Starting phenix.real_space_refine
on Fri Feb 14 06:09:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zka_14760/02_2025/7zka_14760.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zka_14760/02_2025/7zka_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_2025/7zka_14760.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2025/7zka_14760.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2025/7zka_14760.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zka_14760/02_2025/7zka_14760.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.63, per 1000 atoms: 0.70
  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: 2.69
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  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: 1.06
  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: 3.72

  Time building geometry restraints manager: 2.98 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:             3.450
  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:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     25.990
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  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:             0.010
  Load rotamer database and sin/cos tables:12.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.850
-------------------------------------------------------------------------------
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   9587  Z= 0.588
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.008   0.001   TRP A 311 
 HIS   0.003   0.001   HIS A 932 
 PHE   0.025   0.001   PHE A 953 
 TYR   0.010   0.001   TYR A 440 
 ARG   0.003   0.000   ARG A 925 

*********************** 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  : 1.119 
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: 1.3493
  time to fit residues: 208.8858
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  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 30 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 35 optimal weight:   10.0000
   chunk 55 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.8782

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.169666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.126408 restraints weight = 10052.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.70
r_work: 0.3199 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3065 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9587  Z= 0.206
  Angle     :  0.596  10.035  12994  Z= 0.297
  Chirality :  0.043   0.235   1501
  Planarity :  0.004   0.066   1613
  Dihedral  : 14.726 109.567   1702
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.13 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.83 %
    Favored  : 88.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.24), residues: 1173
  helix:  1.78 (0.18), residues: 799
  sheet: -0.04 (0.62), residues: 70
  loop : -0.47 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 158 
 HIS   0.004   0.001   HIS A 608 
 PHE   0.023   0.001   PHE A 508 
 TYR   0.008   0.001   TYR A 440 
 ARG   0.002   0.000   ARG A1188 

*********************** 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
  132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  392 ASN cc_start: 0.7230 (p0) cc_final: 0.6706 (t0)
REVERT: A 1009 GLU cc_start: 0.7653 (mt-10) cc_final: 0.7326 (mp0)
REVERT: A 1152 GLN cc_start: 0.7546 (mt0) cc_final: 0.6595 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7470 (tmt170) cc_final: 0.7201 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7995 (mt0)
  outliers start: 19
  outliers final: 6
  residues processed: 119
  average time/residue: 1.4633
  time to fit residues: 185.5918
Evaluate side-chains
  109 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
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  729 SER
Chi-restraints excluded: chain A residue  844 ILE
Chi-restraints excluded: chain A residue  965 MET
Chi-restraints excluded: chain A residue 1189 GLN
Chi-restraints excluded: chain A residue 1238 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 33 optimal weight:    0.0570
   chunk 98 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 46 optimal weight:    0.0770
   chunk 35 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 93 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    1.0260

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

Flipped N/Q/H residues before XYZ refinement:
A  90 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.162293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.117537 restraints weight = 10215.396|
|-----------------------------------------------------------------------------|
r_work (start): 0.3225 rms_B_bonded: 1.74
r_work: 0.3080 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.08 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9587  Z= 0.209
  Angle     :  0.551   7.454  12994  Z= 0.278
  Chirality :  0.042   0.213   1501
  Planarity :  0.004   0.062   1613
  Dihedral  : 12.268 105.205   1702
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.72 (0.24), residues: 1173
  helix:  1.87 (0.18), residues: 802
  sheet:  0.21 (0.62), residues: 70
  loop : -0.56 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 158 
 HIS   0.005   0.001   HIS A 608 
 PHE   0.020   0.001   PHE A 508 
 TYR   0.009   0.001   TYR A 306 
 ARG   0.003   0.000   ARG A 355 

