Starting phenix.real_space_refine
on Fri Mar 14 02:53:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctf_45904/03_2025/9ctf_45904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctf_45904/03_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_45904/03_2025/9ctf_45904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctf_45904/03_2025/9ctf_45904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctf_45904/03_2025/9ctf_45904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctf_45904/03_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-5624/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: 6.30, per 1000 atoms: 0.67
  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: 2.47
  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: 1.25
  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: 3.15

  Time building geometry restraints manager: 2.90 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     25.510
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.370
-------------------------------------------------------------------------------
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  : 1.103 
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: 0.2469
  time to fit residues: 70.2805
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  : 1.005 
-------------------------------------------------------------------------------
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 = 0.108136 restraints weight = 19066.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106263 restraints weight = 13271.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.107248 restraints weight = 14118.272|
|-----------------------------------------------------------------------------|
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  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8543 (tpp) cc_final: 0.8219 (mpp)
REVERT: A   79 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8113 (t80)
REVERT: A  105 MET cc_start: 0.7801 (tmm) cc_final: 0.7447 (tpp)
REVERT: A  343 PHE cc_start: 0.8013 (m-80) cc_final: 0.7804 (m-80)
REVERT: A  451 VAL cc_start: 0.7466 (t) cc_final: 0.7262 (t)
REVERT: A  538 ARG cc_start: 0.6937 (ptm-80) cc_final: 0.6145 (mtt90)
REVERT: A  541 ILE cc_start: 0.9169 (tt) cc_final: 0.8886 (mt)
REVERT: A  573 LEU cc_start: 0.8901 (mt) cc_final: 0.7778 (pp)
REVERT: A  796 MET cc_start: 0.8589 (mtm) cc_final: 0.8155 (mtm)
REVERT: A  808 LYS cc_start: 0.8562 (tttt) cc_final: 0.7717 (tptt)
REVERT: A  878 MET cc_start: 0.6804 (mmt) cc_final: 0.6467 (mmm)
REVERT: A  888 LYS cc_start: 0.8580 (tptm) cc_final: 0.7824 (tptp)
REVERT: A 1099 LYS cc_start: 0.5976 (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: 0.6808 (m) cc_final: 0.6159 (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: 0.1876
  time to fit residues: 42.2354
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  : 1.024 
-------------------------------------------------------------------------------
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:    7.9990
   chunk 112 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 75 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   overall best weight:    0.8784

-------------------------------------------------------------------------------
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 = 0.3952 r_free = 0.3952 target = 0.147516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.113345 restraints weight = 19034.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.111370 restraints weight = 12933.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.112104 restraints weight = 14650.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9552  Z= 0.172
  Angle     :  0.546   7.239  12811  Z= 0.287
  Chirality :  0.042   0.422   1446
  Planarity :  0.003   0.042   1580
  Dihedral  : 10.257  84.360   1617
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.86 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.66 %
    Favored  : 82.36 %
  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:  1.39 (0.24), residues: 1152
  helix:  1.60 (0.18), residues: 741
  sheet:  0.12 (0.64), residues: 69
  loop : -0.30 (0.33), residues: 342

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   0.013   0.001   TYR A 277 
 ARG   0.004   0.000   ARG A 489 

*********************** 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
  154 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   69 MET cc_start: 0.8448 (tpp) cc_final: 0.8153 (mpp)
REVERT: A   79 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8053 (t80)
REVERT: A  105 MET cc_start: 0.7734 (tmm) cc_final: 0.7417 (tpp)
REVERT: A  339 LEU cc_start: 0.8766 (tp) cc_final: 0.8346 (tp)
REVERT: A  538 ARG cc_start: 0.6928 (ptm-80) cc_final: 0.5929 (mtt90)
REVERT: A  541 ILE cc_start: 0.9073 (tt) cc_final: 0.8810 (mt)
REVERT: A  573 LEU cc_start: 0.8876 (mt) cc_final: 0.7697 (pp)
REVERT: A  796 MET cc_start: 0.8337 (mtm) cc_final: 0.7744 (mtm)
REVERT: A  808 LYS cc_start: 0.8524 (tttt) cc_final: 0.7713 (tptt)
REVERT: A  878 MET cc_start: 0.6961 (mmt) cc_final: 0.6564 (mmm)
REVERT: A  888 LYS cc_start: 0.8541 (tptm) cc_final: 0.8046 (tptp)
REVERT: A 1099 LYS cc_start: 0.5782 (tmtt) cc_final: 0.4817 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8567 (tppt) cc_final: 0.8094 (pttt)
REVERT: A 1133 TYR cc_start: 0.6549 (OUTLIER) cc_final: 0.6336 (t80)
REVERT: A 1167 THR cc_start: 0.6698 (m) cc_final: 0.6049 (p)
  outliers start: 19
  outliers final: 10
  residues processed: 146
  average time/residue: 0.1864
  time to fit residues: 41.0075
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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  345 VAL
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
Chi-restraints excluded: chain A residue 1141 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 91 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 112 optimal weight:    6.9990
   chunk 101 optimal weight:   10.0000
   chunk 84 optimal weight:    5.9990
   chunk 104 optimal weight:    6.9990
   chunk 58 optimal weight:   20.0000
   overall best weight:    2.1784

