Starting phenix.real_space_refine
on Fri Oct 10 22:28:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ctf_45904/10_2025/9ctf_45904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ctf_45904/10_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_45904/10_2025/9ctf_45904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ctf_45904/10_2025/9ctf_45904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ctf_45904/10_2025/9ctf_45904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ctf_45904/10_2025/9ctf_45904.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.46, per 1000 atoms: 0.26
  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: 1.13
  Conformation dependent library (CDL) restraints added in 369.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.34
  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: 1.86

  Time building geometry restraints manager: 1.45 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:             1.110
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.320
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.080
-------------------------------------------------------------------------------
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= 0.120
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (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
 ARG   0.002   0.000   ARG A 538 
 TYR   0.011   0.001   TYR A 920 
 PHE   0.011   0.001   PHE A 193 
 TRP   0.006   0.001   TRP A 698 
 HIS   0.002   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 9552)
  covalent geometry    : angle       0.49490 (12811)
  hydrogen bonds       : bond        0.11596 (  618)
  hydrogen bonds       : angle       4.71652 ( 1797)

*********************** 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  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7693 (t80)
REVERT: A  130 TYR cc_start: 0.8581 (t80) cc_final: 0.8366 (t80)
REVERT: A  416 LYS cc_start: 0.7170 (mmmm) cc_final: 0.6842 (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  717 CYS cc_start: 0.7784 (t) cc_final: 0.7475 (t)
REVERT: A  796 MET cc_start: 0.8810 (mtm) cc_final: 0.8088 (mtm)
REVERT: A  808 LYS cc_start: 0.8692 (tttt) cc_final: 0.7853 (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: 0.7615 (pp)
REVERT: A  888 LYS cc_start: 0.8430 (tptm) cc_final: 0.7633 (tptp)
REVERT: A  956 CYS cc_start: 0.7947 (t) cc_final: 0.7600 (t)
REVERT: A 1027 MET cc_start: 0.7330 (mmt) cc_final: 0.7073 (mmt)
REVERT: A 1099 LYS cc_start: 0.6108 (tmtt) cc_final: 0.5041 (mtmt)
REVERT: A 1167 THR cc_start: 0.6075 (m) cc_final: 0.5632 (p)
REVERT: A 1196 ILE cc_start: 0.7983 (mt) cc_final: 0.7604 (mt)
  outliers start: 5
  outliers final: 2
  residues processed: 199
  average time/residue: 0.0954
  time to fit residues: 26.8140
Evaluate side-chains
  123 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 120
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
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 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:   10.0000
   overall best weight:    1.7586

-------------------------------------------------------------------------------
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
A 842 ASN
A 882 GLN
A 925 GLN
A1182 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.146961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112016 restraints weight = 18998.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.110116 restraints weight = 13748.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.110953 restraints weight = 12638.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.111600 restraints weight = 10236.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111607 restraints weight = 9407.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9552  Z= 0.164
  Angle     :  0.583  11.295  12811  Z= 0.302
  Chirality :  0.042   0.246   1446
  Planarity :  0.004   0.042   1580
  Dihedral  : 11.807  90.303   1617
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 13.67 %
    Favored  : 84.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1152
  helix:  1.72 (0.18), residues: 737
  sheet:  0.11 (0.64), residues: 69
  loop : -0.24 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 929 
 TYR   0.027   0.002   TYR A 277 
 PHE   0.028   0.002   PHE A 759 
 TRP   0.012   0.002   TRP A 232 
 HIS   0.003   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 9552)
  covalent geometry    : angle       0.58329 (12811)
  hydrogen bonds       : bond        0.04742 (  618)
  hydrogen bonds       : angle       4.46686 ( 1797)