*********************** 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
  135 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.977 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.6420 (mpp)
REVERT: A  392 ASN cc_start: 0.7022 (p0) cc_final: 0.6512 (t0)
REVERT: A  424 ASN cc_start: 0.8120 (m-40) cc_final: 0.7641 (m110)
REVERT: A  515 GLN cc_start: 0.7383 (mm110) cc_final: 0.6844 (mp10)
REVERT: A 1009 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7381 (mm-30)
REVERT: A 1152 GLN cc_start: 0.7416 (mt0) cc_final: 0.6421 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7489 (tmt170) cc_final: 0.7149 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.7930 (mt0)
  outliers start: 20
  outliers final: 10
  residues processed: 123
  average time/residue: 1.3315
  time to fit residues: 175.1665
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
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  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  965 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 7 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 83 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 95 optimal weight:    5.9990
   chunk 61 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   chunk 92 optimal weight:    5.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.3749 r_free = 0.3749 target = 0.158638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.113544 restraints weight = 10207.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.75
r_work: 0.3069 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2925 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9587  Z= 0.186
  Angle     :  0.525   8.286  12994  Z= 0.266
  Chirality :  0.041   0.277   1501
  Planarity :  0.004   0.058   1613
  Dihedral  : 11.343  89.396   1702
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.30 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 13.77 %
    Favored  : 83.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.79 (0.24), residues: 1173
  helix:  1.94 (0.18), residues: 804
  sheet:  0.25 (0.62), residues: 70
  loop : -0.62 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 158 
 HIS   0.004   0.001   HIS A 608 
 PHE   0.019   0.001   PHE A 940 
 TYR   0.010   0.001   TYR A 306 
 ARG   0.002   0.000   ARG A 785 

*********************** 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
  133 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
REVERT: A  188 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.6440 (mpp)
REVERT: A  392 ASN cc_start: 0.6963 (p0) cc_final: 0.6474 (t0)
REVERT: A  424 ASN cc_start: 0.8185 (m-40) cc_final: 0.7722 (m110)
REVERT: A  884 LYS cc_start: 0.6549 (mtpp) cc_final: 0.6223 (mtmm)
REVERT: A  940 PHE cc_start: 0.7089 (t80) cc_final: 0.6850 (t80)
REVERT: A 1009 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7386 (mm-30)
REVERT: A 1152 GLN cc_start: 0.7411 (mt0) cc_final: 0.6432 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7950 (mt0)
REVERT: A 1237 ASP cc_start: 0.7865 (t0) cc_final: 0.7658 (t0)
  outliers start: 23
  outliers final: 9
  residues processed: 119
  average time/residue: 1.4020
  time to fit residues: 178.0831
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 77 optimal weight:    5.9990
   chunk 43 optimal weight:    0.0470
   chunk 59 optimal weight:    0.9990
   chunk 56 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 110 optimal weight:    5.9990
   chunk 81 optimal weight:    0.5980
   chunk 111 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    0.6678

-------------------------------------------------------------------------------
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
A1211 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.162292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.121225 restraints weight = 10154.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.64
r_work: 0.3098 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2958 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2958
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9587  Z= 0.165
  Angle     :  0.511   7.081  12994  Z= 0.258
  Chirality :  0.040   0.255   1501
  Planarity :  0.004   0.057   1613
  Dihedral  : 10.293  88.683   1702
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.53 %
    Favored  : 82.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.89 (0.24), residues: 1173
  helix:  2.03 (0.18), residues: 803
  sheet:  0.19 (0.62), residues: 70
  loop : -0.62 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 704 
 HIS   0.003   0.001   HIS A 608 
 PHE   0.016   0.001   PHE A 508 
 TYR   0.010   0.001   TYR A 306 
 ARG   0.003   0.000   ARG A 355 

