Starting phenix.real_space_refine
on Thu Feb 13 23:07:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctf_45904/02_2025/9ctf_45904.cif"
  }
  resolution = 3.9
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      35      5.16       5
     C    6157      2.51       5
     N    1532      2.21       5
     O    1671      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 9398
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1158, 9010
          Classifications: {'peptide': 1158}
          Link IDs: {'PTRANS': 29, 'TRANS': 1128}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 388
          Unusual residues: {'ATP': 1, 'TA1': 1, 'UPL': 22}
          Classifications: {'undetermined': 24}
          Link IDs: {None: 23}
          Unresolved non-hydrogen bonds: 453
          Unresolved non-hydrogen angles: 475
          Unresolved non-hydrogen dihedrals: 497
          Unresolved non-hydrogen chiralities: 22
  Time building chain proxies: 5.99, per 1000 atoms: 0.64
  Number of scatterers: 9398
  At special positions: 0
  Unit cell: (112.548, 119.52, 115.536, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      35     16.00
     P       3     15.00
     O    1671      8.00
     N    1532      7.00
     C    6157      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 5 sheets defined
      71.2% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 40
      removed outlier: 3.880A  pdb=" N   SER A  38 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   PHE A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 87
      removed outlier: 4.107A  pdb=" N   LEU A  65 " --> pdb=" O   HIS A  61 " (cutoff:3.500A)
      Proline residue:  A  66  - end of helix
    Processing helix  chain 'A' and resid 101 through 158
    Processing helix  chain 'A' and resid 159 through 165
      removed outlier: 3.629A  pdb=" N   VAL A 165 " --> pdb=" O   GLY A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
      removed outlier: 3.858A  pdb=" N   LEU A 171 " --> pdb=" O   ASP A 167 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ASN A 172 " --> pdb=" O   VAL A 168 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR A 173 " --> pdb=" O   GLY A 169 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   VAL A 179 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 209
      removed outlier: 4.532A  pdb=" N   GLY A 191 " --> pdb=" O   GLY A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 258
      removed outlier: 3.761A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      Proline residue:  A 223  - end of helix
      removed outlier: 5.000A  pdb=" N   THR A 240 " --> pdb=" O   LEU A 236 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   ASP A 241 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LYS A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 5.093A  pdb=" N   ALA A 250 " --> pdb=" O   ALA A 246 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 253 " --> pdb=" O   LYS A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 268
    Processing helix  chain 'A' and resid 269 through 323
      removed outlier: 4.864A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 347
      removed outlier: 3.841A  pdb=" N   GLY A 346 " --> pdb=" O   ALA A 342 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   GLN A 347 " --> pdb=" O   PHE A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 371
      removed outlier: 4.373A  pdb=" N   GLU A 364 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE A 365 " --> pdb=" O   ALA A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
      removed outlier: 3.729A  pdb=" N   LYS A 405 " --> pdb=" O   PRO A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 441
    Processing helix  chain 'A' and resid 462 through 469
    Processing helix  chain 'A' and resid 483 through 490
    Processing helix  chain 'A' and resid 496 through 507
    Processing helix  chain 'A' and resid 509 through 515
      removed outlier: 3.848A  pdb=" N   MET A 514 " --> pdb=" O   TYR A 510 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   LYS A 515 " --> pdb=" O   ASP A 511 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 522
    Processing helix  chain 'A' and resid 532 through 547
      removed outlier: 3.513A  pdb=" N   LYS A 536 " --> pdb=" O   SER A 532 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   GLN A 537 " --> pdb=" O   GLY A 533 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ARG A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 577
      removed outlier: 4.006A  pdb=" N   VAL A 568 " --> pdb=" O   GLU A 564 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 595
      removed outlier: 4.213A  pdb=" N   ASN A 594 " --> pdb=" O   THR A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 611 through 619
      removed outlier: 3.584A  pdb=" N   LYS A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 630
    Processing helix  chain 'A' and resid 695 through 703
      removed outlier: 4.154A  pdb=" N   ARG A 699 " --> pdb=" O   VAL A 695 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 700 " --> pdb=" O   SER A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 707 through 723
      removed outlier: 3.508A  pdb=" N   PHE A 711 " --> pdb=" O   GLU A 707 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A 720 " --> pdb=" O   PHE A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 739
      removed outlier: 3.969A  pdb=" N   ALA A 727 " --> pdb=" O   GLY A 723 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   PHE A 739 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 799
