pdb=" N04 JIZ A1401 "
    ideal  model  delta    sigma   weight residual
    1.366  1.616 -0.250 2.00e-02 2.50e+03 1.57e+02
  bond pdb=" C13 JIZ A1401 "
       pdb=" N06 JIZ A1401 "
    ideal  model  delta    sigma   weight residual
    1.366  1.615 -0.249 2.00e-02 2.50e+03 1.55e+02
  bond pdb=" C02 JIZ A1401 "
       pdb=" S01 JIZ A1401 "
    ideal  model  delta    sigma   weight residual
    1.728  1.546  0.182 2.00e-02 2.50e+03 8.27e+01
  bond pdb=" C03 JIZ A1401 "
       pdb=" C04 JIZ A1401 "
    ideal  model  delta    sigma   weight residual
    1.360  1.520 -0.160 2.00e-02 2.50e+03 6.39e+01
  ... (remaining 9582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.56: 12845
        3.56 -     7.12: 130
        7.12 -    10.68: 14
       10.68 -    14.24: 1
       14.24 -    17.80: 4
  Bond angle restraints: 12994
  Sorted by residual:
  angle pdb=" N   ILE A 318 "
        pdb=" CA  ILE A 318 "
        pdb=" C   ILE A 318 "
      ideal   model   delta    sigma   weight residual
     111.90   99.57   12.33 8.10e-01 1.52e+00 2.32e+02
  angle pdb=" N   PRO A 741 "
        pdb=" CA  PRO A 741 "
        pdb=" C   PRO A 741 "
      ideal   model   delta    sigma   weight residual
     113.47  131.27  -17.80 1.43e+00 4.89e-01 1.55e+02
  angle pdb=" N   GLN A 746 "
        pdb=" CA  GLN A 746 "
        pdb=" C   GLN A 746 "
      ideal   model   delta    sigma   weight residual
     111.28  103.00    8.28 1.09e+00 8.42e-01 5.77e+01
  angle pdb=" N   PRO A 740 "
        pdb=" CA  PRO A 740 "
        pdb=" C   PRO A 740 "
      ideal   model   delta    sigma   weight residual
     110.70  102.31    8.39 1.22e+00 6.72e-01 4.73e+01
  angle pdb=" N   LYS A  86 "
        pdb=" CA  LYS A  86 "
        pdb=" C   LYS A  86 "
      ideal   model   delta    sigma   weight residual
     112.57  105.01    7.56 1.13e+00 7.83e-01 4.47e+01
  ... (remaining 12989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.39: 5499
       24.39 -    48.78: 363
       48.78 -    73.17: 70
       73.17 -    97.56: 27
       97.56 -   121.95: 22
  Dihedral angle restraints: 5981
    sinusoidal: 2610
      harmonic: 3371
  Sorted by residual:
  dihedral pdb=" C   LEU A 519 "
           pdb=" N   LEU A 519 "
           pdb=" CA  LEU A 519 "
           pdb=" CB  LEU A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.47   14.87     0      2.50e+00 1.60e-01 3.54e+01
  dihedral pdb=" N   LEU A 519 "
           pdb=" C   LEU A 519 "
           pdb=" CA  LEU A 519 "
           pdb=" CB  LEU A 519 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.32  -12.52     0      2.50e+00 1.60e-01 2.51e+01
  dihedral pdb=" C   PHE A 516 "
           pdb=" N   PHE A 516 "
           pdb=" CA  PHE A 516 "
           pdb=" CB  PHE A 516 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.15  -10.45     0      2.50e+00 1.60e-01 1.75e+01
  ... (remaining 5978 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1458
       0.131 -    0.261: 33
       0.261 -    0.392: 7
       0.392 -    0.523: 2
       0.523 -    0.653: 1
  Chirality restraints: 1501
  Sorted by residual:
  chirality pdb=" CA  PRO A 741 "
            pdb=" N   PRO A 741 "
            pdb=" C   PRO A 741 "
            pdb=" CB  PRO A 741 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.06    0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CA  LEU A 519 "
            pdb=" N   LEU A 519 "
            pdb=" C   LEU A 519 "
            pdb=" CB  LEU A 519 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.49e+00
  chirality pdb=" CA  ILE A 318 "
            pdb=" N   ILE A 318 "
            pdb=" C   ILE A 318 "
            pdb=" CB  ILE A 318 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.83   -0.39 2.00e-01 2.50e+01 3.89e+00
  ... (remaining 1498 not shown)

  Planarity restraints: 1613
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 736 "   -0.016 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   THR A 736 "    0.059 2.00e-02 2.50e+03
        pdb=" O   THR A 736 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ASN A 737 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 218 "    0.052 5.00e-02 4.00e+02   7.87e-02 9.92e+00
        pdb=" N   PRO A 219 "   -0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A 219 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 219 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 520 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.24e+00
        pdb=" C   VAL A 520 "    0.047 2.00e-02 2.50e+03
        pdb=" O   VAL A 520 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   GLY A 521 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1610 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 95