-------------------------------------------------------------------------------
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**
** 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 = 0.3918 r_free = 0.3918 target = 0.144779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.110441 restraints weight = 19134.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.107824 restraints weight = 16020.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.108663 restraints weight = 14272.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2607

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= 0.271
  Angle     :  0.578   6.791  12811  Z= 0.306
  Chirality :  0.043   0.311   1446
  Planarity :  0.004   0.042   1580
  Dihedral  : 10.045  83.033   1615
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 15.34 %
    Favored  : 81.63 %
  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:  1.23 (0.24), residues: 1152
  helix:  1.43 (0.18), residues: 749
  sheet: -0.14 (0.61), residues: 75
  loop : -0.25 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 232 
 HIS   0.012   0.001   HIS A 612 
 PHE   0.021   0.002   PHE A 103 
 TYR   0.016   0.002   TYR A 118 
 ARG   0.003   0.000   ARG A 787 

*********************** 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: 29
    poor density    : 121
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8205 (t80)
REVERT: A  105 MET cc_start: 0.7761 (tmm) cc_final: 0.7387 (tpp)
REVERT: A  339 LEU cc_start: 0.8792 (tp) cc_final: 0.8332 (tp)
REVERT: A  538 ARG cc_start: 0.6974 (ptm-80) cc_final: 0.5885 (mtt90)
REVERT: A  541 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8892 (mt)
REVERT: A  796 MET cc_start: 0.8547 (mtm) cc_final: 0.7933 (mtm)
REVERT: A  799 GLN cc_start: 0.8340 (tm-30) cc_final: 0.8016 (tm-30)
REVERT: A  808 LYS cc_start: 0.8564 (tttt) cc_final: 0.7779 (tptt)
REVERT: A  878 MET cc_start: 0.6731 (mmt) cc_final: 0.6414 (mmm)
REVERT: A  888 LYS cc_start: 0.8665 (tptm) cc_final: 0.8081 (tptp)
REVERT: A 1099 LYS cc_start: 0.5818 (tmtt) cc_final: 0.4774 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8620 (tppt) cc_final: 0.8083 (pttt)
REVERT: A 1133 TYR cc_start: 0.6658 (OUTLIER) cc_final: 0.6450 (t80)
  outliers start: 29
  outliers final: 17
  residues processed: 141
  average time/residue: 0.1876
  time to fit residues: 39.2822
Evaluate side-chains
  129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
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  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  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  867 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
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:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 42 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   chunk 70 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 842 ASN
A1043 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 = 0.3972 r_free = 0.3972 target = 0.148891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.114079 restraints weight = 19082.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.114071 restraints weight = 13127.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.115212 restraints weight = 10394.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9552  Z= 0.154
  Angle     :  0.534   7.431  12811  Z= 0.279
  Chirality :  0.041   0.294   1446
  Planarity :  0.003   0.040   1580
  Dihedral  :  9.284  79.459   1615
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 15.97 %
    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:  1.51 (0.24), residues: 1152
  helix:  1.74 (0.18), residues: 738
  sheet: -0.06 (0.61), residues: 75
  loop : -0.30 (0.34), residues: 339