    Processing helix  chain 'A' and resid 800 through 806
      removed outlier: 4.259A  pdb=" N   PHE A 804 " --> pdb=" O   ASP A 800 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP A 806 " --> pdb=" O   SER A 802 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 810 through 820
    Processing helix  chain 'A' and resid 821 through 828
      removed outlier: 3.642A  pdb=" N   VAL A 825 " --> pdb=" O   ALA A 822 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   LYS A 826 " --> pdb=" O   ALA A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 854
      removed outlier: 3.535A  pdb=" N   GLY A 846 " --> pdb=" O   ASN A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 854 through 902
      removed outlier: 3.589A  pdb=" N   THR A 858 " --> pdb=" O   GLY A 854 " (cutoff:3.500A)
      Proline residue:  A 866  - end of helix
      removed outlier: 4.303A  pdb=" N   GLY A 892 " --> pdb=" O   LYS A 888 " (cutoff:3.500A)
      removed outlier: 4.258A  pdb=" N   SER A 893 " --> pdb=" O   GLU A 889 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE A 896 " --> pdb=" O   GLY A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 903 through 910
    Processing helix  chain 'A' and resid 912 through 966
      removed outlier: 3.766A  pdb=" N   GLN A 922 " --> pdb=" O   HIS A 918 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   SER A 923 " --> pdb=" O   MET A 919 " (cutoff:3.500A)
      Proline residue:  A 927  - end of helix
      removed outlier: 4.795A  pdb=" N   MET A 949 " --> pdb=" O   THR A 945 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   TYR A 950 " --> pdb=" O   GLN A 946 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 951 " --> pdb=" O   ALA A 947 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   HIS A 966 " --> pdb=" O   TYR A 962 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 995
      removed outlier: 3.975A  pdb=" N   VAL A 981 " --> pdb=" O   VAL A 977 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   GLY A 984 " --> pdb=" O   ALA A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1014
    Processing helix  chain 'A' and resid 1075 through 1084
    Processing helix  chain 'A' and resid 1102 through 1104
      No H-bonds generated for 'chain 'A' and resid 1102 through 1104'
    Processing helix  chain 'A' and resid 1105 through 1111
    Processing helix  chain 'A' and resid 1127 through 1133
    Processing helix  chain 'A' and resid 1141 through 1152
      removed outlier: 3.650A  pdb=" N   ILE A1145 " --> pdb=" O   SER A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1154 through 1159
    Processing helix  chain 'A' and resid 1163 through 1166
    Processing helix  chain 'A' and resid 1177 through 1192
      removed outlier: 4.151A  pdb=" N   ARG A1192 " --> pdb=" O   ARG A1188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1202 through 1205
      removed outlier: 4.034A  pdb=" N   ALA A1205 " --> pdb=" O   ALA A1202 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1202 through 1205'
    Processing helix  chain 'A' and resid 1207 through 1223
      removed outlier: 3.893A  pdb=" N   VAL A1213 " --> pdb=" O   GLU A1209 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   LYS A1220 " --> pdb=" O   GLU A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing sheet with id=AA1, first strand: chain 'A' and resid 413 through 417
      removed outlier: 4.779A  pdb=" N   LEU A 413 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   PHE A 394 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
      removed outlier: 7.305A  pdb=" N   SER A 452 " --> pdb=" O   PHE A 394 " (cutoff:3.500A)
      removed outlier: 5.338A  pdb=" N   ASN A 396 " --> pdb=" O   MET A 450 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   MET A 450 " --> pdb=" O   ASN A 396 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 473
      removed outlier: 3.591A  pdb=" N   VAL A 584 " --> pdb=" O   VAL A 423 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   GLY A 610 " --> pdb=" O   ILE A 598 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1053 through 1056
      removed outlier: 4.745A  pdb=" N   VAL A1040 " --> pdb=" O   GLY A1055 " (cutoff:3.500A)
      removed outlier: 5.453A  pdb=" N   PHE A1037 " --> pdb=" O   LEU A1095 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   LEU A1095 " --> pdb=" O   PHE A1037 " (cutoff:3.500A)
      removed outlier: 5.463A  pdb=" N   GLU A1039 " --> pdb=" O   LYS A1093 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   LYS A1093 " --> pdb=" O   GLU A1039 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1113 through 1116
      removed outlier: 6.086A  pdb=" N   GLY A1114 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   ASP A1200 " --> pdb=" O   GLY A1114 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL A1116 " --> pdb=" O   ASP A1200 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   ALA A1067 " --> pdb=" O   VAL A1244 " (cutoff:3.500A)
      removed outlier: 7.764A  pdb=" N   PHE A1246 " --> pdb=" O   ALA A1067 " (cutoff:3.500A)
      removed outlier: 7.759A  pdb=" N   VAL A1069 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   GLU A1253 " --> pdb=" O   VAL A1245 " (cutoff:3.500A)
      removed outlier: 6.503A  pdb=" N   GLN A1247 " --> pdb=" O   VAL A1251 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   VAL A1251 " --> pdb=" O   GLN A1247 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1125 through 1126
      removed outlier: 3.803A  pdb=" N   CYS A1125 " --> pdb=" O   VAL A1169 " (cutoff:3.500A)

    618 hydrogen bonds defined for protein.