        2.61 -     3.18: 8453
        3.18 -     3.75: 15131
        3.75 -     4.33: 21212
        4.33 -     4.90: 34202
  Nonbonded interactions: 79093
  Sorted by model distance:
  nonbonded pdb=" OG  SER A1073 "
            pdb="MG    MG A1405 "
     model   vdw
     2.034 2.170
  nonbonded pdb=" O2G ATP A1404 "
            pdb="MG    MG A1405 "
     model   vdw
     2.049 2.170
  nonbonded pdb=" OG  SER A 430 "
            pdb="MG    MG A1403 "
     model   vdw
     2.063 2.170
  nonbonded pdb=" OE1 GLN A1114 "
            pdb="MG    MG A1405 "
     model   vdw
     2.066 2.170
  nonbonded pdb=" O2B ATP A1404 "
            pdb="MG    MG A1405 "
     model   vdw
     2.075 2.170
  ... (remaining 79088 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             4.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.660
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
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      :  0.009   0.272   9588  Z= 0.496
  Angle     :  0.871  17.803  12994  Z= 0.522
  Chirality :  0.057   0.653   1501
  Planarity :  0.005   0.079   1613
  Dihedral  : 19.022 121.954   3821
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.24), residues: 1173
  helix:  1.40 (0.18), residues: 795
  sheet: -0.40 (0.61), residues: 70
  loop : -0.55 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 925 
 TYR   0.010   0.001   TYR A 440 
 PHE   0.025   0.001   PHE A 953 
 TRP   0.008   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 932 

Details of bonding type rmsd
  covalent geometry    : bond        0.00923 ( 9587)
  covalent geometry    : angle       0.87115 (12994)
  hydrogen bonds       : bond        0.13289 (  635)
  hydrogen bonds       : angle       5.59472 ( 1845)
  Misc. bond           : bond        0.02901 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  193 MET cc_start: 0.6753 (mmp) cc_final: 0.6482 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.5673
  time to fit residues: 87.5274
Evaluate side-chains
  105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A  83 GLN
A  90 GLN
A 515 GLN
A 749 ASN
A 835 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.170359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.127215 restraints weight = 10087.981|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 1.69
r_work: 0.3179 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9588  Z= 0.140
  Angle     :  0.595   9.815  12994  Z= 0.294
  Chirality :  0.043   0.324   1501
  Planarity :  0.004   0.065   1613
  Dihedral  : 14.023 107.535   1702
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  1.96 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 10.04 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.59 (0.24), residues: 1173
  helix:  1.75 (0.18), residues: 801
  sheet:  0.05 (0.62), residues: 70
  loop : -0.52 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 745 
 TYR   0.008   0.001   TYR A 440 
 PHE   0.025   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A 158 
 HIS   0.005   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 9587)
  covalent geometry    : angle       0.59514 (12994)
  hydrogen bonds       : bond        0.04904 (  635)
  hydrogen bonds       : angle       4.40655 ( 1845)
  Misc. bond           : bond        0.00000 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 115
  time to evaluate  : 0.244 
Fit side-chains
REVERT: A  392 ASN cc_start: 0.7173 (p0) cc_final: 0.6699 (t0)
REVERT: A 1009 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7258 (mp0)
REVERT: A 1152 GLN cc_start: 0.7515 (mt0) cc_final: 0.6554 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7495 (tmt170) cc_final: 0.7219 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.7967 (mt0)
REVERT: A 1215 ASP cc_start: 0.7089 (m-30) cc_final: 0.6878 (m-30)
  outliers start: 18
  outliers final: 3
  residues processed: 123
  average time/residue: 0.5798
  time to fit residues: 75.8695
Evaluate side-chains
  105 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue 1189 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   chunk 25 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 27 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 99 optimal weight:    0.0050
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
** A 608 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.169649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.126558 restraints weight = 10102.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.70
r_work: 0.3124 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2981 rms_B_bonded: 4.02 restraints_weight: 0.2500