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   0.029   0.001   PHE A 994 
 TYR   0.010   0.001   TYR A 247 
 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
  152 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8189 (t80)
REVERT: A  105 MET cc_start: 0.7777 (tmm) cc_final: 0.7005 (tpp)
REVERT: A  143 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7049 (tm-30)
REVERT: A  339 LEU cc_start: 0.8709 (tp) cc_final: 0.8441 (tp)
REVERT: A  538 ARG cc_start: 0.7029 (ptm-80) cc_final: 0.5852 (mtt90)
REVERT: A  541 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8907 (mt)
REVERT: A  796 MET cc_start: 0.8457 (mtm) cc_final: 0.7893 (mtm)
REVERT: A  808 LYS cc_start: 0.8572 (tttt) cc_final: 0.7633 (tptt)
REVERT: A  878 MET cc_start: 0.6750 (mmt) cc_final: 0.6376 (mmm)
REVERT: A  888 LYS cc_start: 0.8585 (tptm) cc_final: 0.8069 (tptp)
REVERT: A 1064 GLN cc_start: 0.7542 (tp-100) cc_final: 0.7260 (tt0)
REVERT: A 1099 LYS cc_start: 0.5680 (tmtt) cc_final: 0.4717 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8603 (tppt) cc_final: 0.8161 (pttt)
  outliers start: 26
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1889
  time to fit residues: 39.8446
Evaluate side-chains
  122 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  365 ILE
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  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  896 ILE
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
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:    2.9990
   chunk 78 optimal weight:    9.9990
   chunk 109 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 111 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 56 optimal weight:    7.9990
   chunk 113 optimal weight:    5.9990
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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
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: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.142354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.107623 restraints weight = 19366.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.105598 restraints weight = 15833.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.105829 restraints weight = 13898.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054   9552  Z= 0.367
  Angle     :  0.672   8.375  12811  Z= 0.354
  Chirality :  0.045   0.277   1446
  Planarity :  0.004   0.039   1580
  Dihedral  : 10.213  79.786   1614
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 16.91 %
    Favored  : 79.96 %
  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:  1.00 (0.24), residues: 1152
  helix:  1.25 (0.18), residues: 748
  sheet: -0.13 (0.59), residues: 75
  loop : -0.35 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 232 
 HIS   0.013   0.002   HIS A 612 
 PHE   0.031   0.003   PHE A 193 
 TYR   0.020   0.002   TYR A 118 
 ARG   0.004   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
  137 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 107
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  339 LEU cc_start: 0.8767 (tp) cc_final: 0.8544 (tp)
REVERT: A  538 ARG cc_start: 0.7139 (OUTLIER) cc_final: 0.5927 (mtt90)
REVERT: A  541 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8922 (mt)
REVERT: A  796 MET cc_start: 0.8513 (mtm) cc_final: 0.7979 (mtm)
REVERT: A  820 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7596 (t0)
REVERT: A  878 MET cc_start: 0.6589 (mmt) cc_final: 0.6268 (mmm)
REVERT: A  888 LYS cc_start: 0.8665 (tptm) cc_final: 0.8225 (tptp)
REVERT: A 1099 LYS cc_start: 0.5932 (tmtt) cc_final: 0.4886 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8660 (tppt) cc_final: 0.8101 (pttt)
  outliers start: 30
  outliers final: 23
  residues processed: 131
  average time/residue: 0.1924
  time to fit residues: 37.2545
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 101
  time to evaluate  : 1.004 
-------------------------------------------------------------------------------
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  273 GLU
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  433 LYS
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  465 PHE
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  857 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 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:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 94 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 88 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 95 optimal weight:    9.9990
   chunk 48 optimal weight:    8.9990
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   overall best weight:    1.3386