*********************** 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
  132 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.048 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.6591 (mpp)
REVERT: A  392 ASN cc_start: 0.7006 (p0) cc_final: 0.6567 (t0)
REVERT: A  424 ASN cc_start: 0.8264 (m-40) cc_final: 0.7925 (m110)
REVERT: A  884 LYS cc_start: 0.6656 (mtpp) cc_final: 0.6333 (mtmm)
REVERT: A  940 PHE cc_start: 0.7158 (t80) cc_final: 0.6877 (t80)
REVERT: A  953 PHE cc_start: 0.7034 (OUTLIER) cc_final: 0.6745 (t80)
REVERT: A 1009 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7230 (mp0)
REVERT: A 1086 MET cc_start: 0.8373 (ptp) cc_final: 0.8133 (ptm)
REVERT: A 1152 GLN cc_start: 0.7530 (mt0) cc_final: 0.6572 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7564 (tmt170) cc_final: 0.7126 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8010 (mt0)
  outliers start: 22
  outliers final: 8
  residues processed: 121
  average time/residue: 1.3145
  time to fit residues: 170.2421
Evaluate side-chains
  114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 103
  time to evaluate  : 1.007 
-------------------------------------------------------------------------------
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  872 MET
Chi-restraints excluded: chain A residue  953 PHE
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 55 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   chunk 3 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 = 0.3750 r_free = 0.3750 target = 0.157824 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.116205 restraints weight = 10260.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.63
r_work: 0.3036 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2896 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9587  Z= 0.249
  Angle     :  0.546   7.321  12994  Z= 0.279
  Chirality :  0.042   0.195   1501
  Planarity :  0.004   0.056   1613
  Dihedral  : 10.079  85.777   1702
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.47 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.15 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.24), residues: 1173
  helix:  1.92 (0.18), residues: 804
  sheet:  0.19 (0.62), residues: 70
  loop : -0.69 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 158 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.021   0.002   PHE A 508 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.007   0.000   ARG A 745 

*********************** 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
  128 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.994 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8156 (OUTLIER) cc_final: 0.6984 (mpp)
REVERT: A  424 ASN cc_start: 0.8301 (m-40) cc_final: 0.7784 (m110)
REVERT: A  884 LYS cc_start: 0.6703 (mtpp) cc_final: 0.6369 (mtmm)
REVERT: A  940 PHE cc_start: 0.7254 (t80) cc_final: 0.6952 (t80)
REVERT: A  948 SER cc_start: 0.8198 (t) cc_final: 0.7821 (p)
REVERT: A 1009 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7499 (mm-30)
REVERT: A 1055 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7428 (tt0)
REVERT: A 1086 MET cc_start: 0.8371 (ptp) cc_final: 0.8148 (ptm)
REVERT: A 1152 GLN cc_start: 0.7565 (mt0) cc_final: 0.6595 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8025 (mt0)
  outliers start: 22
  outliers final: 9
  residues processed: 117
  average time/residue: 1.4294
  time to fit residues: 178.6119
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
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  293 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  872 MET
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 1232 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 96 optimal weight:    3.9990
   chunk 39 optimal weight:    0.1980
   chunk 50 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   chunk 53 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9990
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.164001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.122624 restraints weight = 10265.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.70
r_work: 0.3126 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.2997 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9587  Z= 0.167
  Angle     :  0.501   7.186  12994  Z= 0.259
  Chirality :  0.040   0.208   1501
  Planarity :  0.004   0.056   1613
  Dihedral  :  9.842  86.970   1702
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 16.98 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.24), residues: 1173
  helix:  2.06 (0.18), residues: 806
  sheet:  0.18 (0.63), residues: 70
  loop : -0.62 (0.35), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1104 
 HIS   0.003   0.001   HIS A 608 
 PHE   0.016   0.001   PHE A 508 
 TYR   0.010   0.001   TYR A 306 
 ARG   0.003   0.000   ARG A 745 