r_work (final): 0.2981
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.1672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9588  Z= 0.125
  Angle     :  0.526   7.183  12994  Z= 0.264
  Chirality :  0.041   0.218   1501
  Planarity :  0.004   0.061   1613
  Dihedral  : 11.972 103.432   1702
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 11.80 %
    Favored  : 85.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.24), residues: 1173
  helix:  1.95 (0.18), residues: 801
  sheet:  0.18 (0.62), residues: 70
  loop : -0.56 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 355 
 TYR   0.010   0.001   TYR A 306 
 PHE   0.020   0.001   PHE A 619 
 TRP   0.005   0.001   TRP A 158 
 HIS   0.012   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9587)
  covalent geometry    : angle       0.52599 (12994)
  hydrogen bonds       : bond        0.04682 (  635)
  hydrogen bonds       : angle       4.14385 ( 1845)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.6399 (mpp)
REVERT: A  392 ASN cc_start: 0.6916 (p0) cc_final: 0.6492 (t0)
REVERT: A  424 ASN cc_start: 0.8117 (m-40) cc_final: 0.7635 (m110)
REVERT: A  619 PHE cc_start: 0.6137 (t80) cc_final: 0.5892 (t80)
REVERT: A  940 PHE cc_start: 0.7101 (t80) cc_final: 0.6889 (t80)
REVERT: A 1009 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7143 (mp0)
REVERT: A 1152 GLN cc_start: 0.7388 (mt0) cc_final: 0.6421 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7467 (tmt170) cc_final: 0.7133 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.7901 (mt0)
REVERT: A 1215 ASP cc_start: 0.7040 (m-30) cc_final: 0.6833 (m-30)
  outliers start: 25
  outliers final: 11
  residues processed: 118
  average time/residue: 0.5515
  time to fit residues: 69.4607
Evaluate side-chains
  113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  519 LEU
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  860 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1232 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 47 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 72 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A  60 HIS
A 139 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.156869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.111402 restraints weight = 10359.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3181 rms_B_bonded: 1.76
r_work: 0.3033 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 4.12 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9588  Z= 0.177
  Angle     :  0.574   8.557  12994  Z= 0.289
  Chirality :  0.043   0.298   1501
  Planarity :  0.004   0.059   1613
  Dihedral  : 11.264  85.968   1702
  Min Nonbonded Distance : 1.899

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.47 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 14.70 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.24), residues: 1173
  helix:  1.81 (0.18), residues: 804
  sheet:  0.12 (0.60), residues: 70
  loop : -0.67 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 785 
 TYR   0.011   0.001   TYR A 306 
 PHE   0.021   0.002   PHE A 508 
 TRP   0.007   0.001   TRP A 158 
 HIS   0.006   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 9587)
  covalent geometry    : angle       0.57412 (12994)
  hydrogen bonds       : bond        0.05383 (  635)
  hydrogen bonds       : angle       4.20734 ( 1845)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.6527 (mpp)
REVERT: A  424 ASN cc_start: 0.8207 (m-40) cc_final: 0.7735 (m110)
REVERT: A  619 PHE cc_start: 0.6143 (t80) cc_final: 0.5891 (t80)
REVERT: A  884 LYS cc_start: 0.6596 (mtpp) cc_final: 0.6264 (mtmm)
REVERT: A  940 PHE cc_start: 0.7190 (t80) cc_final: 0.6902 (t80)
REVERT: A 1009 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7445 (mm-30)
REVERT: A 1152 GLN cc_start: 0.7461 (mt0) cc_final: 0.6486 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7984 (mt0)
REVERT: A 1215 ASP cc_start: 0.7053 (m-30) cc_final: 0.6835 (m-30)
REVERT: A 1237 ASP cc_start: 0.7908 (t0) cc_final: 0.7678 (t0)
  outliers start: 25
  outliers final: 11
  residues processed: 123
  average time/residue: 0.5108
  time to fit residues: 67.0010
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  496 ILE
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  860 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 17 optimal weight:    5.9990
   chunk 88 optimal weight:    0.7980
   chunk 114 optimal weight:    7.9990
   chunk 110 optimal weight:    0.8980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