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.146413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111352 restraints weight = 19235.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111778 restraints weight = 12283.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112877 restraints weight = 9857.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9552  Z= 0.199
  Angle     :  0.568   7.265  12811  Z= 0.300
  Chirality :  0.042   0.272   1446
  Planarity :  0.003   0.040   1580
  Dihedral  :  9.583  82.251   1614
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 18.06 %
    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:  1.28 (0.24), residues: 1152
  helix:  1.53 (0.18), residues: 745
  sheet: -0.11 (0.59), residues: 75
  loop : -0.36 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 232 
 HIS   0.008   0.001   HIS A 612 
 PHE   0.021   0.001   PHE A 759 
 TYR   0.010   0.001   TYR A 118 
 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
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 111
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8477 (OUTLIER) cc_final: 0.8113 (t80)
REVERT: A  239 PHE cc_start: 0.7251 (OUTLIER) cc_final: 0.7028 (t80)
REVERT: A  538 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.5791 (mtt90)
REVERT: A  573 LEU cc_start: 0.8943 (mt) cc_final: 0.7791 (pp)
REVERT: A  808 LYS cc_start: 0.8553 (tttt) cc_final: 0.7734 (tptt)
REVERT: A  820 ASN cc_start: 0.7868 (OUTLIER) cc_final: 0.7496 (t0)
REVERT: A  878 MET cc_start: 0.6508 (mmt) cc_final: 0.6250 (mmm)
REVERT: A  888 LYS cc_start: 0.8612 (tptm) cc_final: 0.8090 (tptp)
REVERT: A 1064 GLN cc_start: 0.7883 (tp-100) cc_final: 0.6527 (tm-30)
REVERT: A 1065 THR cc_start: 0.8025 (m) cc_final: 0.7377 (m)
REVERT: A 1099 LYS cc_start: 0.5815 (tmtt) cc_final: 0.4786 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8622 (tppt) cc_final: 0.8156 (pttt)
  outliers start: 24
  outliers final: 15
  residues processed: 127
  average time/residue: 0.2225
  time to fit residues: 41.2309
Evaluate side-chains
  120 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 1.058 
-------------------------------------------------------------------------------
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  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
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  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 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 1141 SER
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 113 optimal weight:    9.9990
   chunk 29 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 47 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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
** 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 = 0.3947 r_free = 0.3947 target = 0.147231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112064 restraints weight = 19509.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112000 restraints weight = 13521.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.113302 restraints weight = 10241.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3456
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9552  Z= 0.181
  Angle     :  0.574   8.662  12811  Z= 0.300
  Chirality :  0.042   0.260   1446
  Planarity :  0.003   0.037   1580
  Dihedral  :  9.253  85.728   1614
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 17.75 %
    Favored  : 79.23 %
  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:  1.64 (0.18), residues: 746
  sheet: -0.10 (0.59), residues: 75
  loop : -0.36 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A1108 
 HIS   0.009   0.001   HIS A 612 
 PHE   0.035   0.001   PHE A 994 
 TYR   0.010   0.001   TYR A 307 
 ARG   0.002   0.000   ARG A 489 

*********************** 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
  140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.956 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8133 (t80)
REVERT: A  143 GLN cc_start: 0.8043 (tm-30) cc_final: 0.7110 (tm-30)
REVERT: A  239 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6950 (t80)
REVERT: A  538 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5429 (mtt90)
REVERT: A  573 LEU cc_start: 0.8944 (mt) cc_final: 0.7590 (pp)
REVERT: A  820 ASN cc_start: 0.7880 (OUTLIER) cc_final: 0.7443 (t0)
REVERT: A  878 MET cc_start: 0.6652 (mmt) cc_final: 0.6334 (mmm)
REVERT: A  888 LYS cc_start: 0.8605 (tptm) cc_final: 0.8060 (tptp)
REVERT: A 1042 PHE cc_start: 0.6444 (t80) cc_final: 0.6195 (t80)
REVERT: A 1065 THR cc_start: 0.7843 (m) cc_final: 0.7484 (m)
REVERT: A 1099 LYS cc_start: 0.5809 (tmtt) cc_final: 0.4701 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8645 (tppt) cc_final: 0.8168 (pttt)
  outliers start: 29
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1891
  time to fit residues: 37.4245
Evaluate side-chains
  128 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
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  332 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
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  820 ASN
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  898 THR
Chi-restraints excluded: chain A residue 1044 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 51 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 23 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 41 optimal weight:    9.9990
   chunk 56 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.148162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.113441 restraints weight = 19175.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.113453 restraints weight = 12639.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.114345 restraints weight = 10107.315|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.3292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9552  Z= 0.179
  Angle     :  0.584  12.899  12811  Z= 0.300
  Chirality :  0.042   0.319   1446
  Planarity :  0.003   0.036   1580
  Dihedral  :  9.084  89.047   1614
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 18.48 %
    Favored  : 78.81 %
  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:  1.69 (0.18), residues: 746
  sheet: -0.02 (0.59), residues: 75
  loop : -0.35 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A1108 
 HIS   0.010   0.001   HIS A 612 
 PHE   0.030   0.002   PHE A 994 
 TYR   0.009   0.001   TYR A 307 
 ARG   0.003   0.000   ARG A 817 