*********************** 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
  154 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7864 (t80)
REVERT: A  105 MET cc_start: 0.7711 (tmm) cc_final: 0.7427 (tpp)
REVERT: A  339 LEU cc_start: 0.8772 (tp) cc_final: 0.8458 (mt)
REVERT: A  451 VAL cc_start: 0.7356 (t) cc_final: 0.7155 (t)
REVERT: A  538 ARG cc_start: 0.7057 (ptm-80) cc_final: 0.6150 (mtt90)
REVERT: A  541 ILE cc_start: 0.9104 (tt) cc_final: 0.8791 (mt)
REVERT: A  573 LEU cc_start: 0.8805 (mt) cc_final: 0.7736 (pp)
REVERT: A  717 CYS cc_start: 0.7383 (t) cc_final: 0.7044 (t)
REVERT: A  796 MET cc_start: 0.8537 (mtm) cc_final: 0.8060 (mtm)
REVERT: A  808 LYS cc_start: 0.8599 (tttt) cc_final: 0.7760 (tptt)
REVERT: A  878 MET cc_start: 0.7128 (mmt) cc_final: 0.6691 (mmm)
REVERT: A  884 LEU cc_start: 0.7901 (tp) cc_final: 0.7645 (pp)
REVERT: A  888 LYS cc_start: 0.8553 (tptm) cc_final: 0.8012 (tptp)
REVERT: A 1099 LYS cc_start: 0.5977 (tmtt) cc_final: 0.4903 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8472 (tppt) cc_final: 0.7930 (pttt)
REVERT: A 1167 THR cc_start: 0.6607 (m) cc_final: 0.6011 (p)
REVERT: A 1182 GLN cc_start: 0.5459 (OUTLIER) cc_final: 0.5145 (tp-100)
REVERT: A 1223 GLU cc_start: 0.7612 (tp30) cc_final: 0.6823 (pp20)
  outliers start: 22
  outliers final: 14
  residues processed: 149
  average time/residue: 0.0748
  time to fit residues: 16.3296
Evaluate side-chains
  132 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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  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  521 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain A residue  867 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue 1124 ASP
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1182 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 106 optimal weight:   10.0000
   chunk 110 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 751 ASN
A1130 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.149170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.114603 restraints weight = 19028.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.114725 restraints weight = 12691.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.115471 restraints weight = 11400.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.116115 restraints weight = 8537.344|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.116116 restraints weight = 8026.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9552  Z= 0.121
  Angle     :  0.533   8.505  12811  Z= 0.277
  Chirality :  0.041   0.417   1446
  Planarity :  0.003   0.041   1580
  Dihedral  :  9.747  83.810   1615
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 14.09 %
    Favored  : 83.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.24), residues: 1152
  helix:  1.85 (0.18), residues: 739
  sheet:  0.21 (0.65), residues: 69
  loop : -0.29 (0.33), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 929 
 TYR   0.009   0.001   TYR A 118 
 PHE   0.023   0.001   PHE A 103 
 TRP   0.028   0.002   TRP A 232 
 HIS   0.010   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 9552)
  covalent geometry    : angle       0.53296 (12811)
  hydrogen bonds       : bond        0.04392 (  618)
  hydrogen bonds       : angle       4.26057 ( 1797)