    1797 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: 3.31

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1533
        1.32 -     1.44: 2380
        1.44 -     1.57: 5567
        1.57 -     1.69: 9
        1.69 -     1.81: 63
  Bond restraints: 9552
  Sorted by residual:
  bond pdb=" C   VAL A 926 "
       pdb=" N   PRO A 927 "
    ideal  model  delta    sigma   weight residual
    1.335  1.354 -0.019 1.19e-02 7.06e+03 2.56e+00
  bond pdb=" CA  VAL A 926 "
       pdb=" C   VAL A 926 "
    ideal  model  delta    sigma   weight residual
    1.523  1.533 -0.010 9.20e-03 1.18e+04 1.21e+00
  bond pdb=" C   ALA A 995 "
       pdb=" N   PRO A 996 "
    ideal  model  delta    sigma   weight residual
    1.334  1.356 -0.022 2.34e-02 1.83e+03 8.88e-01
  bond pdb=" CA  PRO A 996 "
       pdb=" C   PRO A 996 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.012 1.42e-02 4.96e+03 7.08e-01
  bond pdb=" CA  PRO A 996 "
       pdb=" CB  PRO A 996 "
    ideal  model  delta    sigma   weight residual
    1.533  1.522  0.011 1.42e-02 4.96e+03 6.52e-01
  ... (remaining 9547 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 12578
        1.42 -     2.83: 180
        2.83 -     4.25: 33
        4.25 -     5.67: 14
        5.67 -     7.08: 6
  Bond angle restraints: 12811
  Sorted by residual:
  angle pdb=" C   HIS A 518 "
        pdb=" N   LYS A 519 "
        pdb=" CA  LYS A 519 "
      ideal   model   delta    sigma   weight residual
     121.54  125.53   -3.99 1.91e+00 2.74e-01 4.36e+00
  angle pdb=" C   ASN A1163 "
        pdb=" N   LYS A1164 "
        pdb=" CA  LYS A1164 "
      ideal   model   delta    sigma   weight residual
     121.54  125.48   -3.94 1.91e+00 2.74e-01 4.26e+00
  angle pdb=" C18 TA1 A1324 "
        pdb=" C20 TA1 A1324 "
        pdb=" C21 TA1 A1324 "
      ideal   model   delta    sigma   weight residual
     124.82  130.99   -6.17 3.00e+00 1.11e-01 4.23e+00
  angle pdb=" CA  LEU A 784 "
        pdb=" CB  LEU A 784 "
        pdb=" CG  LEU A 784 "
      ideal   model   delta    sigma   weight residual
     116.30  123.38   -7.08 3.50e+00 8.16e-02 4.10e+00
  angle pdb=" C   ALA A 995 "
        pdb=" N   PRO A 996 "
        pdb=" CA  PRO A 996 "
      ideal   model   delta    sigma   weight residual
     119.84  122.29   -2.45 1.25e+00 6.40e-01 3.85e+00
  ... (remaining 12806 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.51: 5610
       27.51 -    55.02: 186
       55.02 -    82.53: 24
       82.53 -   110.03: 8
      110.03 -   137.54: 12
  Dihedral angle restraints: 5840
    sinusoidal: 2519
      harmonic: 3321
  Sorted by residual:
  dihedral pdb=" O08 TA1 A1324 "
           pdb=" C20 TA1 A1324 "
           pdb=" C21 TA1 A1324 "
           pdb=" O09 TA1 A1324 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.50    9.04 -137.54     1      3.00e+01 1.11e-03 1.85e+01
  dihedral pdb=" C24 TA1 A1324 "
           pdb=" C20 TA1 A1324 "
           pdb=" C21 TA1 A1324 "
           pdb=" O08 TA1 A1324 "
      ideal   model   delta sinusoidal    sigma   weight residual
     254.51  117.20  137.31     1      3.00e+01 1.11e-03 1.85e+01
  dihedral pdb=" C19 TA1 A1324 "
           pdb=" C18 TA1 A1324 "
           pdb=" C20 TA1 A1324 "
           pdb=" O08 TA1 A1324 "
      ideal   model   delta sinusoidal    sigma   weight residual
     140.52    8.29  132.23     1      3.00e+01 1.11e-03 1.78e+01
  ... (remaining 5837 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1166
       0.045 -    0.091: 228
       0.091 -    0.136: 51
       0.136 -    0.182: 0
       0.182 -    0.227: 1
  Chirality restraints: 1446
  Sorted by residual:
  chirality pdb=" C10 TA1 A1324 "
            pdb=" C02 TA1 A1324 "
            pdb=" C11 TA1 A1324 "
            pdb=" C18 TA1 A1324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.54    2.32    0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CA  TRP A 708 "
            pdb=" N   TRP A 708 "
            pdb=" C   TRP A 708 "
            pdb=" CB  TRP A 708 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.54e-01
  chirality pdb=" CA  ILE A1230 "
            pdb=" N   ILE A1230 "
            pdb=" C   ILE A1230 "
            pdb=" CB  ILE A1230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.31e-01
  ... (remaining 1443 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 995 "    0.027 5.00e-02 4.00e+02   4.06e-02 2.63e+00
        pdb=" N   PRO A 996 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 996 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 996 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A 174 "    0.005 2.00e-02 2.50e+03   1.07e-02 1.14e+00
        pdb=" C   ARG A 174 "   -0.018 2.00e-02 2.50e+03
        pdb=" O   ARG A 174 "    0.007 2.00e-02 2.50e+03
        pdb=" N   LEU A 175 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "    0.018 5.00e-02 4.00e+02   2.65e-02 1.12e+00
        pdb=" N   PRO A  66 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "    0.015 5.00e-02 4.00e+02
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1074
        2.75 -     3.29: 9853
        3.29 -     3.82: 15555
        3.82 -     4.36: 17185
        4.36 -     4.90: 29856
  Nonbonded interactions: 73523
  Sorted by model distance:
  nonbonded pdb=" O   PHE A1157 "
            pdb=" OG  SER A1160 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   THR A 333 "
            pdb=" OG  SER A 337 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" NH1 ARG A 489 "