A1020 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.157431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.115610 restraints weight = 10326.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3212 rms_B_bonded: 1.66
r_work: 0.3027 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.2270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   9588  Z= 0.172
  Angle     :  0.557   7.542  12994  Z= 0.283
  Chirality :  0.042   0.205   1501
  Planarity :  0.004   0.057   1613
  Dihedral  : 10.312  84.070   1702
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.42 %
    Favored  : 81.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.24), residues: 1173
  helix:  1.82 (0.18), residues: 804
  sheet:  0.02 (0.62), residues: 70
  loop : -0.69 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 745 
 TYR   0.011   0.001   TYR A 306 
 PHE   0.021   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A 158 
 HIS   0.006   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 9587)
  covalent geometry    : angle       0.55687 (12994)
  hydrogen bonds       : bond        0.05364 (  635)
  hydrogen bonds       : angle       4.18190 ( 1845)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 107
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7099 (mpp)
REVERT: A  392 ASN cc_start: 0.7105 (p0) cc_final: 0.6668 (t0)
REVERT: A  424 ASN cc_start: 0.8260 (m-40) cc_final: 0.7883 (m110)
REVERT: A  619 PHE cc_start: 0.6257 (t80) cc_final: 0.5974 (t80)
REVERT: A  884 LYS cc_start: 0.6712 (mtpp) cc_final: 0.6386 (mtmm)
REVERT: A 1009 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7558 (mm-30)
REVERT: A 1152 GLN cc_start: 0.7549 (mt0) cc_final: 0.6578 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8071 (mt0)
REVERT: A 1215 ASP cc_start: 0.7078 (m-30) cc_final: 0.6858 (m-30)
REVERT: A 1237 ASP cc_start: 0.7944 (t0) cc_final: 0.7698 (t0)
  outliers start: 26
  outliers final: 12
  residues processed: 123
  average time/residue: 0.5455
  time to fit residues: 71.4630
Evaluate side-chains
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 104
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue   84 VAL
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  860 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 94 optimal weight:    0.8980
   chunk 72 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 7 optimal weight:    9.9990
   chunk 39 optimal weight:    0.0870
   chunk 6 optimal weight:    0.8980
   chunk 32 optimal weight:    0.5980
   chunk 30 optimal weight:    6.9990
   chunk 90 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.6358

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

Flipped N/Q/H residues before XYZ refinement:
A1020 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.164414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.123121 restraints weight = 10260.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.68
r_work: 0.3082 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.88 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.2335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9588  Z= 0.120
  Angle     :  0.497   7.237  12994  Z= 0.255
  Chirality :  0.039   0.203   1501
  Planarity :  0.004   0.057   1613
  Dihedral  :  9.873  87.117   1702
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.25 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.24), residues: 1173
  helix:  2.03 (0.18), residues: 805
  sheet:  0.10 (0.62), residues: 70
  loop : -0.62 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 925 
 TYR   0.010   0.001   TYR A 306 
 PHE   0.016   0.001   PHE A 508 
 TRP   0.005   0.001   TRP A 704 
 HIS   0.005   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9587)
  covalent geometry    : angle       0.49706 (12994)
  hydrogen bonds       : bond        0.04666 (  635)
  hydrogen bonds       : angle       4.00288 ( 1845)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.367 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.6657 (mpp)
REVERT: A  392 ASN cc_start: 0.6934 (p0) cc_final: 0.6659 (t0)
REVERT: A  424 ASN cc_start: 0.8287 (m-40) cc_final: 0.7757 (m110)
REVERT: A  511 LYS cc_start: 0.8130 (mtpp) cc_final: 0.7920 (ttmm)
REVERT: A  592 ASP cc_start: 0.7627 (m-30) cc_final: 0.7346 (m-30)
REVERT: A  619 PHE cc_start: 0.6324 (t80) cc_final: 0.6058 (t80)
REVERT: A  884 LYS cc_start: 0.6624 (mtpp) cc_final: 0.6299 (mtmm)
REVERT: A  940 PHE cc_start: 0.7167 (t80) cc_final: 0.6928 (t80)
REVERT: A  948 SER cc_start: 0.8026 (t) cc_final: 0.7741 (p)
REVERT: A 1009 GLU cc_start: 0.7657 (mt-10) cc_final: 0.7432 (mm-30)
REVERT: A 1055 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7405 (tt0)