*********************** 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
  156 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 136
  time to evaluate  : 0.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8291 (OUTLIER) cc_final: 0.7878 (t80)
REVERT: A  105 MET cc_start: 0.7587 (tmm) cc_final: 0.7196 (tpp)
REVERT: A  538 ARG cc_start: 0.6936 (ptm-80) cc_final: 0.6042 (mtt90)
REVERT: A  541 ILE cc_start: 0.9054 (tt) cc_final: 0.8775 (mt)
REVERT: A  573 LEU cc_start: 0.8766 (mt) cc_final: 0.7652 (pp)
REVERT: A  616 MET cc_start: 0.3687 (mpp) cc_final: 0.3438 (mpp)
REVERT: A  717 CYS cc_start: 0.7338 (t) cc_final: 0.7009 (t)
REVERT: A  796 MET cc_start: 0.8488 (mtm) cc_final: 0.7896 (mtm)
REVERT: A  808 LYS cc_start: 0.8519 (tttt) cc_final: 0.7714 (tptt)
REVERT: A  878 MET cc_start: 0.6981 (mmt) cc_final: 0.6553 (mmm)
REVERT: A  884 LEU cc_start: 0.7914 (tp) cc_final: 0.7661 (pp)
REVERT: A  888 LYS cc_start: 0.8557 (tptm) cc_final: 0.8046 (tptp)
REVERT: A 1099 LYS cc_start: 0.5765 (tmtt) cc_final: 0.4717 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8443 (tppt) cc_final: 0.8004 (pttt)
REVERT: A 1167 THR cc_start: 0.6712 (m) cc_final: 0.6095 (p)
REVERT: A 1182 GLN cc_start: 0.6180 (mm-40) cc_final: 0.5787 (tp-100)
REVERT: A 1223 GLU cc_start: 0.7658 (tp30) cc_final: 0.6945 (pp20)
  outliers start: 20
  outliers final: 10
  residues processed: 150
  average time/residue: 0.0808
  time to fit residues: 17.9768
Evaluate side-chains
  129 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 118
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
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  345 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  521 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 87 optimal weight:    0.8980
   chunk 55 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 530 GLN
A1182 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.147361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.113159 restraints weight = 19283.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.110227 restraints weight = 15775.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111183 restraints weight = 14276.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112055 restraints weight = 10644.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.112303 restraints weight = 9294.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9552  Z= 0.147
  Angle     :  0.549   7.109  12811  Z= 0.288
  Chirality :  0.042   0.322   1446
  Planarity :  0.003   0.040   1580
  Dihedral  :  9.496  82.169   1615
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 13.78 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.24), residues: 1152
  helix:  1.71 (0.18), residues: 740
  sheet:  0.17 (0.65), residues: 69
  loop : -0.31 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 794 
 TYR   0.014   0.001   TYR A 277 
 PHE   0.024   0.002   PHE A 103 
 TRP   0.020   0.002   TRP A 232 
 HIS   0.006   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9552)
  covalent geometry    : angle       0.54906 (12811)
  hydrogen bonds       : bond        0.04466 (  618)
  hydrogen bonds       : angle       4.30509 ( 1797)

*********************** 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
  158 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 MET cc_start: 0.8628 (tpt) cc_final: 0.8405 (tpp)
REVERT: A   79 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (t80)
REVERT: A  538 ARG cc_start: 0.7015 (ptm-80) cc_final: 0.5829 (mtt90)
REVERT: A  541 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8800 (mt)
REVERT: A  573 LEU cc_start: 0.8851 (mt) cc_final: 0.7721 (pp)
REVERT: A  616 MET cc_start: 0.3240 (OUTLIER) cc_final: 0.2907 (mpp)
REVERT: A  717 CYS cc_start: 0.7347 (t) cc_final: 0.7017 (t)
REVERT: A  796 MET cc_start: 0.8499 (mtm) cc_final: 0.7864 (mtm)
REVERT: A  799 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7951 (tm-30)
REVERT: A  808 LYS cc_start: 0.8558 (tttt) cc_final: 0.7707 (tptt)
REVERT: A  878 MET cc_start: 0.6809 (mmt) cc_final: 0.6389 (mmm)
REVERT: A  884 LEU cc_start: 0.7936 (tp) cc_final: 0.7654 (pp)
REVERT: A  888 LYS cc_start: 0.8571 (tptm) cc_final: 0.8032 (tptp)
REVERT: A 1099 LYS cc_start: 0.5910 (tmtt) cc_final: 0.4841 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8601 (tppt) cc_final: 0.8075 (pttt)
REVERT: A 1167 THR cc_start: 0.6461 (m) cc_final: 0.5820 (p)
REVERT: A 1223 GLU cc_start: 0.7913 (tp30) cc_final: 0.7143 (pp20)
  outliers start: 30
  outliers final: 15
  residues processed: 148
  average time/residue: 0.0855
  time to fit residues: 18.7669
Evaluate side-chains
  136 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  214 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  365 ILE
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  616 MET
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 35 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 842 ASN
A1155 HIS
A1182 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.142536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.107092 restraints weight = 19313.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.105650 restraints weight = 16457.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.106158 restraints weight = 12627.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.106920 restraints weight = 10689.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.107234 restraints weight = 9694.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060   9552  Z= 0.258
  Angle     :  0.671   7.856  12811  Z= 0.350
  Chirality :  0.045   0.284   1446
  Planarity :  0.004   0.041   1580
  Dihedral  : 10.487  85.334   1615
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.76 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.24), residues: 1152
  helix:  1.17 (0.18), residues: 756
  sheet: -0.13 (0.60), residues: 75
  loop : -0.30 (0.35), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 787 
 TYR   0.019   0.002   TYR A 118 
 PHE   0.024   0.002   PHE A 103 
 TRP   0.015   0.002   TRP A 232 
 HIS   0.006   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00594 ( 9552)
  covalent geometry    : angle       0.67074 (12811)
  hydrogen bonds       : bond        0.05312 (  618)
  hydrogen bonds       : angle       4.81921 ( 1797)

