Starting phenix.real_space_refine
on Tue May 13 08:16:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9exh_50038/05_2025/9exh_50038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9exh_50038/05_2025/9exh_50038.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/9exh_50038/05_2025/9exh_50038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9exh_50038/05_2025/9exh_50038.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9exh_50038/05_2025/9exh_50038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9exh_50038/05_2025/9exh_50038.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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: 4
    Type Number    sf(0)   Gaussians
     S      42      5.16       5
     C    6195      2.51       5
     N    1660      2.21       5
     O    1831      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 9728
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9728
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1205, 9728
          Classifications: {'peptide': 1205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 40, 'TRANS': 1164}
  Time building chain proxies: 5.17, per 1000 atoms: 0.53
  Number of scatterers: 9728
  At special positions: 0
  Unit cell: (77.52, 104.72, 137.36, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      42     16.00
     O    1831      8.00
     N    1660      7.00
     C    6195      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.27
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 6 sheets defined
      56.9% alpha, 6.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 6
      removed outlier: 3.817A  pdb=" N   ASN A   5 " --> pdb=" O   MET A   1 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 28
      removed outlier: 3.611A  pdb=" N   ASN A  15 " --> pdb=" O   PRO A  11 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ARG A  18 " --> pdb=" O   ARG A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 75
      removed outlier: 3.597A  pdb=" N   GLN A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 102
    Processing helix  chain 'A' and resid 121 through 124
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 137 through 148
    Processing helix  chain 'A' and resid 150 through 168
      removed outlier: 4.249A  pdb=" N   HIS A 168 " --> pdb=" O   HIS A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 183
    Processing helix  chain 'A' and resid 194 through 201
      removed outlier: 4.064A  pdb=" N   GLY A 198 " --> pdb=" O   SER A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 210
      removed outlier: 3.752A  pdb=" N   GLU A 209 " --> pdb=" O   GLU A 206 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   GLN A 210 " --> pdb=" O   ASP A 207 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 221
      removed outlier: 3.872A  pdb=" N   GLY A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   TYR A 218 " --> pdb=" O   ILE A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 229
      removed outlier: 3.753A  pdb=" N   ALA A 228 " --> pdb=" O   GLU A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 243
      removed outlier: 4.074A  pdb=" N   ALA A 242 " --> pdb=" O   ILE A 239 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   THR A 243 " --> pdb=" O   PRO A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 258
      removed outlier: 3.559A  pdb=" N   ASN A 258 " --> pdb=" O   TYR A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 3.640A  pdb=" N   GLN A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   THR A 267 " --> pdb=" O   GLN A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.994A  pdb=" N   ILE A 307 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 335
    Processing helix  chain 'A' and resid 337 through 339
      No H-bonds generated for 'chain 'A' and resid 337 through 339'
    Processing helix  chain 'A' and resid 340 through 349
      removed outlier: 3.712A  pdb=" N   LEU A 344 " --> pdb=" O   ASP A 340 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASN A 348 " --> pdb=" O   LEU A 344 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ASN A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 375
      removed outlier: 3.968A  pdb=" N   ASP A 374 " --> pdb=" O   LEU A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 405
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 3.569A  pdb=" N   HIS A 409 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 442
      removed outlier: 3.781A  pdb=" N   LEU A 442 " --> pdb=" O   ARG A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 445 through 450
    Processing helix  chain 'A' and resid 459 through 474
    Processing helix  chain 'A' and resid 478 through 499
      Proline residue:  A 490  - end of helix
    Processing helix  chain 'A' and resid 518 through 529
    Processing helix  chain 'A' and resid 535 through 545
      removed outlier: 3.602A  pdb=" N   MET A 539 " --> pdb=" O   ASP A 535 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   PHE A 545 " --> pdb=" O   MET A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 564
      removed outlier: 3.623A  pdb=" N   PHE A 564 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 561 through 564'
    Processing helix  chain 'A' and resid 565 through 567
      No H-bonds generated for 'chain 'A' and resid 565 through 567'
    Processing helix  chain 'A' and resid 568 through 579
      removed outlier: 3.951A  pdb=" N   ASN A 578 " --> pdb=" O   TRP A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 637
    Processing helix  chain 'A' and resid 645 through 651
    Processing helix  chain 'A' and resid 662 through 671