            pdb=" O   VAL A 495 "
     model   vdw
     2.219 3.120
  nonbonded pdb=" NH2 ARG A 489 "
            pdb=" O   GLU A 493 "
     model   vdw
     2.287 3.120
  nonbonded pdb=" O   SER A1071 "
            pdb=" NZ  LYS A1076 "
     model   vdw
     2.302 3.120
  ... (remaining 73518 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.700
  Find NCS groups from input model:        0.100
  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:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9552  Z= 0.156
  Angle     :  0.495   7.084  12811  Z= 0.255
  Chirality :  0.038   0.227   1446
  Planarity :  0.003   0.041   1580
  Dihedral  : 15.185 137.542   3708
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.52 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  6.58 %
    Favored  : 92.90 %
  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:  1.77 (0.25), residues: 1152
  helix:  1.92 (0.19), residues: 738
  sheet:  0.13 (0.61), residues: 72
  loop : -0.17 (0.34), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 698 
 HIS   0.002   0.001   HIS A 612 
 PHE   0.011   0.001   PHE A 193 
 TYR   0.011   0.001   TYR A 920 
 ARG   0.002   0.000   ARG A 538 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 195
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7694 (t80)
REVERT: A  130 TYR cc_start: 0.8581 (t80) cc_final: 0.8366 (t80)
REVERT: A  193 PHE cc_start: 0.8481 (t80) cc_final: 0.8246 (t80)
REVERT: A  416 LYS cc_start: 0.7170 (mmmm) cc_final: 0.6843 (mptt)
REVERT: A  538 ARG cc_start: 0.6855 (ptm-80) cc_final: 0.6336 (mtt90)
REVERT: A  541 ILE cc_start: 0.8899 (tt) cc_final: 0.8568 (mt)
REVERT: A  616 MET cc_start: 0.2266 (mpp) cc_final: 0.1993 (mtp)
REVERT: A  717 CYS cc_start: 0.7784 (t) cc_final: 0.7475 (t)
REVERT: A  796 MET cc_start: 0.8810 (mtm) cc_final: 0.8089 (mtm)
REVERT: A  808 LYS cc_start: 0.8692 (tttt) cc_final: 0.7854 (tptt)
REVERT: A  857 LEU cc_start: 0.8598 (mt) cc_final: 0.8277 (mm)
REVERT: A  878 MET cc_start: 0.6856 (mmt) cc_final: 0.6502 (mmm)
REVERT: A  884 LEU cc_start: 0.7905 (tp) cc_final: 0.7616 (pp)
REVERT: A  888 LYS cc_start: 0.8430 (tptm) cc_final: 0.7634 (tptp)
REVERT: A  956 CYS cc_start: 0.7947 (t) cc_final: 0.7599 (t)
REVERT: A 1027 MET cc_start: 0.7330 (mmt) cc_final: 0.7074 (mmt)
REVERT: A 1099 LYS cc_start: 0.6108 (tmtt) cc_final: 0.5040 (mtmt)
REVERT: A 1167 THR cc_start: 0.6075 (m) cc_final: 0.5631 (p)
REVERT: A 1196 ILE cc_start: 0.7983 (mt) cc_final: 0.7605 (mt)
  outliers start: 5
  outliers final: 2
  residues processed: 199
  average time/residue: 0.2257
  time to fit residues: 62.8412
Evaluate side-chains
  124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  345 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:   10.0000
   chunk 87 optimal weight:    2.9990
   chunk 48 optimal weight:    8.9990
   chunk 29 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 90 optimal weight:    8.9990
   chunk 34 optimal weight:    9.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    8.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 882 GLN
A 925 GLN
A1153 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.142809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.108137 restraints weight = 19066.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.106249 restraints weight = 13269.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.107234 restraints weight = 14119.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.049   9552  Z= 0.403
  Angle     :  0.700  11.331  12811  Z= 0.364
  Chirality :  0.046   0.225   1446
  Planarity :  0.005   0.044   1580
  Dihedral  : 12.477  89.720   1617
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 13.57 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.98 (0.24), residues: 1152
  helix:  1.21 (0.18), residues: 746
  sheet: -0.02 (0.64), residues: 69
  loop : -0.30 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  45 
 HIS   0.006   0.001   HIS A 918 
 PHE   0.029   0.003   PHE A 193 
 TYR   0.030   0.002   TYR A 277 
 ARG   0.005   0.000   ARG A 492 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8544 (tpp) cc_final: 0.8219 (mpp)
REVERT: A   79 PHE cc_start: 0.8554 (OUTLIER) cc_final: 0.8113 (t80)
REVERT: A  105 MET cc_start: 0.7800 (tmm) cc_final: 0.7446 (tpp)
REVERT: A  343 PHE cc_start: 0.8012 (m-80) cc_final: 0.7804 (m-80)
REVERT: A  451 VAL cc_start: 0.7467 (t) cc_final: 0.7262 (t)
REVERT: A  538 ARG cc_start: 0.6938 (ptm-80) cc_final: 0.6146 (mtt90)
REVERT: A  541 ILE cc_start: 0.9170 (tt) cc_final: 0.8887 (mt)
REVERT: A  573 LEU cc_start: 0.8901 (mt) cc_final: 0.7778 (pp)
REVERT: A  796 MET cc_start: 0.8588 (mtm) cc_final: 0.8154 (mtm)
REVERT: A  808 LYS cc_start: 0.8563 (tttt) cc_final: 0.7717 (tptt)
REVERT: A  878 MET cc_start: 0.6805 (mmt) cc_final: 0.6467 (mmm)
REVERT: A  888 LYS cc_start: 0.8581 (tptm) cc_final: 0.7824 (tptp)
REVERT: A 1099 LYS cc_start: 0.5977 (tmtt) cc_final: 0.4900 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8590 (tppt) cc_final: 0.8018 (pttt)
REVERT: A 1167 THR cc_start: 0.6810 (m) cc_final: 0.6161 (p)
REVERT: A 1223 GLU cc_start: 0.7728 (tp30) cc_final: 0.7034 (pp20)
  outliers start: 29
  outliers final: 22
  residues processed: 153
  average time/residue: 0.1974
  time to fit residues: 43.9018