*********************** 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
  143 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 112
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8061 (t80)
REVERT: A  497 MET cc_start: 0.6775 (mmm) cc_final: 0.6428 (tpp)
REVERT: A  538 ARG cc_start: 0.6928 (ptm-80) cc_final: 0.5673 (mtt90)
REVERT: A  541 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8957 (mt)
REVERT: A  717 CYS cc_start: 0.7668 (t) cc_final: 0.7252 (t)
REVERT: A  796 MET cc_start: 0.8558 (mtm) cc_final: 0.8001 (mtm)
REVERT: A  878 MET cc_start: 0.6638 (mmt) cc_final: 0.6329 (mmm)
REVERT: A  888 LYS cc_start: 0.8647 (tptm) cc_final: 0.8220 (tptp)
REVERT: A 1099 LYS cc_start: 0.5966 (tmtt) cc_final: 0.4833 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8636 (tppt) cc_final: 0.8078 (pttt)
REVERT: A 1223 GLU cc_start: 0.7753 (tp30) cc_final: 0.7101 (pp20)
  outliers start: 31
  outliers final: 21
  residues processed: 134
  average time/residue: 0.0776
  time to fit residues: 15.8845
Evaluate side-chains
  125 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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  192 MET
Chi-restraints excluded: chain A residue  214 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  762 LEU
Chi-restraints excluded: chain A residue  772 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  867 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1199 LEU
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 54 optimal weight:    0.7980
   chunk 114 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 842 ASN
A1155 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.147711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112133 restraints weight = 19312.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112518 restraints weight = 13754.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.112605 restraints weight = 9829.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113322 restraints weight = 9659.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.113321 restraints weight = 8433.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9552  Z= 0.124
  Angle     :  0.541   6.829  12811  Z= 0.283
  Chirality :  0.041   0.286   1446
  Planarity :  0.003   0.041   1580
  Dihedral  :  9.503  81.415   1615
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 17.12 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1152
  helix:  1.65 (0.18), residues: 742
  sheet: -0.04 (0.60), residues: 75
  loop : -0.33 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 794 
 TYR   0.009   0.001   TYR A 247 
 PHE   0.032   0.001   PHE A 994 
 TRP   0.016   0.002   TRP A1108 
 HIS   0.016   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 9552)
  covalent geometry    : angle       0.54060 (12811)
  hydrogen bonds       : bond        0.04391 (  618)
  hydrogen bonds       : angle       4.26332 ( 1797)