      removed outlier: 4.071A  pdb=" N   ILE A 666 " --> pdb=" O   THR A 662 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS A 671 " --> pdb=" O   ASN A 667 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 693
      removed outlier: 3.564A  pdb=" N   PHE A 692 " --> pdb=" O   SER A 688 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU A 693 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 688 through 693'
    Processing helix  chain 'A' and resid 695 through 699
      removed outlier: 3.673A  pdb=" N   VAL A 699 " --> pdb=" O   TRP A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 747
    Processing helix  chain 'A' and resid 752 through 756
    Processing helix  chain 'A' and resid 784 through 786
      No H-bonds generated for 'chain 'A' and resid 784 through 786'
    Processing helix  chain 'A' and resid 798 through 807
      removed outlier: 3.640A  pdb=" N   ASN A 807 " --> pdb=" O   LEU A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 808 through 819
    Processing helix  chain 'A' and resid 825 through 830
    Processing helix  chain 'A' and resid 838 through 856
      removed outlier: 3.934A  pdb=" N   ASP A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 872
      removed outlier: 4.021A  pdb=" N   HIS A 872 " --> pdb=" O   LEU A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 910
    Processing helix  chain 'A' and resid 927 through 933
    Processing helix  chain 'A' and resid 942 through 962
    Processing helix  chain 'A' and resid 976 through 980
      removed outlier: 4.035A  pdb=" N   ASN A 979 " --> pdb=" O   HIS A 976 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS A 980 " --> pdb=" O   GLU A 977 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 976 through 980'
    Processing helix  chain 'A' and resid 981 through 989
    Processing helix  chain 'A' and resid 1013 through 1027
    Processing helix  chain 'A' and resid 1030 through 1046
      removed outlier: 4.178A  pdb=" N   TYR A1045 " --> pdb=" O   SER A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1066
    Processing helix  chain 'A' and resid 1066 through 1076
    Processing helix  chain 'A' and resid 1104 through 1135
      removed outlier: 4.278A  pdb=" N   VAL A1115 " --> pdb=" O   THR A1111 " (cutoff:3.500A)
      Proline residue:  A1116  - end of helix
      removed outlier: 3.973A  pdb=" N   ASP A1133 " --> pdb=" O   ASN A1129 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU A1134 " --> pdb=" O   ASP A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1136 through 1170
      removed outlier: 3.547A  pdb=" N   ALA A1140 " --> pdb=" O   SER A1136 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A1143 " --> pdb=" O   GLU A1139 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLU A1146 " --> pdb=" O   ARG A1142 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ARG A1147 " --> pdb=" O   LEU A1143 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   MET A1170 " --> pdb=" O   HIS A1166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1175 through 1178
    Processing helix  chain 'A' and resid 1179 through 1184
    Processing helix  chain 'A' and resid 1185 through 1188
      removed outlier: 4.026A  pdb=" N   GLY A1188 " --> pdb=" O   GLY A1185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1185 through 1188'
    Processing helix  chain 'A' and resid 1193 through 1199
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46
      removed outlier: 3.553A  pdb=" N   PHE A  55 " --> pdb=" O   TYR A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 389
      removed outlier: 8.507A  pdb=" N   VAL A 388 " --> pdb=" O   ILE A 350 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   GLY A 352 " --> pdb=" O   VAL A 388 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   VAL A 309 " --> pdb=" O   PHE A 351 " (cutoff:3.500A)
      removed outlier: 8.057A  pdb=" N   LEU A 353 " --> pdb=" O   VAL A 309 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   ASP A 311 " --> pdb=" O   LEU A 353 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   VAL A 506 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   ASP A 503 " --> pdb=" O   PHE A 553 " (cutoff:3.500A)
      removed outlier: 8.007A  pdb=" N   ALA A 555 " --> pdb=" O   ASP A 503 " (cutoff:3.500A)
      removed outlier: 6.367A  pdb=" N   VAL A 505 " --> pdb=" O   ALA A 555 " (cutoff:3.500A)
      removed outlier: 8.281A  pdb=" N   VAL A 557 " --> pdb=" O   VAL A 505 " (cutoff:3.500A)
      removed outlier: 7.488A  pdb=" N   ALA A 507 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
      removed outlier: 9.706A  pdb=" N   MET A 559 " --> pdb=" O   ALA A 507 " (cutoff:3.500A)
      removed outlier: 5.830A  pdb=" N   THR A 602 " --> pdb=" O   LEU A 587 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 620
      removed outlier: 3.830A  pdb=" N   PHE A 641 " --> pdb=" O   PHE A 619 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 680
      removed outlier: 3.561A  pdb=" N   ALA A 788 " --> pdb=" O   VAL A 680 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 733 through 735
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1001 through 1004
      removed outlier: 4.138A  pdb=" N   GLU A1093 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.02

  Time building geometry restraints manager: 2.65 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3218
        1.34 -     1.46: 2190
        1.46 -     1.58: 4463
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 9943
  Sorted by residual:
  bond pdb=" C   ALA A  10 "
       pdb=" N   PRO A  11 "
    ideal  model  delta    sigma   weight residual
    1.335  1.351 -0.015 1.30e-02 5.92e+03 1.40e+00
  bond pdb=" CB  PRO A 656 "
       pdb=" CG  PRO A 656 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.39e-01