*********************** 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
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 110
  time to evaluate  : 0.943 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8433 (OUTLIER) cc_final: 0.8138 (t80)
REVERT: A  143 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7091 (tm-30)
REVERT: A  239 PHE cc_start: 0.7275 (OUTLIER) cc_final: 0.6943 (t80)
REVERT: A  538 ARG cc_start: 0.6871 (OUTLIER) cc_final: 0.5380 (mtt90)
REVERT: A  757 LEU cc_start: 0.7963 (tp) cc_final: 0.7750 (tp)
REVERT: A  808 LYS cc_start: 0.8563 (tttt) cc_final: 0.7737 (tptt)
REVERT: A  820 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7384 (t0)
REVERT: A  878 MET cc_start: 0.6631 (mmt) cc_final: 0.6293 (mmm)
REVERT: A  888 LYS cc_start: 0.8579 (tptm) cc_final: 0.8107 (tptp)
REVERT: A 1064 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6685 (pp30)
REVERT: A 1065 THR cc_start: 0.7786 (m) cc_final: 0.7216 (m)
REVERT: A 1099 LYS cc_start: 0.5847 (tmtt) cc_final: 0.4763 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8648 (tppt) cc_final: 0.8157 (pttt)
  outliers start: 26
  outliers final: 17
  residues processed: 129
  average time/residue: 0.1922
  time to fit residues: 36.3256
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
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  332 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
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  820 ASN
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  898 THR
Chi-restraints excluded: chain A residue 1064 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 68 optimal weight:    0.5980
   chunk 90 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 78 optimal weight:    9.9990
   chunk 60 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0020
   chunk 16 optimal weight:    3.9990
   chunk 36 optimal weight:   10.0000
   chunk 20 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    1.1194

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.147030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111949 restraints weight = 19496.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112446 restraints weight = 12355.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.113429 restraints weight = 9828.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3468
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9552  Z= 0.189
  Angle     :  0.582  11.466  12811  Z= 0.300
  Chirality :  0.043   0.300   1446
  Planarity :  0.003   0.036   1580
  Dihedral  :  9.039  86.908   1614
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.10 %
    Favored  : 78.60 %
  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:  1.50 (0.24), residues: 1152
  helix:  1.69 (0.18), residues: 747
  sheet:  0.31 (0.61), residues: 69
  loop : -0.36 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1108 
 HIS   0.012   0.001   HIS A 612 
 PHE   0.028   0.001   PHE A 994 
 TYR   0.010   0.001   TYR A 118 
 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
  132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.011 
Fit side-chains
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8427 (OUTLIER) cc_final: 0.8137 (t80)
REVERT: A  143 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7104 (tm-30)
REVERT: A  239 PHE cc_start: 0.7296 (OUTLIER) cc_final: 0.6903 (t80)
REVERT: A  416 LYS cc_start: 0.7111 (mmmm) cc_final: 0.6868 (mptt)
REVERT: A  538 ARG cc_start: 0.6869 (OUTLIER) cc_final: 0.5318 (mtt90)
REVERT: A  757 LEU cc_start: 0.7919 (tp) cc_final: 0.7712 (tp)
REVERT: A  808 LYS cc_start: 0.8577 (tttt) cc_final: 0.7720 (tptt)
REVERT: A  820 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7358 (t0)
REVERT: A  878 MET cc_start: 0.6703 (mmt) cc_final: 0.6343 (mmm)
REVERT: A  888 LYS cc_start: 0.8577 (tptm) cc_final: 0.8108 (tptp)
REVERT: A 1064 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.6596 (pp30)
REVERT: A 1065 THR cc_start: 0.7845 (m) cc_final: 0.7294 (m)
REVERT: A 1099 LYS cc_start: 0.5825 (tmtt) cc_final: 0.4647 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8661 (tppt) cc_final: 0.8171 (pttt)
  outliers start: 22
  outliers final: 16
  residues processed: 125
  average time/residue: 0.2021
  time to fit residues: 36.8730
Evaluate side-chains
  129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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  332 LEU
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  695 VAL
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  884 LEU
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1064 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 46 optimal weight:    7.9990
   chunk 18 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 102 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 100 optimal weight:    0.5980
   chunk 56 optimal weight:    9.9990
   chunk 109 optimal weight:    7.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.8984

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.147817 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.113723 restraints weight = 19465.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112570 restraints weight = 14274.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.112900 restraints weight = 12682.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3462
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.3438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9552  Z= 0.174
  Angle     :  0.579  11.029  12811  Z= 0.297
  Chirality :  0.042   0.288   1446
  Planarity :  0.003   0.036   1580
  Dihedral  :  8.895  84.150   1614
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 19.10 %
    Favored  : 78.60 %
  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:  1.61 (0.25), residues: 1152
  helix:  1.75 (0.18), residues: 746
  sheet:  0.61 (0.62), residues: 65
  loop : -0.28 (0.35), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A1108 
 HIS   0.007   0.001   HIS A 612 
 PHE   0.027   0.001   PHE A 994 
 TYR   0.009   0.001   TYR A 307 
 ARG   0.002   0.000   ARG A 489 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2703.03 seconds
wall clock time: 48 minutes 51.05 seconds (2931.05 seconds total)