*********************** 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
  149 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.8173 (t80)
REVERT: A  105 MET cc_start: 0.7327 (tpp) cc_final: 0.6800 (tpp)
REVERT: A  143 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7098 (tm-30)
REVERT: A  492 ARG cc_start: 0.6751 (ttp-170) cc_final: 0.6528 (ttp80)
REVERT: A  497 MET cc_start: 0.6709 (mmm) cc_final: 0.5874 (tpp)
REVERT: A  538 ARG cc_start: 0.6896 (ptm-80) cc_final: 0.5455 (mtt90)
REVERT: A  541 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8866 (mt)
REVERT: A  573 LEU cc_start: 0.8808 (mt) cc_final: 0.7710 (pp)
REVERT: A  717 CYS cc_start: 0.7389 (t) cc_final: 0.6991 (t)
REVERT: A  796 MET cc_start: 0.8544 (mtm) cc_final: 0.7990 (mtm)
REVERT: A  799 GLN cc_start: 0.8351 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: A  808 LYS cc_start: 0.8597 (tttt) cc_final: 0.7793 (tptt)
REVERT: A  878 MET cc_start: 0.6730 (mmt) cc_final: 0.6374 (mmm)
REVERT: A  888 LYS cc_start: 0.8578 (tptm) cc_final: 0.8049 (tptp)
REVERT: A 1099 LYS cc_start: 0.5852 (tmtt) cc_final: 0.4832 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8644 (tppt) cc_final: 0.8110 (pttt)
REVERT: A 1223 GLU cc_start: 0.7716 (tp30) cc_final: 0.7036 (pp20)
  outliers start: 23
  outliers final: 13
  residues processed: 142
  average time/residue: 0.0861
  time to fit residues: 17.6771
Evaluate side-chains
  127 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  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 1140 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 98 optimal weight:    0.0020
   chunk 112 optimal weight:   10.0000
   chunk 20 optimal weight:    0.8980
   chunk 49 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 92 optimal weight:    7.9990
   chunk 69 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 55 optimal weight:    4.9990
   chunk 58 optimal weight:   10.0000
   chunk 10 optimal weight:    3.9990
   overall best weight:    1.5592

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

Flipped N/Q/H residues before XYZ refinement:
A 820 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.146693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.111180 restraints weight = 19457.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.111318 restraints weight = 13338.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.111166 restraints weight = 9992.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111608 restraints weight = 9819.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.112130 restraints weight = 8761.901|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9552  Z= 0.150
  Angle     :  0.568   7.721  12811  Z= 0.297
  Chirality :  0.042   0.266   1446
  Planarity :  0.003   0.038   1580
  Dihedral  :  9.353  79.579   1614
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.43 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1152
  helix:  1.67 (0.18), residues: 743
  sheet: -0.10 (0.59), residues: 75
  loop : -0.33 (0.35), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 787 
 TYR   0.011   0.001   TYR A 118 
 PHE   0.039   0.002   PHE A 343 
 TRP   0.019   0.002   TRP A 232 
 HIS   0.012   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9552)
  covalent geometry    : angle       0.56754 (12811)
  hydrogen bonds       : bond        0.04521 (  618)
  hydrogen bonds       : angle       4.36373 ( 1797)