  bond pdb=" CA  VAL A 600 "
       pdb=" CB  VAL A 600 "
    ideal  model  delta    sigma   weight residual
    1.540  1.530  0.010 1.36e-02 5.41e+03 5.16e-01
  bond pdb=" N   PRO A 342 "
       pdb=" CA  PRO A 342 "
    ideal  model  delta    sigma   weight residual
    1.469  1.478 -0.009 1.28e-02 6.10e+03 4.73e-01
  bond pdb=" N   GLN A 150 "
       pdb=" CA  GLN A 150 "
    ideal  model  delta    sigma   weight residual
    1.461  1.472 -0.010 1.52e-02 4.33e+03 4.70e-01
  ... (remaining 9938 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.03: 13095
        1.03 -     2.05: 272
        2.05 -     3.08: 52
        3.08 -     4.10: 15
        4.10 -     5.13: 11
  Bond angle restraints: 13445
  Sorted by residual:
  angle pdb=" N   GLY A 728 "
        pdb=" CA  GLY A 728 "
        pdb=" C   GLY A 728 "
      ideal   model   delta    sigma   weight residual
     111.63  115.28   -3.65 1.15e+00 7.56e-01 1.01e+01
  angle pdb=" CA  TYR A  86 "
        pdb=" CB  TYR A  86 "
        pdb=" CG  TYR A  86 "
      ideal   model   delta    sigma   weight residual
     113.90  119.03   -5.13 1.80e+00 3.09e-01 8.12e+00
  angle pdb=" N   PHE A 727 "
        pdb=" CA  PHE A 727 "
        pdb=" C   PHE A 727 "
      ideal   model   delta    sigma   weight residual
     108.52  112.79   -4.27 1.52e+00 4.33e-01 7.89e+00
  angle pdb=" C   PRO A 114 "
        pdb=" N   GLU A 115 "
        pdb=" CA  GLU A 115 "
      ideal   model   delta    sigma   weight residual
     121.54  125.67   -4.13 1.91e+00 2.74e-01 4.67e+00
  angle pdb=" N   LYS A   8 "
        pdb=" CA  LYS A   8 "
        pdb=" C   LYS A   8 "
      ideal   model   delta    sigma   weight residual
     113.72  110.66    3.06 1.52e+00 4.33e-01 4.07e+00
  ... (remaining 13440 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.87: 5440
       10.87 -    21.73: 372
       21.73 -    32.60: 111
       32.60 -    43.47: 38
       43.47 -    54.33: 7
  Dihedral angle restraints: 5968
    sinusoidal: 2444
      harmonic: 3524
  Sorted by residual:
  dihedral pdb=" CA  SER A 430 "
           pdb=" C   SER A 430 "
           pdb=" N   ALA A 431 "
           pdb=" CA  ALA A 431 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.08   15.92     0      5.00e+00 4.00e-02 1.01e+01
  dihedral pdb=" CA  ARG A1017 "
           pdb=" CB  ARG A1017 "
           pdb=" CG  ARG A1017 "
           pdb=" CD  ARG A1017 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.50  -53.50     3      1.50e+01 4.44e-03 9.21e+00
  dihedral pdb=" CA  LYS A1153 "
           pdb=" CB  LYS A1153 "
           pdb=" CG  LYS A1153 "
           pdb=" CD  LYS A1153 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -113.47   53.47     3      1.50e+01 4.44e-03 9.21e+00
  ... (remaining 5965 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 983
       0.030 -    0.060: 325
       0.060 -    0.091: 86
       0.091 -    0.121: 44
       0.121 -    0.151: 6
  Chirality restraints: 1444
  Sorted by residual:
  chirality pdb=" CA  TRP A 696 "
            pdb=" N   TRP A 696 "
            pdb=" C   TRP A 696 "
            pdb=" CB  TRP A 696 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.69e-01
  chirality pdb=" CA  VAL A 557 "
            pdb=" N   VAL A 557 "
            pdb=" C   VAL A 557 "
            pdb=" CB  VAL A 557 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.21e-01
  chirality pdb=" CA  ILE A1001 "
            pdb=" N   ILE A1001 "
            pdb=" C   ILE A1001 "
            pdb=" CB  ILE A1001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1441 not shown)

  Planarity restraints: 1749
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  86 "    0.011 2.00e-02 2.50e+03   9.65e-03 1.86e+00
        pdb=" CG  TYR A  86 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  86 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  86 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  86 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  86 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  86 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A  86 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A1148 "    0.007 2.00e-02 2.50e+03   1.34e-02 1.80e+00
        pdb=" C   ASP A1148 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ASP A1148 "    0.009 2.00e-02 2.50e+03
        pdb=" N   SER A1149 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 832 "   -0.020 5.00e-02 4.00e+02   3.08e-02 1.52e+00
        pdb=" N   PRO A 833 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO A 833 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 833 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1746 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 705
        2.74 -     3.28: 10282
        3.28 -     3.82: 15929
        3.82 -     4.36: 18325
        4.36 -     4.90: 30798
  Nonbonded interactions: 76039
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 420 "
            pdb=" OG1 THR A 423 "
     model   vdw
     2.199 3.040
  nonbonded pdb=" OG  SER A1054 "
            pdb=" OE1 GLU A1057 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   LYS A1152 "
            pdb=" OG  SER A1155 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   HIS A 318 "
            pdb=" OG1 THR A 321 "
     model   vdw
     2.240 3.040
  nonbonded pdb=" O   GLU A1156 "
            pdb=" OG  SER A1159 "
     model   vdw
     2.253 3.040
  ... (remaining 76034 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.550
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8531
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   0.043   9943  Z= 0.090
  Angle     :  0.414   5.128  13445  Z= 0.231
  Chirality :  0.036   0.151   1444
  Planarity :  0.003   0.031   1749