REVERT: A 1152 GLN cc_start: 0.7532 (mt0) cc_final: 0.6528 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7552 (tmt170) cc_final: 0.7282 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8058 (mt0)
REVERT: A 1215 ASP cc_start: 0.7069 (m-30) cc_final: 0.6841 (m-30)
REVERT: A 1237 ASP cc_start: 0.7886 (t0) cc_final: 0.7658 (t0)
  outliers start: 22
  outliers final: 12
  residues processed: 120
  average time/residue: 0.5175
  time to fit residues: 66.4864
Evaluate side-chains
  119 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  853 LEU
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1055 GLU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 7 optimal weight:    9.9990
   chunk 5 optimal weight:    2.9990
   chunk 97 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 105 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 42 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    2.1788

-------------------------------------------------------------------------------
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 = 0.3713 r_free = 0.3713 target = 0.154313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.112798 restraints weight = 10368.458|
|-----------------------------------------------------------------------------|
r_work (start): 0.3179 rms_B_bonded: 1.63
r_work: 0.2988 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2848 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2848
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.2585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9588  Z= 0.226
  Angle     :  0.592   9.710  12994  Z= 0.305
  Chirality :  0.044   0.185   1501
  Planarity :  0.004   0.056   1613
  Dihedral  : 10.146  82.344   1702
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 16.36 %
    Favored  : 81.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.24), residues: 1173
  helix:  1.72 (0.18), residues: 806
  sheet: -0.14 (0.63), residues: 70
  loop : -0.62 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 925 
 TYR   0.013   0.001   TYR A 126 
 PHE   0.026   0.002   PHE A 508 
 TRP   0.008   0.001   TRP A 158 
 HIS   0.006   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 9587)
  covalent geometry    : angle       0.59214 (12994)
  hydrogen bonds       : bond        0.05943 (  635)
  hydrogen bonds       : angle       4.27230 ( 1845)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 112
  time to evaluate  : 0.356 
Fit side-chains
REVERT: A   74 MET cc_start: 0.3370 (mpp) cc_final: 0.2789 (mmt)
REVERT: A  188 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7399 (mpp)
REVERT: A  424 ASN cc_start: 0.8234 (m-40) cc_final: 0.7839 (m-40)
REVERT: A  511 LYS cc_start: 0.8174 (mtpp) cc_final: 0.7956 (ttmm)
REVERT: A  619 PHE cc_start: 0.6391 (t80) cc_final: 0.6130 (t80)
REVERT: A  836 ILE cc_start: 0.7297 (mm) cc_final: 0.7065 (mt)
REVERT: A  884 LYS cc_start: 0.6766 (mtpp) cc_final: 0.6422 (mtmm)
REVERT: A  940 PHE cc_start: 0.7234 (t80) cc_final: 0.6968 (t80)
REVERT: A  948 SER cc_start: 0.8297 (t) cc_final: 0.7816 (p)
REVERT: A 1009 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7643 (mm-30)
REVERT: A 1152 GLN cc_start: 0.7577 (mt0) cc_final: 0.6603 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8105 (mt0)
REVERT: A 1215 ASP cc_start: 0.7047 (m-30) cc_final: 0.6816 (m-30)
REVERT: A 1237 ASP cc_start: 0.7983 (t0) cc_final: 0.7723 (t0)
  outliers start: 25
  outliers final: 12
  residues processed: 126
  average time/residue: 0.5571
  time to fit residues: 74.9443
Evaluate side-chains
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 107
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  593 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1232 THR
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 22 optimal weight:    0.7980
   chunk 42 optimal weight:    0.5980
   chunk 5 optimal weight:   30.0000
   chunk 108 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3766 r_free = 0.3766 target = 0.159116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.115710 restraints weight = 10317.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 2.05
r_work: 0.3076 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9588  Z= 0.133
  Angle     :  0.517   7.443  12994  Z= 0.266
  Chirality :  0.040   0.211   1501
  Planarity :  0.004   0.056   1613
  Dihedral  :  9.820  85.174   1702
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.08 %
    Favored  : 80.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.25), residues: 1173
  helix:  1.98 (0.18), residues: 807
  sheet: -0.16 (0.63), residues: 70
  loop : -0.59 (0.36), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 925 
 TYR   0.011   0.001   TYR A 306 