*********************** 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
  141 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.8185 (t80)
REVERT: A  105 MET cc_start: 0.7340 (tpp) cc_final: 0.6924 (tpp)
REVERT: A  538 ARG cc_start: 0.6912 (ptm-80) cc_final: 0.5512 (mtt90)
REVERT: A  541 ILE cc_start: 0.9150 (OUTLIER) cc_final: 0.8894 (mt)
REVERT: A  573 LEU cc_start: 0.8783 (mt) cc_final: 0.7683 (pp)
REVERT: A  717 CYS cc_start: 0.7292 (t) cc_final: 0.6934 (t)
REVERT: A  796 MET cc_start: 0.8502 (mtm) cc_final: 0.7976 (mtm)
REVERT: A  799 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8175 (tm-30)
REVERT: A  820 ASN cc_start: 0.7828 (OUTLIER) cc_final: 0.7449 (t0)
REVERT: A  878 MET cc_start: 0.6746 (mmt) cc_final: 0.6354 (mmm)
REVERT: A  888 LYS cc_start: 0.8579 (tptm) cc_final: 0.8108 (tptp)
REVERT: A 1064 GLN cc_start: 0.7892 (tp-100) cc_final: 0.6466 (tm-30)
REVERT: A 1099 LYS cc_start: 0.5814 (tmtt) cc_final: 0.4800 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8600 (tppt) cc_final: 0.8096 (pttt)
REVERT: A 1223 GLU cc_start: 0.7756 (tp30) cc_final: 0.7078 (pp20)
  outliers start: 28
  outliers final: 19
  residues processed: 132
  average time/residue: 0.0862
  time to fit residues: 16.9583
Evaluate side-chains
  131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  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 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 1208 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 82 optimal weight:    0.7980
   chunk 36 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 94 optimal weight:    7.9990
   chunk 48 optimal weight:    6.9990
   chunk 60 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 809 ASN
A 820 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.146207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.111414 restraints weight = 19419.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.111559 restraints weight = 12967.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.111516 restraints weight = 9793.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.112185 restraints weight = 9640.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.112302 restraints weight = 8228.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9552  Z= 0.146
  Angle     :  0.557   6.965  12811  Z= 0.294
  Chirality :  0.042   0.261   1446
  Planarity :  0.003   0.038   1580
  Dihedral  :  9.243  84.774   1614
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.95 %
    Favored  : 79.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1152
  helix:  1.64 (0.18), residues: 746
  sheet: -0.08 (0.58), residues: 75
  loop : -0.29 (0.35), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 787 
 TYR   0.011   0.001   TYR A 118 
 PHE   0.019   0.002   PHE A 994 
 TRP   0.019   0.002   TRP A1108 
 HIS   0.006   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 9552)
  covalent geometry    : angle       0.55749 (12811)
  hydrogen bonds       : bond        0.04458 (  618)
  hydrogen bonds       : angle       4.31430 ( 1797)

*********************** 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
  142 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8442 (OUTLIER) cc_final: 0.8147 (t80)
REVERT: A  105 MET cc_start: 0.7284 (tpp) cc_final: 0.6947 (tpp)
REVERT: A  143 GLN cc_start: 0.8082 (tm-30) cc_final: 0.7134 (tm-30)
REVERT: A  538 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.5589 (mtt90)
REVERT: A  541 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8876 (mt)
REVERT: A  573 LEU cc_start: 0.8727 (mt) cc_final: 0.7640 (pp)
REVERT: A  717 CYS cc_start: 0.7205 (t) cc_final: 0.6860 (t)
REVERT: A  796 MET cc_start: 0.8492 (mtm) cc_final: 0.7998 (mtm)
REVERT: A  799 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8208 (tm-30)
REVERT: A  808 LYS cc_start: 0.8530 (tttt) cc_final: 0.7690 (tptt)
REVERT: A  820 ASN cc_start: 0.7845 (OUTLIER) cc_final: 0.7521 (t0)
REVERT: A  878 MET cc_start: 0.6766 (mmt) cc_final: 0.6383 (mmm)
REVERT: A  888 LYS cc_start: 0.8568 (tptm) cc_final: 0.8114 (tptp)
REVERT: A  913 GLU cc_start: 0.7028 (pp20) cc_final: 0.6447 (pp20)
REVERT: A 1064 GLN cc_start: 0.7879 (tp-100) cc_final: 0.6517 (tm-30)
REVERT: A 1099 LYS cc_start: 0.5784 (tmtt) cc_final: 0.4680 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8573 (tppt) cc_final: 0.8085 (pttt)
REVERT: A 1223 GLU cc_start: 0.7774 (tp30) cc_final: 0.7103 (pp20)
  outliers start: 28
  outliers final: 21
  residues processed: 135
  average time/residue: 0.0791
  time to fit residues: 15.8947
Evaluate side-chains
  135 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  112 THR
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain A residue  319 THR
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  809 ASN
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1060 VAL
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 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 73 optimal weight:    2.9990
   chunk 114 optimal weight:    7.9990
   chunk 88 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 41 optimal weight:    0.9980
   chunk 93 optimal weight:    8.9990
   chunk 63 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 39 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 809 ASN
A 820 ASN