  Dihedral  :  8.923  54.334   3700
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.11 %
    Favored  : 94.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.25), residues: 1203
  helix:  1.78 (0.23), residues: 570
  sheet: -0.27 (0.70), residues: 58
  loop : -0.67 (0.26), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 862 
 HIS   0.003   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A 537 
 TYR   0.024   0.001   TYR A  86 
 ARG   0.001   0.000   ARG A1147 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17395 (  442)
  hydrogen bonds       : angle       6.50050 ( 1263)
  covalent geometry    : bond        0.00174 ( 9943)
  covalent geometry    : angle       0.41413 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 61
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
REVERT: A  409 HIS cc_start: 0.7616 (t-90) cc_final: 0.7078 (t-90)
REVERT: A  410 MET cc_start: 0.7418 (mtm) cc_final: 0.6805 (mtm)
REVERT: A  437 MET cc_start: 0.9072 (mmm) cc_final: 0.8714 (mmm)
REVERT: A  512 MET cc_start: 0.8350 (ttm) cc_final: 0.8146 (tmm)
REVERT: A  517 MET cc_start: 0.7741 (mtp) cc_final: 0.7235 (mtp)
REVERT: A  584 MET cc_start: 0.8796 (ttm) cc_final: 0.8400 (tmm)
REVERT: A  638 MET cc_start: 0.8460 (mmp) cc_final: 0.8197 (mmm)
REVERT: A  773 MET cc_start: 0.8944 (ttm) cc_final: 0.8720 (ttm)
REVERT: A  948 ASP cc_start: 0.8970 (m-30) cc_final: 0.8680 (m-30)
REVERT: A 1109 MET cc_start: 0.9545 (ttm) cc_final: 0.9243 (tmm)
  outliers start: 3
  outliers final: 1
  residues processed: 64
  average time/residue: 0.2834
  time to fit residues: 25.3005
Evaluate side-chains
  38 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 37
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  340 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    0.3980
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 94 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 70 optimal weight:    4.9990
   chunk 108 optimal weight:    6.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A  90 ASN
A 253 GLN
** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 626 ASN
A1071 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.050979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.035998 restraints weight = 66117.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037243 restraints weight = 39148.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.038118 restraints weight = 29120.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8543
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9943  Z= 0.132
  Angle     :  0.522  11.953  13445  Z= 0.276
  Chirality :  0.039   0.160   1444
  Planarity :  0.003   0.034   1749
  Dihedral  :  3.723  16.119   1322
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  6.74 %
    Favored  : 92.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.19 (0.25), residues: 1203
  helix:  2.37 (0.22), residues: 576
  sheet: -0.54 (0.68), residues: 60
  loop : -0.76 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 216 
 HIS   0.005   0.001   HIS A 586 
 PHE   0.009   0.001   PHE A1154 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.008   0.001   ARG A1145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04472 (  442)
  hydrogen bonds       : angle       4.76504 ( 1263)
  covalent geometry    : bond        0.00287 ( 9943)
  covalent geometry    : angle       0.52218 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9394 (tpp) cc_final: 0.9011 (tpp)
REVERT: A  437 MET cc_start: 0.9009 (mmm) cc_final: 0.8589 (mmm)
REVERT: A  512 MET cc_start: 0.8418 (ttm) cc_final: 0.7731 (tmm)
REVERT: A  517 MET cc_start: 0.7791 (mtp) cc_final: 0.7177 (mpp)
REVERT: A  584 MET cc_start: 0.8862 (ttm) cc_final: 0.8416 (tmm)
REVERT: A  638 MET cc_start: 0.8485 (mmp) cc_final: 0.8154 (mmm)
REVERT: A  948 ASP cc_start: 0.8907 (m-30) cc_final: 0.8658 (m-30)
REVERT: A 1072 MET cc_start: 0.9252 (mtm) cc_final: 0.8970 (mtm)
REVERT: A 1109 MET cc_start: 0.9551 (ttm) cc_final: 0.9249 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 46
  average time/residue: 0.2190
  time to fit residues: 15.2324
Evaluate side-chains
  37 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 35
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  539 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 72 optimal weight:    5.9990
   chunk 23 optimal weight:    5.9990
   chunk 74 optimal weight:    7.9990
   chunk 101 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 91 optimal weight:    8.9990
   chunk 32 optimal weight:    0.8980
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 409 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.050460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2765 r_free = 0.2765 target = 0.035159 restraints weight = 68076.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2811 r_free = 0.2811 target = 0.036476 restraints weight = 40898.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2841 r_free = 0.2841 target = 0.037333 restraints weight = 30382.496|
|-----------------------------------------------------------------------------|
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9943  Z= 0.149
  Angle     :  0.501   6.803  13445  Z= 0.266
  Chirality :  0.039   0.144   1444
  Planarity :  0.003   0.038   1749
  Dihedral  :  3.752  15.717   1320
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 6.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.36 %
    Favored  : 92.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.25), residues: 1203
  helix:  2.45 (0.22), residues: 582
  sheet: -0.65 (0.68), residues: 60
  loop : -0.81 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 862 
 HIS   0.005   0.001   HIS A1166 