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 0.934 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  470 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  762 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 112 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 30 optimal weight:    0.8980
   chunk 32 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0170
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.6418

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

Flipped N/Q/H residues before XYZ refinement:
A 475 GLN
A 530 GLN
A 842 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.148349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.114259 restraints weight = 19016.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.112548 restraints weight = 12974.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113104 restraints weight = 14475.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9552  Z= 0.163
  Angle     :  0.541   7.054  12811  Z= 0.284
  Chirality :  0.042   0.420   1446
  Planarity :  0.003   0.042   1580
  Dihedral  : 10.067  83.135   1617
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.66 %
    Favored  : 82.57 %
  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:  1.46 (0.24), residues: 1152
  helix:  1.68 (0.18), residues: 738
  sheet:  0.13 (0.64), residues: 69
  loop : -0.30 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 232 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.023   0.001   PHE A 103 
 TYR   0.012   0.001   TYR A 277 
 ARG   0.008   0.000   ARG A 492 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8417 (tpp) cc_final: 0.8161 (mpp)
REVERT: A   79 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8026 (t80)
REVERT: A  105 MET cc_start: 0.7709 (tmm) cc_final: 0.7040 (tpp)
REVERT: A  339 LEU cc_start: 0.8774 (tp) cc_final: 0.8299 (tp)
REVERT: A  538 ARG cc_start: 0.6977 (ptm-80) cc_final: 0.5916 (mtt90)
REVERT: A  541 ILE cc_start: 0.9100 (tt) cc_final: 0.8805 (mt)
REVERT: A  573 LEU cc_start: 0.8862 (mt) cc_final: 0.7687 (pp)
REVERT: A  717 CYS cc_start: 0.7045 (t) cc_final: 0.6825 (t)
REVERT: A  796 MET cc_start: 0.8324 (mtm) cc_final: 0.7760 (mtm)
REVERT: A  808 LYS cc_start: 0.8519 (tttt) cc_final: 0.7713 (tptt)
REVERT: A  878 MET cc_start: 0.6926 (mmt) cc_final: 0.6533 (mmm)
REVERT: A  888 LYS cc_start: 0.8537 (tptm) cc_final: 0.8048 (tptp)
REVERT: A 1099 LYS cc_start: 0.5763 (tmtt) cc_final: 0.4798 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8590 (tppt) cc_final: 0.8120 (pttt)
REVERT: A 1133 TYR cc_start: 0.6421 (OUTLIER) cc_final: 0.6216 (t80)
REVERT: A 1167 THR cc_start: 0.6631 (m) cc_final: 0.5968 (p)
  outliers start: 17
  outliers final: 8
  residues processed: 146
  average time/residue: 0.1799
  time to fit residues: 38.8187
Evaluate side-chains
  124 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1133 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 82 optimal weight:    0.0980
   chunk 79 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 101 optimal weight:   20.0000
   chunk 84 optimal weight:    8.9990
   chunk 104 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    1.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 751 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.145472 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111134 restraints weight = 19096.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.108709 restraints weight = 15924.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.109426 restraints weight = 13362.403|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   9552  Z= 0.244
  Angle     :  0.562   6.694  12811  Z= 0.297
  Chirality :  0.043   0.309   1446
  Planarity :  0.003   0.039   1580
  Dihedral  :  9.832  82.760   1614
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.55 %
    Favored  : 81.73 %
  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:  1.36 (0.24), residues: 1152
  helix:  1.58 (0.18), residues: 740
  sheet: -0.12 (0.61), residues: 75
  loop : -0.26 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 232 
 HIS   0.010   0.001   HIS A 612 
 PHE   0.021   0.002   PHE A 103 
 TYR   0.015   0.002   TYR A 118 
 ARG   0.003   0.000   ARG A 489 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8828 (tp) cc_final: 0.8427 (tp)
REVERT: A  538 ARG cc_start: 0.6960 (ptm-80) cc_final: 0.5900 (mtt90)
REVERT: A  541 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8885 (mt)
REVERT: A  796 MET cc_start: 0.8403 (mtm) cc_final: 0.7831 (mtm)
REVERT: A  799 GLN cc_start: 0.8277 (tm-30) cc_final: 0.8003 (tm-30)
REVERT: A  808 LYS cc_start: 0.8544 (tttt) cc_final: 0.7711 (tptt)
REVERT: A  878 MET cc_start: 0.6887 (mmt) cc_final: 0.6530 (mmm)
REVERT: A  888 LYS cc_start: 0.8634 (tptm) cc_final: 0.8097 (tptp)
REVERT: A 1099 LYS cc_start: 0.5762 (tmtt) cc_final: 0.4695 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8585 (tppt) cc_final: 0.8073 (pttt)
  outliers start: 26
  outliers final: 16
  residues processed: 141
  average time/residue: 0.1945
  time to fit residues: 40.4417
Evaluate side-chains
  132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1191 VAL
Chi-restraints excluded: chain A residue 1199 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    5.9990
   chunk 113 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 106 optimal weight:    4.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A1043 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.147190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113362 restraints weight = 19256.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111746 restraints weight = 15161.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.112281 restraints weight = 12486.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9552  Z= 0.199