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 = 0.147002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.110354 restraints weight = 19202.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110780 restraints weight = 13969.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.112233 restraints weight = 9756.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.112858 restraints weight = 7717.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.113073 restraints weight = 7192.574|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9552  Z= 0.128
  Angle     :  0.561   7.616  12811  Z= 0.295
  Chirality :  0.041   0.256   1446
  Planarity :  0.003   0.038   1580
  Dihedral  :  9.085  87.678   1614
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.54 %
    Favored  : 79.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.24), residues: 1152
  helix:  1.72 (0.18), residues: 745
  sheet:  0.23 (0.60), residues: 69
  loop : -0.33 (0.35), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 538 
 TYR   0.013   0.001   TYR A 277 
 PHE   0.019   0.001   PHE A 103 
 TRP   0.021   0.002   TRP A1108 
 HIS   0.006   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 9552)
  covalent geometry    : angle       0.56133 (12811)
  hydrogen bonds       : bond        0.04337 (  618)
  hydrogen bonds       : angle       4.25380 ( 1797)

*********************** 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
  140 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8380 (OUTLIER) cc_final: 0.8154 (t80)
REVERT: A  105 MET cc_start: 0.7347 (tpp) cc_final: 0.7007 (tpp)
REVERT: A  143 GLN cc_start: 0.8014 (tm-30) cc_final: 0.6963 (tm-30)
REVERT: A  343 PHE cc_start: 0.7601 (m-80) cc_final: 0.7376 (m-80)
REVERT: A  416 LYS cc_start: 0.7112 (mmmm) cc_final: 0.6827 (mptt)
REVERT: A  538 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.5478 (mtt90)
REVERT: A  541 ILE cc_start: 0.9116 (OUTLIER) cc_final: 0.8851 (mt)
REVERT: A  717 CYS cc_start: 0.7519 (t) cc_final: 0.7188 (t)
REVERT: A  799 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: A  820 ASN cc_start: 0.7745 (OUTLIER) cc_final: 0.7323 (t0)
REVERT: A  878 MET cc_start: 0.6731 (mmt) cc_final: 0.6342 (mmm)
REVERT: A  888 LYS cc_start: 0.8552 (tptm) cc_final: 0.8098 (tptp)
REVERT: A  913 GLU cc_start: 0.6978 (pp20) cc_final: 0.6442 (pp20)
REVERT: A 1064 GLN cc_start: 0.7872 (tp-100) cc_final: 0.6517 (pp30)
REVERT: A 1065 THR cc_start: 0.7926 (m) cc_final: 0.7299 (m)
REVERT: A 1099 LYS cc_start: 0.5920 (tmtt) cc_final: 0.4882 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8641 (tppt) cc_final: 0.8108 (pttt)
REVERT: A 1223 GLU cc_start: 0.7772 (tp30) cc_final: 0.7111 (pp20)
  outliers start: 27
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0805
  time to fit residues: 16.1187
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  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  112 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  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  809 ASN
Chi-restraints excluded: chain A residue  820 ASN
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 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 9 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 15 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 96 optimal weight:    0.4980
   chunk 37 optimal weight:    5.9990
   chunk 82 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 110 optimal weight:   10.0000
   chunk 77 optimal weight:    0.7980
   chunk 41 optimal weight:    3.9990
   overall best weight:    1.2182

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

Flipped N/Q/H residues before XYZ refinement:
A 809 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.147181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.111622 restraints weight = 19156.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.112177 restraints weight = 12811.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.113115 restraints weight = 9373.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.113528 restraints weight = 7994.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.113858 restraints weight = 7228.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.3199

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= 0.137
  Angle     :  0.569   9.143  12811  Z= 0.300
  Chirality :  0.042   0.250   1446
  Planarity :  0.003   0.037   1580
  Dihedral  :  9.013  87.777   1614
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 17.95 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.24), residues: 1152
  helix:  1.71 (0.18), residues: 746
  sheet:  0.27 (0.60), residues: 69
  loop : -0.34 (0.35), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 538 
 TYR   0.011   0.001   TYR A 277 
 PHE   0.019   0.002   PHE A 103 
 TRP   0.022   0.002   TRP A1108 
 HIS   0.016   0.001   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9552)
  covalent geometry    : angle       0.56945 (12811)
  hydrogen bonds       : bond        0.04348 (  618)
  hydrogen bonds       : angle       4.26173 ( 1797)