*********************** 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
  130 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.050 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8161 (OUTLIER) cc_final: 0.6606 (mpp)
REVERT: A  392 ASN cc_start: 0.6941 (p0) cc_final: 0.6644 (t0)
REVERT: A  424 ASN cc_start: 0.8299 (m-40) cc_final: 0.7959 (m110)
REVERT: A  511 LYS cc_start: 0.8165 (mtpp) cc_final: 0.7933 (ttmm)
REVERT: A  592 ASP cc_start: 0.7710 (m-30) cc_final: 0.7432 (m-30)
REVERT: A  884 LYS cc_start: 0.6700 (mtpp) cc_final: 0.6386 (mtmm)
REVERT: A  940 PHE cc_start: 0.7173 (t80) cc_final: 0.6871 (t80)
REVERT: A  948 SER cc_start: 0.8272 (t) cc_final: 0.7912 (p)
REVERT: A 1009 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7410 (mm-30)
REVERT: A 1055 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7403 (tt0)
REVERT: A 1152 GLN cc_start: 0.7553 (mt0) cc_final: 0.6570 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8031 (mt0)
  outliers start: 19
  outliers final: 9
  residues processed: 121
  average time/residue: 1.3739
  time to fit residues: 177.9033
Evaluate side-chains
  117 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
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  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  872 MET
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 1232 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 86 optimal weight:    6.9990
   chunk 73 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 110 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 6 optimal weight:    0.4980
   chunk 114 optimal weight:    2.9990
   chunk 113 optimal weight:    0.7980
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3752 r_free = 0.3752 target = 0.157931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.113868 restraints weight = 10364.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.04
r_work: 0.3026 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7788
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9587  Z= 0.231
  Angle     :  0.535   7.457  12994  Z= 0.275
  Chirality :  0.041   0.205   1501
  Planarity :  0.004   0.057   1613
  Dihedral  :  9.871  85.853   1702
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.29 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.24), residues: 1173
  helix:  1.96 (0.18), residues: 806
  sheet:  0.12 (0.63), residues: 70
  loop : -0.53 (0.36), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 158 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.021   0.001   PHE A 508 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.003   0.000   ARG A 925 

*********************** 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
  126 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.923 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8026 (OUTLIER) cc_final: 0.6949 (mpp)
REVERT: A  392 ASN cc_start: 0.6765 (p0) cc_final: 0.6475 (t0)
REVERT: A  424 ASN cc_start: 0.8194 (m-40) cc_final: 0.7651 (m110)
REVERT: A  511 LYS cc_start: 0.7989 (mtpp) cc_final: 0.7768 (ttmm)
REVERT: A  884 LYS cc_start: 0.6519 (mtpp) cc_final: 0.6175 (mtmm)
REVERT: A  948 SER cc_start: 0.8172 (t) cc_final: 0.7789 (p)
REVERT: A  965 MET cc_start: 0.6960 (ttp) cc_final: 0.6629 (tmm)
REVERT: A 1009 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7462 (mm-30)
REVERT: A 1055 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7376 (tt0)
REVERT: A 1152 GLN cc_start: 0.7445 (mt0) cc_final: 0.6454 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8422 (OUTLIER) cc_final: 0.7960 (mt0)
  outliers start: 18
  outliers final: 10
  residues processed: 115
  average time/residue: 1.4235
  time to fit residues: 174.7414
Evaluate side-chains
  118 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 105
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 MET
Chi-restraints excluded: chain A residue  495 GLU
Chi-restraints excluded: chain A residue  496 ILE
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  872 MET
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 1232 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 107 optimal weight:    0.0970
   chunk 30 optimal weight:    1.9990
   chunk 103 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 40 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0000
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.7184

-------------------------------------------------------------------------------
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 = 0.165347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.123861 restraints weight = 10199.204|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 1.79
r_work: 0.3082 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.2475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9587  Z= 0.171
  Angle     :  0.500   7.191  12994  Z= 0.259
  Chirality :  0.040   0.221   1501
  Planarity :  0.004   0.056   1613
  Dihedral  :  9.714  87.282   1702
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 17.60 %
    Favored  : 80.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.25), residues: 1173
  helix:  2.09 (0.18), residues: 805
  sheet:  0.11 (0.63), residues: 70
  loop : -0.52 (0.36), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A1104 
 HIS   0.002   0.001   HIS A 608 
 PHE   0.016   0.001   PHE A 508 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.004   0.000   ARG A 925 