 PHE   0.011   0.001   PHE A 174 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.009   0.000   ARG A1127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04004 (  442)
  hydrogen bonds       : angle       4.41111 ( 1263)
  covalent geometry    : bond        0.00324 ( 9943)
  covalent geometry    : angle       0.50076 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 35
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ILE cc_start: 0.8535 (mm) cc_final: 0.8305 (mp)
REVERT: A   98 MET cc_start: 0.9454 (tpp) cc_final: 0.9078 (tpp)
REVERT: A  406 PHE cc_start: 0.7669 (OUTLIER) cc_final: 0.7420 (t80)
REVERT: A  437 MET cc_start: 0.9117 (mmm) cc_final: 0.8737 (mmm)
REVERT: A  512 MET cc_start: 0.8451 (ttm) cc_final: 0.7766 (tmm)
REVERT: A  517 MET cc_start: 0.7654 (mtp) cc_final: 0.7095 (mpp)
REVERT: A  584 MET cc_start: 0.8832 (ttm) cc_final: 0.8397 (tmm)
REVERT: A  638 MET cc_start: 0.8569 (mmp) cc_final: 0.8234 (mmm)
REVERT: A 1072 MET cc_start: 0.9233 (mtm) cc_final: 0.8918 (mtm)
REVERT: A 1109 MET cc_start: 0.9512 (ttm) cc_final: 0.9221 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 43
  average time/residue: 0.1998
  time to fit residues: 13.9308
Evaluate side-chains
  42 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 66 optimal weight:    5.9990
   chunk 70 optimal weight:    0.5980
   chunk 0 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 64 optimal weight:    0.7980
   chunk 117 optimal weight:   10.0000
   chunk 39 optimal weight:    8.9990
   chunk 36 optimal weight:    0.9990
   chunk 62 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   overall best weight:    2.2786

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

Flipped N/Q/H residues before XYZ refinement:
A 325 ASN
A 409 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.049973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.034812 restraints weight = 66696.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.036060 restraints weight = 40473.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.036910 restraints weight = 30294.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.2788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9943  Z= 0.174
  Angle     :  0.526  12.656  13445  Z= 0.274
  Chirality :  0.040   0.334   1444
  Planarity :  0.003   0.032   1749
  Dihedral  :  3.807  19.770   1320
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.23 %
    Favored  : 91.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.25), residues: 1203
  helix:  2.42 (0.22), residues: 582
  sheet: -0.79 (0.66), residues: 60
  loop : -0.84 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 862 
 HIS   0.004   0.001   HIS A 409 
 PHE   0.009   0.001   PHE A 886 
 TYR   0.020   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A1127 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  442)
  hydrogen bonds       : angle       4.39142 ( 1263)
  covalent geometry    : bond        0.00382 ( 9943)
  covalent geometry    : angle       0.52588 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 35
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8037 (mmm) cc_final: 0.7677 (mmm)
REVERT: A    6 ILE cc_start: 0.8574 (mm) cc_final: 0.8323 (mp)
REVERT: A   98 MET cc_start: 0.9376 (tpp) cc_final: 0.9053 (tpp)
REVERT: A  277 MET cc_start: 0.8858 (mpp) cc_final: 0.8531 (mpp)
REVERT: A  406 PHE cc_start: 0.7714 (OUTLIER) cc_final: 0.7471 (t80)
REVERT: A  437 MET cc_start: 0.9127 (mmm) cc_final: 0.8733 (mmm)
REVERT: A  512 MET cc_start: 0.8501 (ttm) cc_final: 0.7801 (tmm)
REVERT: A  517 MET cc_start: 0.7708 (mtp) cc_final: 0.7133 (mpp)
REVERT: A  584 MET cc_start: 0.8828 (ttm) cc_final: 0.8379 (tmm)
REVERT: A  638 MET cc_start: 0.8596 (mmp) cc_final: 0.8260 (mmm)
REVERT: A  962 MET cc_start: 0.8695 (tpp) cc_final: 0.8458 (ttm)
REVERT: A 1072 MET cc_start: 0.9235 (mtm) cc_final: 0.8917 (mtm)
REVERT: A 1109 MET cc_start: 0.9520 (ttm) cc_final: 0.9226 (tmm)
  outliers start: 11
  outliers final: 7
  residues processed: 44
  average time/residue: 0.2095
  time to fit residues: 14.7991
Evaluate side-chains
  43 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 35
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LYS
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  752 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 65 optimal weight:    0.3980
   chunk 63 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 27 optimal weight:    0.3980
   chunk 83 optimal weight:    6.9990
   chunk 98 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 67 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 961 GLN
A1166 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.051153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2792 r_free = 0.2792 target = 0.035919 restraints weight = 66308.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037245 restraints weight = 40226.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.038120 restraints weight = 29987.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9943  Z= 0.089
  Angle     :  0.460  11.196  13445  Z= 0.241
  Chirality :  0.038   0.258   1444
  Planarity :  0.003   0.030   1749
  Dihedral  :  3.653  19.435   1320
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  7.51 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.25), residues: 1203
  helix:  2.58 (0.22), residues: 582
  sheet: -0.53 (0.66), residues: 55
  loop : -0.75 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 496 
 HIS   0.008   0.001   HIS A 409 
 PHE   0.010   0.001   PHE A 537 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.002   0.000   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03345 (  442)
  hydrogen bonds       : angle       4.02307 ( 1263)
  covalent geometry    : bond        0.00185 ( 9943)