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

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

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

  2304 Ramachandran restraints generated.
    1152 Oldfield, 0 Emsley, 1152 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   79 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.8163 (t80)
REVERT: A  105 MET cc_start: 0.7383 (tpp) cc_final: 0.7042 (tpp)
REVERT: A  143 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7157 (tm-30)
REVERT: A  239 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6904 (t80)
REVERT: A  538 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.5473 (mtt90)
REVERT: A  541 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8886 (mt)
REVERT: A  717 CYS cc_start: 0.7505 (t) cc_final: 0.7178 (t)
REVERT: A  799 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8211 (tm-30)
REVERT: A  808 LYS cc_start: 0.8524 (tttt) cc_final: 0.7670 (tptt)
REVERT: A  878 MET cc_start: 0.6732 (mmt) cc_final: 0.6354 (mmm)
REVERT: A  888 LYS cc_start: 0.8552 (tptm) cc_final: 0.8098 (tptp)
REVERT: A 1064 GLN cc_start: 0.7881 (tp-100) cc_final: 0.6614 (pp30)
REVERT: A 1099 LYS cc_start: 0.5901 (tmtt) cc_final: 0.4882 (mtmt)
REVERT: A 1102 LYS cc_start: 0.8619 (tppt) cc_final: 0.8157 (pttt)
REVERT: A 1223 GLU cc_start: 0.7789 (tp30) cc_final: 0.7165 (pp20)
  outliers start: 22
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0838
  time to fit residues: 15.6958
Evaluate side-chains
  131 residues out of total 958 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 PHE
Chi-restraints excluded: chain A residue  192 MET
Chi-restraints excluded: chain A residue  239 PHE
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  433 LYS
Chi-restraints excluded: chain A residue  437 VAL
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  538 ARG
Chi-restraints excluded: chain A residue  541 ILE
Chi-restraints excluded: chain A residue  574 ASP
Chi-restraints excluded: chain A residue  695 VAL
Chi-restraints excluded: chain A residue  772 LEU
Chi-restraints excluded: chain A residue  829 ILE
Chi-restraints excluded: chain A residue  896 ILE
Chi-restraints excluded: chain A residue  898 THR
Chi-restraints excluded: chain A residue 1076 LYS
Chi-restraints excluded: chain A residue 1140 VAL
Chi-restraints excluded: chain A residue 1141 SER
Chi-restraints excluded: chain A residue 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 9 optimal weight:    4.9990
   chunk 13 optimal weight:    0.9990
   chunk 72 optimal weight:    4.9990
   chunk 110 optimal weight:   10.0000
   chunk 19 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 81 optimal weight:    0.6980
   chunk 112 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 107 optimal weight:    3.9990
   chunk 43 optimal weight:    7.9990
   overall best weight:    2.9388

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.142669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.107493 restraints weight = 19329.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.106500 restraints weight = 16876.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.107702 restraints weight = 12854.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.108469 restraints weight = 10139.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.108637 restraints weight = 8903.981|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   9552  Z= 0.231
  Angle     :  0.658   8.091  12811  Z= 0.347
  Chirality :  0.045   0.261   1446
  Planarity :  0.004   0.039   1580
  Dihedral  :  9.866  80.863   1614
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 17.64 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.24), residues: 1152
  helix:  1.34 (0.18), residues: 748
  sheet:  0.55 (0.60), residues: 65
  loop : -0.39 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1047 
 TYR   0.017   0.002   TYR A 118 
 PHE   0.018   0.002   PHE A 103 
 TRP   0.023   0.003   TRP A 232 
 HIS   0.018   0.002   HIS A 612 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 ( 9552)
  covalent geometry    : angle       0.65845 (12811)
  hydrogen bonds       : bond        0.05145 (  618)
  hydrogen bonds       : angle       4.66998 ( 1797)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1465.29 seconds
wall clock time: 26 minutes 10.30 seconds (1570.30 seconds total)