 PHE   0.017   0.001   PHE A 508 
 TRP   0.005   0.001   TRP A 208 
 HIS   0.004   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 9587)
  covalent geometry    : angle       0.51687 (12994)
  hydrogen bonds       : bond        0.04949 (  635)
  hydrogen bonds       : angle       4.05827 ( 1845)
  Misc. bond           : bond        0.00013 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A   74 MET cc_start: 0.3305 (mpp) cc_final: 0.2727 (mmt)
REVERT: A  188 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7231 (mpp)
REVERT: A  392 ASN cc_start: 0.7007 (p0) cc_final: 0.6724 (t0)
REVERT: A  424 ASN cc_start: 0.8283 (m-40) cc_final: 0.7750 (m-40)
REVERT: A  511 LYS cc_start: 0.8139 (mtpp) cc_final: 0.7926 (ttmm)
REVERT: A  619 PHE cc_start: 0.6438 (t80) cc_final: 0.6114 (t80)
REVERT: A  884 LYS cc_start: 0.6736 (mtpp) cc_final: 0.6409 (mtmm)
REVERT: A  940 PHE cc_start: 0.7147 (t80) cc_final: 0.6862 (t80)
REVERT: A  948 SER cc_start: 0.8322 (t) cc_final: 0.7890 (p)
REVERT: A 1009 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7514 (mm-30)
REVERT: A 1086 MET cc_start: 0.8411 (ptp) cc_final: 0.8119 (ptm)
REVERT: A 1152 GLN cc_start: 0.7537 (mt0) cc_final: 0.6522 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7621 (tmt170) cc_final: 0.7369 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8105 (mt0)
REVERT: A 1215 ASP cc_start: 0.7077 (m-30) cc_final: 0.6850 (m-30)
REVERT: A 1237 ASP cc_start: 0.7952 (t0) cc_final: 0.7718 (t0)
  outliers start: 19
  outliers final: 11
  residues processed: 118
  average time/residue: 0.5992
  time to fit residues: 75.4437
Evaluate side-chains
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  377 SER
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 6 optimal weight:    8.9990
   chunk 0 optimal weight:    3.9990
   chunk 87 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 963 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.162892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.121642 restraints weight = 10278.248|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.69
r_work: 0.3089 rms_B_bonded: 2.35 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9588  Z= 0.147
  Angle     :  0.522   7.476  12994  Z= 0.269
  Chirality :  0.041   0.215   1501
  Planarity :  0.004   0.055   1613
  Dihedral  :  9.823  85.907   1702
  Min Nonbonded Distance : 1.933

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 17.81 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.25), residues: 1173
  helix:  1.96 (0.18), residues: 806
  sheet: -0.16 (0.64), residues: 70
  loop : -0.51 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 925 
 TYR   0.010   0.001   TYR A 306 
 PHE   0.019   0.001   PHE A 508 
 TRP   0.005   0.001   TRP A 704 
 HIS   0.005   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9587)
  covalent geometry    : angle       0.52208 (12994)
  hydrogen bonds       : bond        0.05074 (  635)
  hydrogen bonds       : angle       4.05968 ( 1845)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   74 MET cc_start: 0.3377 (mpp) cc_final: 0.2795 (mmt)
REVERT: A   91 MET cc_start: 0.5131 (mmt) cc_final: 0.4913 (mmm)
REVERT: A  188 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7285 (mpp)
REVERT: A  392 ASN cc_start: 0.7020 (p0) cc_final: 0.6772 (t0)
REVERT: A  424 ASN cc_start: 0.8253 (m-40) cc_final: 0.7876 (m-40)
REVERT: A  511 LYS cc_start: 0.8176 (mtpp) cc_final: 0.7958 (ttmm)
REVERT: A  619 PHE cc_start: 0.6476 (t80) cc_final: 0.6210 (t80)
REVERT: A  836 ILE cc_start: 0.7315 (mm) cc_final: 0.7085 (mt)
REVERT: A  884 LYS cc_start: 0.6748 (mtpp) cc_final: 0.6425 (mtmm)
REVERT: A  940 PHE cc_start: 0.7154 (t80) cc_final: 0.6903 (t80)
REVERT: A  948 SER cc_start: 0.8355 (t) cc_final: 0.7876 (p)
REVERT: A 1009 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7501 (mm-30)
REVERT: A 1086 MET cc_start: 0.8369 (ptp) cc_final: 0.8084 (ptm)
REVERT: A 1152 GLN cc_start: 0.7569 (mt0) cc_final: 0.6563 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7584 (tmt170) cc_final: 0.7322 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8088 (mt0)
REVERT: A 1215 ASP cc_start: 0.7096 (m-30) cc_final: 0.6866 (m-30)
REVERT: A 1237 ASP cc_start: 0.8003 (t0) cc_final: 0.7765 (t0)
  outliers start: 17
  outliers final: 10
  residues processed: 119
  average time/residue: 0.6451
  time to fit residues: 81.8174
Evaluate side-chains
  123 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  500 VAL
Chi-restraints excluded: chain A residue  729 SER
Chi-restraints excluded: chain A residue  813 ARG
Chi-restraints excluded: chain A residue  832 ILE