  covalent geometry    : angle       0.45991 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ILE cc_start: 0.8465 (mm) cc_final: 0.8214 (mp)
REVERT: A   98 MET cc_start: 0.9352 (tpp) cc_final: 0.9031 (tpp)
REVERT: A  277 MET cc_start: 0.8846 (mpp) cc_final: 0.8565 (mpp)
REVERT: A  415 MET cc_start: 0.6803 (mmp) cc_final: 0.6434 (mmp)
REVERT: A  437 MET cc_start: 0.9120 (mmm) cc_final: 0.8698 (mmm)
REVERT: A  453 ILE cc_start: 0.8763 (mt) cc_final: 0.8411 (tp)
REVERT: A  512 MET cc_start: 0.8337 (ttm) cc_final: 0.7720 (tmm)
REVERT: A  517 MET cc_start: 0.7602 (mtp) cc_final: 0.7046 (mpp)
REVERT: A  584 MET cc_start: 0.8772 (ttm) cc_final: 0.8378 (tmm)
REVERT: A  638 MET cc_start: 0.8513 (mmp) cc_final: 0.8215 (mmm)
REVERT: A  962 MET cc_start: 0.8734 (tpp) cc_final: 0.8531 (ttm)
REVERT: A 1072 MET cc_start: 0.9203 (mtm) cc_final: 0.8935 (mtm)
REVERT: A 1093 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8757 (mp0)
REVERT: A 1109 MET cc_start: 0.9501 (ttm) cc_final: 0.9201 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 46
  average time/residue: 0.1951
  time to fit residues: 14.6155
Evaluate side-chains
  43 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 37
  time to evaluate  : 1.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  705 ASP
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    0.0670
   chunk 43 optimal weight:    0.2980
   chunk 72 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0670
   chunk 1 optimal weight:    0.6980
   chunk 35 optimal weight:    3.9990
   chunk 71 optimal weight:    6.9990
   overall best weight:    0.3856

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.051571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.036305 restraints weight = 66034.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.037664 restraints weight = 39490.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.038565 restraints weight = 29082.904|
|-----------------------------------------------------------------------------|
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9943  Z= 0.083
  Angle     :  0.448  11.403  13445  Z= 0.233
  Chirality :  0.038   0.206   1444
  Planarity :  0.002   0.030   1749
  Dihedral  :  3.524  19.698   1320
  Min Nonbonded Distance : 2.634

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  8.38 %
    Favored  : 90.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.25), residues: 1203
  helix:  2.63 (0.22), residues: 583
  sheet: -0.40 (0.62), residues: 67
  loop : -0.71 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.009   0.001   PHE A 537 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.002   0.000   ARG A 372 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03038 (  442)
  hydrogen bonds       : angle       3.87058 ( 1263)
  covalent geometry    : bond        0.00173 ( 9943)
  covalent geometry    : angle       0.44833 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 38
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    6 ILE cc_start: 0.8373 (mm) cc_final: 0.8146 (mp)
REVERT: A   50 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8803 (p)
REVERT: A   98 MET cc_start: 0.9360 (tpp) cc_final: 0.8910 (tpp)
REVERT: A  415 MET cc_start: 0.6830 (mmp) cc_final: 0.6444 (mmp)
REVERT: A  437 MET cc_start: 0.9113 (mmm) cc_final: 0.8704 (mmm)
REVERT: A  512 MET cc_start: 0.8381 (ttm) cc_final: 0.7754 (tmm)
REVERT: A  517 MET cc_start: 0.7579 (mtp) cc_final: 0.7050 (mpp)
REVERT: A  584 MET cc_start: 0.8805 (ttm) cc_final: 0.8405 (tmm)
REVERT: A  638 MET cc_start: 0.8492 (mmp) cc_final: 0.8209 (mmm)
REVERT: A  696 TRP cc_start: 0.9395 (OUTLIER) cc_final: 0.8753 (p-90)
REVERT: A  962 MET cc_start: 0.8624 (tpp) cc_final: 0.8417 (ttm)
REVERT: A 1072 MET cc_start: 0.9184 (mtm) cc_final: 0.8929 (mtm)
REVERT: A 1093 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8867 (mp0)
REVERT: A 1109 MET cc_start: 0.9509 (ttm) cc_final: 0.9203 (tmm)
  outliers start: 7
  outliers final: 3
  residues processed: 44
  average time/residue: 0.2076
  time to fit residues: 14.4756
Evaluate side-chains
  42 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 37
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 80 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 23 optimal weight:    0.0870
   chunk 75 optimal weight:    9.9990
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    6.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
A 961 GLN
A 976 HIS
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.048962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.033549 restraints weight = 67183.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.034807 restraints weight = 40123.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.035632 restraints weight = 29665.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8596
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   9943  Z= 0.255
  Angle     :  0.609   8.671  13445  Z= 0.320
  Chirality :  0.041   0.212   1444
  Planarity :  0.004   0.033   1749
  Dihedral  :  3.950  22.078   1320
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.29 %
    Favored  : 90.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1203
  helix:  2.16 (0.22), residues: 596
  sheet: -0.70 (0.67), residues: 60
  loop : -1.03 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 855 
 HIS   0.006   0.001   HIS A 976 
 PHE   0.011   0.002   PHE A1187 
 TYR   0.018   0.002   TYR A  86 
 ARG   0.003   0.001   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  442)
  hydrogen bonds       : angle       4.38996 ( 1263)
  covalent geometry    : bond        0.00554 ( 9943)
  covalent geometry    : angle       0.60905 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8086 (mmm) cc_final: 0.7541 (mmm)