  Angle     :  0.550   6.519  12811  Z= 0.289
  Chirality :  0.042   0.294   1446
  Planarity :  0.003   0.039   1580
  Dihedral  :  9.405  80.924   1612
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.18 %
    Favored  : 81.32 %
  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:  1.41 (0.24), residues: 1152
  helix:  1.62 (0.18), residues: 743
  sheet: -0.04 (0.61), residues: 75
  loop : -0.29 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 232 
 HIS   0.011   0.001   HIS A 612 
 PHE   0.018   0.001   PHE A 103 
 TYR   0.011   0.001   TYR A 118 
 ARG   0.002   0.000   ARG A 489 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 0.959 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 MET cc_start: 0.7392 (tpp) cc_final: 0.6859 (tpp)
REVERT: A  339 LEU cc_start: 0.8742 (tp) cc_final: 0.8499 (tp)
REVERT: A  538 ARG cc_start: 0.7093 (ptm-80) cc_final: 0.5890 (mtt90)
REVERT: A  541 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8902 (mt)
REVERT: A  796 MET cc_start: 0.8479 (mtm) cc_final: 0.7927 (mtm)
REVERT: A  808 LYS cc_start: 0.8621 (tttt) cc_final: 0.7728 (tptt)
REVERT: A  878 MET cc_start: 0.6736 (mmt) cc_final: 0.6381 (mmm)
REVERT: A  888 LYS cc_start: 0.8596 (tptm) cc_final: 0.8038 (tptp)
REVERT: A 1099 LYS cc_start: 0.5814 (tmtt) cc_final: 0.4801 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8665 (tppt) cc_final: 0.8167 (pttt)
  outliers start: 24
  outliers final: 14
  residues processed: 137
  average time/residue: 0.2038
  time to fit residues: 41.1098
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  365 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 78 optimal weight:    8.9990
   chunk 109 optimal weight:    4.9990
   chunk 106 optimal weight:    4.9990
   chunk 111 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 113 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
A 842 ASN
A1155 HIS
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1248 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.141816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.107638 restraints weight = 19302.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.106416 restraints weight = 14152.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107158 restraints weight = 14753.928|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.3278

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056   9552  Z= 0.399
  Angle     :  0.691   8.329  12811  Z= 0.364
  Chirality :  0.047   0.272   1446
  Planarity :  0.004   0.041   1580
  Dihedral  : 10.584  83.828   1612
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.39 %
    Favored  : 80.06 %
  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:  0.80 (0.24), residues: 1152
  helix:  1.10 (0.18), residues: 748
  sheet: -0.19 (0.59), residues: 75
  loop : -0.43 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.003   TRP A 232 
 HIS   0.014   0.002   HIS A 612 
 PHE   0.032   0.003   PHE A 193 
 TYR   0.022   0.002   TYR A 118 
 ARG   0.005   0.000   ARG A 787 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 105
  time to evaluate  : 1.084 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8202 (t80)
REVERT: A  105 MET cc_start: 0.7415 (tpp) cc_final: 0.7105 (tpp)
REVERT: A  538 ARG cc_start: 0.7131 (OUTLIER) cc_final: 0.5901 (mtt90)
REVERT: A  541 ILE cc_start: 0.9193 (OUTLIER) cc_final: 0.8922 (mt)
REVERT: A  796 MET cc_start: 0.8555 (mtm) cc_final: 0.8025 (mtm)
REVERT: A  820 ASN cc_start: 0.7975 (OUTLIER) cc_final: 0.7580 (t0)
REVERT: A  878 MET cc_start: 0.6622 (mmt) cc_final: 0.6269 (mmm)
REVERT: A  888 LYS cc_start: 0.8639 (tptm) cc_final: 0.8239 (tptp)
REVERT: A 1042 PHE cc_start: 0.6635 (t80) cc_final: 0.6358 (t80)
REVERT: A 1099 LYS cc_start: 0.5827 (tmtt) cc_final: 0.4710 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8657 (tppt) cc_final: 0.8151 (pttt)
  outliers start: 34
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1965
  time to fit residues: 38.4220
Evaluate side-chains
  126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 1.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1191 VAL
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 54 optimal weight:    5.9990
   chunk 94 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 95 optimal weight:    7.9990
   chunk 48 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0070
   chunk 30 optimal weight:    0.0770
   overall best weight:    0.5356

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
A 842 ASN
A1155 HIS
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1248 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.148080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113354 restraints weight = 19220.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.113826 restraints weight = 12685.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.114829 restraints weight = 10461.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9552  Z= 0.159
  Angle     :  0.558   7.338  12811  Z= 0.293
  Chirality :  0.042   0.281   1446
  Planarity :  0.003   0.040   1580
  Dihedral  :  9.399  87.492   1612
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 17.75 %
    Favored  : 79.75 %
  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:  1.40 (0.24), residues: 1152