*********************** 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
  121 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6704 (mpp)
REVERT: A  295 MET cc_start: 0.8362 (ttt) cc_final: 0.8100 (ttt)
REVERT: A  424 ASN cc_start: 0.8232 (m-40) cc_final: 0.7872 (m110)
REVERT: A  511 LYS cc_start: 0.8133 (mtpp) cc_final: 0.7926 (ttmm)
REVERT: A  592 ASP cc_start: 0.7632 (m-30) cc_final: 0.7286 (m-30)
REVERT: A  884 LYS cc_start: 0.6641 (mtpp) cc_final: 0.6306 (mtmm)
REVERT: A  948 SER cc_start: 0.8271 (t) cc_final: 0.7906 (p)
REVERT: A  965 MET cc_start: 0.7078 (ttp) cc_final: 0.6700 (tmm)
REVERT: A 1009 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7264 (mp0)
REVERT: A 1055 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7403 (tt0)
REVERT: A 1152 GLN cc_start: 0.7555 (mt0) cc_final: 0.6549 (mp-120)
REVERT: A 1164 ARG cc_start: 0.7543 (tmt170) cc_final: 0.7194 (tmm-80)
REVERT: A 1189 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8043 (mt0)
REVERT: A 1203 ASP cc_start: 0.6033 (m-30) cc_final: 0.5822 (m-30)
  outliers start: 15
  outliers final: 7
  residues processed: 113
  average time/residue: 1.4516
  time to fit residues: 174.6317
Evaluate side-chains
  114 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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  844 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 73 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 63 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9980
   chunk 88 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
** A 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.158922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.117648 restraints weight = 10363.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.59
r_work: 0.3093 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9587  Z= 0.220
  Angle     :  0.530   7.303  12994  Z= 0.277
  Chirality :  0.041   0.212   1501
  Planarity :  0.004   0.057   1613
  Dihedral  :  9.787  86.499   1702
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  : 17.91 %
    Favored  : 80.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.87 (0.24), residues: 1173
  helix:  1.99 (0.18), residues: 807
  sheet:  0.08 (0.65), residues: 70
  loop : -0.54 (0.35), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 158 
 HIS   0.003   0.001   HIS A 141 
 PHE   0.020   0.001   PHE A 508 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.005   0.000   ARG A 925 

********************** 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
  120 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.001 
Fit side-chains
REVERT: A  188 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7231 (mpp)
REVERT: A  424 ASN cc_start: 0.8284 (m-40) cc_final: 0.7934 (m-40)
REVERT: A  511 LYS cc_start: 0.8192 (mtpp) cc_final: 0.7971 (ttmm)
REVERT: A  884 LYS cc_start: 0.6743 (mtpp) cc_final: 0.6421 (mtmm)
REVERT: A  948 SER cc_start: 0.8363 (t) cc_final: 0.7983 (p)
REVERT: A 1009 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7449 (mm-30)
REVERT: A 1055 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7433 (tt0)
REVERT: A 1152 GLN cc_start: 0.7575 (mt0) cc_final: 0.6615 (mp-120)
REVERT: A 1189 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8043 (mt0)
REVERT: A 1203 ASP cc_start: 0.6033 (m-30) cc_final: 0.5831 (m-30)
  outliers start: 13
  outliers final: 7
  residues processed: 112
  average time/residue: 1.5168
  time to fit residues: 181.0149
Evaluate side-chains
  116 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.024 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  844 ILE
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 64 optimal weight:    0.1980
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0870
   chunk 35 optimal weight:    2.9990
   chunk 28 optimal weight:    0.3980
   chunk 26 optimal weight:    0.8980
   chunk 113 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.4158

-------------------------------------------------------------------------------
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 = 0.3854 r_free = 0.3854 target = 0.166421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.125595 restraints weight = 10228.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.66
r_work: 0.3145 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9587  Z= 0.141
  Angle     :  0.492   7.055  12994  Z= 0.257
  Chirality :  0.039   0.226   1501
  Planarity :  0.004   0.056   1613
  Dihedral  :  9.631  88.636   1702
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 18.63 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.25), residues: 1173
  helix:  2.17 (0.18), residues: 805
  sheet:  0.11 (0.65), residues: 70
  loop : -0.54 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 704 
 HIS   0.002   0.001   HIS A 608 
 PHE   0.014   0.001   PHE A 508 
 TYR   0.011   0.001   TYR A 306 
 ARG   0.004   0.000   ARG A 925 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7725.25 seconds
wall clock time: 137 minutes 14.15 seconds (8234.15 seconds total)