REVERT: A    6 ILE cc_start: 0.8579 (mm) cc_final: 0.8335 (mp)
REVERT: A   50 VAL cc_start: 0.9197 (OUTLIER) cc_final: 0.8843 (p)
REVERT: A   98 MET cc_start: 0.9458 (tpp) cc_final: 0.9053 (tpp)
REVERT: A  277 MET cc_start: 0.8953 (mpp) cc_final: 0.8668 (mpp)
REVERT: A  437 MET cc_start: 0.9012 (mmm) cc_final: 0.8569 (mmm)
REVERT: A  512 MET cc_start: 0.8596 (ttm) cc_final: 0.7820 (tmm)
REVERT: A  517 MET cc_start: 0.7827 (mtp) cc_final: 0.7185 (mpp)
REVERT: A  584 MET cc_start: 0.8867 (ttm) cc_final: 0.8195 (tmm)
REVERT: A  638 MET cc_start: 0.8705 (mmp) cc_final: 0.8320 (mmm)
REVERT: A  755 MET cc_start: 0.8320 (mmm) cc_final: 0.7867 (mmm)
REVERT: A  962 MET cc_start: 0.8750 (tpp) cc_final: 0.8522 (ttm)
REVERT: A 1072 MET cc_start: 0.9237 (mtm) cc_final: 0.8937 (mtm)
REVERT: A 1109 MET cc_start: 0.9560 (ttm) cc_final: 0.9260 (tmm)
  outliers start: 10
  outliers final: 7
  residues processed: 45
  average time/residue: 0.1794
  time to fit residues: 13.2137
Evaluate side-chains
  42 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  539 MET
Chi-restraints excluded: chain A residue  705 ASP
Chi-restraints excluded: chain A residue  717 ILE
Chi-restraints excluded: chain A residue  752 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 48 optimal weight:    7.9990
   chunk 32 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 118 optimal weight:    7.9990
   chunk 54 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 411 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.050402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.034884 restraints weight = 66418.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.036252 restraints weight = 38979.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.037141 restraints weight = 28518.925|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9943  Z= 0.093
  Angle     :  0.474  11.678  13445  Z= 0.250
  Chirality :  0.039   0.264   1444
  Planarity :  0.003   0.033   1749
  Dihedral  :  3.706  19.887   1320
  Min Nonbonded Distance : 2.632

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.67 %
    Favored  : 90.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.25), residues: 1203
  helix:  2.56 (0.22), residues: 587
  sheet: -0.58 (0.68), residues: 55
  loop : -0.82 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 496 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.010   0.001   PHE A 537 
 TYR   0.022   0.001   TYR A  86 
 ARG   0.002   0.000   ARG A 469 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03442 (  442)
  hydrogen bonds       : angle       3.92859 ( 1263)
  covalent geometry    : bond        0.00197 ( 9943)
  covalent geometry    : angle       0.47440 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 34
  time to evaluate  : 1.181 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8130 (mmm) cc_final: 0.7662 (mmm)
REVERT: A    6 ILE cc_start: 0.8505 (mm) cc_final: 0.8248 (mp)
REVERT: A   50 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8798 (p)
REVERT: A   98 MET cc_start: 0.9431 (tpp) cc_final: 0.9079 (tpp)
REVERT: A  277 MET cc_start: 0.8983 (mpp) cc_final: 0.8658 (mpp)
REVERT: A  409 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7812 (m90)
REVERT: A  410 MET cc_start: 0.7495 (pmm) cc_final: 0.7285 (pmm)
REVERT: A  437 MET cc_start: 0.9090 (mmm) cc_final: 0.8661 (mmm)
REVERT: A  512 MET cc_start: 0.8491 (ttm) cc_final: 0.7862 (tmm)
REVERT: A  517 MET cc_start: 0.7666 (mtp) cc_final: 0.7031 (mtp)
REVERT: A  584 MET cc_start: 0.8823 (ttm) cc_final: 0.8220 (tmm)
REVERT: A  638 MET cc_start: 0.8543 (mmp) cc_final: 0.8172 (mmm)
REVERT: A  755 MET cc_start: 0.8283 (mmm) cc_final: 0.7821 (mmm)
REVERT: A 1072 MET cc_start: 0.9243 (mtm) cc_final: 0.8951 (mtm)
REVERT: A 1109 MET cc_start: 0.9516 (ttm) cc_final: 0.9206 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 41
  average time/residue: 0.1834
  time to fit residues: 12.3375
Evaluate side-chains
  41 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 34
  time to evaluate  : 0.968 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  415 MET
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 31 optimal weight:    0.9990
   chunk 75 optimal weight:    0.0470
   chunk 59 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 119 optimal weight:    0.0980
   chunk 11 optimal weight:    6.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    0.5882

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

Flipped N/Q/H residues before XYZ refinement:
A 961 GLN
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.050868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.035524 restraints weight = 64887.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.036910 restraints weight = 37904.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.037816 restraints weight = 27578.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   9943  Z= 0.088
  Angle     :  0.459  11.599  13445  Z= 0.240
  Chirality :  0.038   0.243   1444
  Planarity :  0.002   0.031   1749
  Dihedral  :  3.564  19.883   1320
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  8.77 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.25), residues: 1203
  helix:  2.64 (0.22), residues: 587
  sheet: -0.40 (0.64), residues: 67
  loop : -0.76 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.009   0.001   PHE A1021 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.008   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  442)
  hydrogen bonds       : angle       3.80305 ( 1263)
  covalent geometry    : bond        0.00190 ( 9943)
  covalent geometry    : angle       0.45926 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8139 (mmm) cc_final: 0.7776 (mmm)