  helix:  1.61 (0.18), residues: 746
  sheet: -0.10 (0.60), residues: 75
  loop : -0.28 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 232 
 HIS   0.010   0.001   HIS A 612 
 PHE   0.039   0.001   PHE A 994 
 TYR   0.011   0.001   TYR A 998 
 ARG   0.003   0.000   ARG A 489 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 1.000 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8378 (OUTLIER) cc_final: 0.7871 (t80)
REVERT: A  105 MET cc_start: 0.7282 (tpp) cc_final: 0.6965 (tpp)
REVERT: A  143 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7044 (tm-30)
REVERT: A  538 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.5821 (mtt90)
REVERT: A  573 LEU cc_start: 0.8916 (mt) cc_final: 0.7778 (pp)
REVERT: A  796 MET cc_start: 0.8509 (mtm) cc_final: 0.7973 (mtm)
REVERT: A  799 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: A  808 LYS cc_start: 0.8568 (tttt) cc_final: 0.7751 (tptt)
REVERT: A  820 ASN cc_start: 0.7844 (OUTLIER) cc_final: 0.7400 (t0)
REVERT: A  878 MET cc_start: 0.6579 (mmt) cc_final: 0.6270 (mmm)
REVERT: A  886 ASP cc_start: 0.7813 (m-30) cc_final: 0.7452 (m-30)
REVERT: A  888 LYS cc_start: 0.8602 (tptm) cc_final: 0.8073 (tptp)
REVERT: A 1064 GLN cc_start: 0.8058 (tp-100) cc_final: 0.6564 (tm-30)
REVERT: A 1065 THR cc_start: 0.8030 (m) cc_final: 0.7317 (m)
REVERT: A 1099 LYS cc_start: 0.5711 (tmtt) cc_final: 0.4713 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8638 (tppt) cc_final: 0.8188 (pttt)
  outliers start: 24
  outliers final: 12
  residues processed: 139
  average time/residue: 0.1890
  time to fit residues: 38.4010
Evaluate side-chains
  126 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1199 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 47 optimal weight:    8.9990
   chunk 80 optimal weight:    3.9990
   chunk 39 optimal weight:    1.9990
   chunk 12 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A1182 GLN ** 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 = 0.3937 r_free = 0.3937 target = 0.146532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.111692 restraints weight = 19563.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111455 restraints weight = 13830.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112444 restraints weight = 11717.151|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9552  Z= 0.210
  Angle     :  0.567   7.894  12811  Z= 0.297
  Chirality :  0.041   0.260   1446
  Planarity :  0.003   0.038   1580
  Dihedral  :  9.310  87.918   1612
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 18.68 %
    Favored  : 79.44 %
  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:  1.45 (0.24), residues: 1152
  helix:  1.68 (0.18), residues: 745
  sheet: -0.10 (0.59), residues: 75
  loop : -0.34 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.025   0.002   PHE A 994 
 TYR   0.011   0.001   TYR A 118 
 ARG   0.002   0.000   ARG A 817 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7899 (t80)
REVERT: A  105 MET cc_start: 0.7294 (tpp) cc_final: 0.6970 (tpp)
REVERT: A  143 GLN cc_start: 0.8065 (tm-30) cc_final: 0.7142 (tm-30)
REVERT: A  239 PHE cc_start: 0.7285 (OUTLIER) cc_final: 0.7069 (t80)
REVERT: A  538 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.5550 (mtt90)
REVERT: A  799 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: A  808 LYS cc_start: 0.8574 (tttt) cc_final: 0.7752 (tptt)
REVERT: A  878 MET cc_start: 0.6488 (mmt) cc_final: 0.6182 (mmm)
REVERT: A  888 LYS cc_start: 0.8608 (tptm) cc_final: 0.8074 (tptp)
REVERT: A 1065 THR cc_start: 0.8023 (m) cc_final: 0.7616 (m)
REVERT: A 1099 LYS cc_start: 0.5784 (tmtt) cc_final: 0.4639 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8613 (tppt) cc_final: 0.8163 (pttt)
  outliers start: 18
  outliers final: 13
  residues processed: 127
  average time/residue: 0.1866
  time to fit residues: 34.5424
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 92 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 103 optimal weight:    6.9990
   chunk 69 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 56 optimal weight:    5.9990
   chunk 3 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3958 r_free = 0.3958 target = 0.148052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.113348 restraints weight = 19196.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.113168 restraints weight = 12410.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.114319 restraints weight = 10326.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9552  Z= 0.176
  Angle     :  0.574  12.692  12811  Z= 0.297
  Chirality :  0.042   0.333   1446
  Planarity :  0.003   0.037   1580
  Dihedral  :  8.854  81.056   1612
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.95 %
    Favored  : 79.65 %
  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:  1.57 (0.24), residues: 1152
  helix:  1.77 (0.18), residues: 745
  sheet: -0.04 (0.59), residues: 75
  loop : -0.31 (0.35), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1108 
 HIS   0.012   0.001   HIS A 612 
 PHE   0.025   0.001   PHE A 994 
 TYR   0.015   0.001   TYR A 277 
 ARG   0.002   0.000   ARG A 489 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.973 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7910 (t80)
REVERT: A  105 MET cc_start: 0.7313 (tpp) cc_final: 0.6982 (tpp)
REVERT: A  143 GLN cc_start: 0.7945 (tm-30) cc_final: 0.6922 (tm-30)
REVERT: A  239 PHE cc_start: 0.7237 (OUTLIER) cc_final: 0.6887 (t80)