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 15 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 24 optimal weight:    0.6980
   chunk 10 optimal weight:    0.6980
   chunk 27 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0040
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.3842 r_free = 0.3842 target = 0.165353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124596 restraints weight = 10208.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 1.85
r_work: 0.3076 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9588  Z= 0.117
  Angle     :  0.493   7.236  12994  Z= 0.255
  Chirality :  0.040   0.226   1501
  Planarity :  0.004   0.055   1613
  Dihedral  :  9.660  88.326   1702
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 18.32 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.95 (0.25), residues: 1173
  helix:  2.08 (0.18), residues: 805
  sheet: -0.10 (0.64), residues: 70
  loop : -0.51 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 925 
 TYR   0.010   0.001   TYR A 306 
 PHE   0.015   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A 704 
 HIS   0.005   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 9587)
  covalent geometry    : angle       0.49318 (12994)
  hydrogen bonds       : bond        0.04568 (  635)
  hydrogen bonds       : angle       3.94475 ( 1845)
  Misc. bond           : bond        0.00008 (    1)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.391 
Fit side-chains
REVERT: A   74 MET cc_start: 0.3307 (mpp) cc_final: 0.2734 (mmt)
REVERT: A   91 MET cc_start: 0.5013 (mmt) cc_final: 0.4794 (mmm)
REVERT: A  188 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7182 (mpp)
REVERT: A  424 ASN cc_start: 0.8256 (m-40) cc_final: 0.7704 (m-40)
REVERT: A  619 PHE cc_start: 0.6334 (t80) cc_final: 0.6065 (t80)
REVERT: A  884 LYS cc_start: 0.6664 (mtpp) cc_final: 0.6324 (mtmm)
REVERT: A  940 PHE cc_start: 0.7033 (t80) cc_final: 0.6727 (t80)
REVERT: A  948 SER cc_start: 0.8289 (t) cc_final: 0.7874 (p)
REVERT: A 1009 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7422 (mm-30)
REVERT: A 1086 MET cc_start: 0.8369 (ptp) cc_final: 0.8091 (ptm)
REVERT: A 1152 GLN cc_start: 0.7556 (mt0) cc_final: 0.6540 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7576 (tmt170) cc_final: 0.7320 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8091 (mt0)
REVERT: A 1215 ASP cc_start: 0.7082 (m-30) cc_final: 0.6861 (m-30)
REVERT: A 1237 ASP cc_start: 0.7925 (t0) cc_final: 0.7669 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 115
  average time/residue: 0.6562
  time to fit residues: 80.4280
Evaluate side-chains
  113 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 104
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 MET
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  813 ARG
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  872 MET
Chi-restraints excluded: chain A residue 1019 THR
Chi-restraints excluded: chain A residue 1027 LEU
Chi-restraints excluded: chain A residue 1189 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 45 optimal weight:    0.5980
   chunk 55 optimal weight:   10.0000
   chunk 87 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 90 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 107 optimal weight:    0.4980
   chunk 13 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.4184

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.160962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.118609 restraints weight = 10265.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.93
r_work: 0.3024 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.04 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.2661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9588  Z= 0.167
  Angle     :  0.541   7.410  12994  Z= 0.282
  Chirality :  0.041   0.216   1501
  Planarity :  0.004   0.055   1613
  Dihedral  :  9.831  86.407   1702
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.01 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.82 (0.25), residues: 1173
  helix:  1.96 (0.18), residues: 806
  sheet: -0.18 (0.64), residues: 70
  loop : -0.51 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 925 
 TYR   0.011   0.001   TYR A 306 
 PHE   0.022   0.001   PHE A 508 
 TRP   0.006   0.001   TRP A 158 
 HIS   0.005   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 9587)
  covalent geometry    : angle       0.54063 (12994)
  hydrogen bonds       : bond        0.05191 (  635)
  hydrogen bonds       : angle       4.05415 ( 1845)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3363.11 seconds
wall clock time: 57 minutes 57.53 seconds (3477.53 seconds total)