REVERT: A    6 ILE cc_start: 0.8590 (mm) cc_final: 0.8320 (mp)
REVERT: A   50 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8757 (p)
REVERT: A  409 HIS cc_start: 0.8053 (OUTLIER) cc_final: 0.7808 (m90)
REVERT: A  437 MET cc_start: 0.9107 (mmm) cc_final: 0.8704 (mmm)
REVERT: A  512 MET cc_start: 0.8455 (ttm) cc_final: 0.7827 (tmm)
REVERT: A  517 MET cc_start: 0.7624 (mtp) cc_final: 0.7032 (mtp)
REVERT: A  584 MET cc_start: 0.8849 (ttm) cc_final: 0.8213 (tmm)
REVERT: A  638 MET cc_start: 0.8561 (mmp) cc_final: 0.8196 (mmm)
REVERT: A  696 TRP cc_start: 0.9429 (OUTLIER) cc_final: 0.8795 (p-90)
REVERT: A  755 MET cc_start: 0.8259 (mmm) cc_final: 0.7838 (mmm)
REVERT: A 1093 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8920 (mp0)
REVERT: A 1109 MET cc_start: 0.9512 (ttm) cc_final: 0.9197 (tmm)
  outliers start: 9
  outliers final: 4
  residues processed: 43
  average time/residue: 0.2073
  time to fit residues: 15.2355
Evaluate side-chains
  42 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 35
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  411 GLN
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 87 optimal weight:    0.3980
   chunk 21 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0170
   chunk 51 optimal weight:    3.9990
   chunk 13 optimal weight:   10.0000
   chunk 117 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 106 optimal weight:    0.2980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.051095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.035637 restraints weight = 65278.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.037024 restraints weight = 38257.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.037947 restraints weight = 27940.234|
|-----------------------------------------------------------------------------|
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   9943  Z= 0.086
  Angle     :  0.469  11.699  13445  Z= 0.244
  Chirality :  0.039   0.305   1444
  Planarity :  0.002   0.029   1749
  Dihedral  :  3.513  18.908   1320
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.06 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.25), residues: 1203
  helix:  2.58 (0.22), residues: 589
  sheet: -0.34 (0.64), residues: 67
  loop : -0.73 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 
 PHE   0.009   0.001   PHE A 537 
 TYR   0.021   0.001   TYR A  86 
 ARG   0.003   0.000   ARG A 438 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02960 (  442)
  hydrogen bonds       : angle       3.78142 ( 1263)
  covalent geometry    : bond        0.00183 ( 9943)
  covalent geometry    : angle       0.46872 (13445)

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

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

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2406 Ramachandran restraints generated.
    1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 35
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8169 (mmm) cc_final: 0.7837 (mmm)
REVERT: A    6 ILE cc_start: 0.8572 (mm) cc_final: 0.8310 (mp)
REVERT: A   50 VAL cc_start: 0.9166 (OUTLIER) cc_final: 0.8764 (p)
REVERT: A  144 MET cc_start: 0.9012 (ptp) cc_final: 0.8755 (ptm)
REVERT: A  437 MET cc_start: 0.9037 (mmm) cc_final: 0.8658 (mmm)
REVERT: A  512 MET cc_start: 0.8534 (ttm) cc_final: 0.7908 (tmm)
REVERT: A  517 MET cc_start: 0.7636 (mtp) cc_final: 0.7092 (mtp)
REVERT: A  584 MET cc_start: 0.8866 (ttm) cc_final: 0.8310 (tmm)
REVERT: A  638 MET cc_start: 0.8536 (mmp) cc_final: 0.8184 (mmm)
REVERT: A  696 TRP cc_start: 0.9389 (OUTLIER) cc_final: 0.8779 (p-90)
REVERT: A  755 MET cc_start: 0.8286 (mmm) cc_final: 0.7874 (mmm)
REVERT: A 1093 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8914 (mp0)
REVERT: A 1109 MET cc_start: 0.9494 (ttm) cc_final: 0.9174 (tmm)
  outliers start: 6
  outliers final: 3
  residues processed: 41
  average time/residue: 0.2147
  time to fit residues: 14.2971
Evaluate side-chains
  40 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 35
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   50 VAL
Chi-restraints excluded: chain A residue  155 TYR
Chi-restraints excluded: chain A residue  409 HIS
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    8.9990
   chunk 28 optimal weight:    0.0270
   chunk 3 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.3642

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.050607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.035157 restraints weight = 65348.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2807 r_free = 0.2807 target = 0.036515 restraints weight = 38766.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037399 restraints weight = 28404.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9943  Z= 0.116
  Angle     :  0.490  11.889  13445  Z= 0.256
  Chirality :  0.039   0.302   1444
  Planarity :  0.003   0.030   1749
  Dihedral  :  3.556  19.173   1320
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  8.96 %
    Favored  : 90.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.25), residues: 1203
  helix:  2.61 (0.22), residues: 588
  sheet: -0.50 (0.63), residues: 72
  loop : -0.79 (0.26), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 696 
 HIS   0.005   0.001   HIS A 101 
 PHE   0.008   0.001   PHE A 886 
 TYR   0.020   0.001   TYR A  86 
 ARG   0.004   0.000   ARG A  65 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  442)
  hydrogen bonds       : angle       3.83978 ( 1263)
  covalent geometry    : bond        0.00257 ( 9943)
  covalent geometry    : angle       0.48994 (13445)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3060.48 seconds
wall clock time: 54 minutes 23.42 seconds (3263.42 seconds total)