REVERT: A  416 LYS cc_start: 0.7091 (mmmm) cc_final: 0.6871 (mptt)
REVERT: A  538 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.5459 (mtt90)
REVERT: A  799 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8090 (tm-30)
REVERT: A  808 LYS cc_start: 0.8579 (tttt) cc_final: 0.7763 (tptt)
REVERT: A  820 ASN cc_start: 0.7841 (OUTLIER) cc_final: 0.7456 (t0)
REVERT: A  878 MET cc_start: 0.6701 (mmt) cc_final: 0.6330 (mmm)
REVERT: A  888 LYS cc_start: 0.8573 (tptm) cc_final: 0.8063 (tptp)
REVERT: A 1064 GLN cc_start: 0.7915 (tp-100) cc_final: 0.6688 (pp30)
REVERT: A 1065 THR cc_start: 0.7835 (m) cc_final: 0.7273 (m)
REVERT: A 1099 LYS cc_start: 0.5800 (tmtt) cc_final: 0.4770 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8625 (tppt) cc_final: 0.8151 (pttt)
  outliers start: 23
  outliers final: 15
  residues processed: 131
  average time/residue: 0.1973
  time to fit residues: 37.5988
Evaluate side-chains
  131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 90 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 78 optimal weight:    8.9990
   chunk 60 optimal weight:    2.9990
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:    0.0470
   chunk 20 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.9682

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN
A1130 ASN
** A1182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.148123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.113302 restraints weight = 19402.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113544 restraints weight = 12988.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.114706 restraints weight = 10282.144|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9552  Z= 0.182
  Angle     :  0.579  11.809  12811  Z= 0.299
  Chirality :  0.042   0.325   1446
  Planarity :  0.003   0.037   1580
  Dihedral  :  8.713  77.332   1612
  Min Nonbonded Distance : 2.336

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.68 %
    Favored  : 79.02 %
  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:  1.60 (0.24), residues: 1152
  helix:  1.80 (0.18), residues: 746
  sheet:  0.30 (0.62), residues: 69
  loop : -0.37 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1108 
 HIS   0.008   0.001   HIS A 612 
 PHE   0.023   0.001   PHE A 994 
 TYR   0.009   0.001   TYR A 247 
 ARG   0.002   0.000   ARG A 489 

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7865 (t80)
REVERT: A  105 MET cc_start: 0.7299 (tpp) cc_final: 0.6971 (tpp)
REVERT: A  143 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7123 (tm-30)
REVERT: A  239 PHE cc_start: 0.7223 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: A  416 LYS cc_start: 0.7083 (mmmm) cc_final: 0.6848 (mptt)
REVERT: A  538 ARG cc_start: 0.6932 (OUTLIER) cc_final: 0.5436 (mtt90)
REVERT: A  757 LEU cc_start: 0.7963 (tp) cc_final: 0.7749 (tp)
REVERT: A  808 LYS cc_start: 0.8567 (tttt) cc_final: 0.7750 (tptt)
REVERT: A  820 ASN cc_start: 0.7930 (OUTLIER) cc_final: 0.7476 (t0)
REVERT: A  888 LYS cc_start: 0.8571 (tptm) cc_final: 0.8071 (tptp)
REVERT: A 1064 GLN cc_start: 0.7920 (tp-100) cc_final: 0.6643 (pp30)
REVERT: A 1065 THR cc_start: 0.7827 (m) cc_final: 0.7287 (m)
REVERT: A 1099 LYS cc_start: 0.5751 (tmtt) cc_final: 0.4651 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8617 (tppt) cc_final: 0.8160 (pttt)
  outliers start: 22
  outliers final: 17
  residues processed: 128
  average time/residue: 0.2049
  time to fit residues: 38.0223
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.955 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  784 LEU
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  908 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 102 optimal weight:    0.0370
   chunk 74 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 100 optimal weight:    8.9990
   chunk 56 optimal weight:    6.9990
   chunk 109 optimal weight:   10.0000
   chunk 14 optimal weight:    3.9990
   overall best weight:    1.9864

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

Flipped N/Q/H residues before XYZ refinement:
** A1182 GLN ** 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 = 0.3921 r_free = 0.3921 target = 0.144957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.110856 restraints weight = 19555.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.110665 restraints weight = 12745.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111501 restraints weight = 11988.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
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Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.3521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063   9552  Z= 0.256
  Angle     :  0.603  10.809  12811  Z= 0.313
  Chirality :  0.043   0.301   1446
  Planarity :  0.003   0.037   1580
  Dihedral  :  8.935  75.784   1612
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 18.68 %
    Favored  : 79.02 %
  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:  1.48 (0.25), residues: 1152
  helix:  1.67 (0.18), residues: 746
  sheet:  0.31 (0.61), residues: 69
  loop : -0.34 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A1108 
 HIS   0.007   0.001   HIS A 612 
 PHE   0.020   0.002   PHE A 994 
 TYR   0.014   0.002   TYR A 118 
 ARG   0.002   0.000   ARG A 787 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2610.73 seconds
wall clock time: 47 minutes 50.34 seconds (2870.34 seconds total)