Starting phenix.real_space_refine
on Sat Aug 23 05:08:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9exh_50038/08_2025/9exh_50038.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9exh_50038/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9exh_50038/08_2025/9exh_50038.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9exh_50038/08_2025/9exh_50038.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9exh_50038/08_2025/9exh_50038.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9exh_50038/08_2025/9exh_50038.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.26, per 1000 atoms: 0.23
  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: 0.87
  Conformation dependent library (CDL) restraints added in 349.9 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.34
  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: 1.63

  Time building geometry restraints manager: 1.09 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:             1.420
  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:             0.020
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.760
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (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
 ARG   0.001   0.000   ARG A1147 
 TYR   0.024   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A 537 
 TRP   0.007   0.001   TRP A 862 
 HIS   0.003   0.001   HIS A 167 

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

*********************** 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  : 0.378 
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: 0.1038
  time to fit residues: 9.1984
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  : 0.290 
-------------------------------------------------------------------------------
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 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 117 optimal weight:    8.9990
   overall best weight:    1.4184

-------------------------------------------------------------------------------
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 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 = 0.3293 r_free = 0.3293 target = 0.050873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.035769 restraints weight = 66843.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.037090 restraints weight = 40414.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.037943 restraints weight = 30064.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2877 r_free = 0.2877 target = 0.038422 restraints weight = 25112.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.038800 restraints weight = 22621.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9943  Z= 0.139
  Angle     :  0.526  12.214  13445  Z= 0.278
  Chirality :  0.039   0.146   1444
  Planarity :  0.003   0.035   1749
  Dihedral  :  3.739  16.207   1322
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.25), residues: 1203
  helix:  2.36 (0.22), residues: 576
  sheet: -0.55 (0.67), residues: 60
  loop : -0.76 (0.26), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A1145 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A 537 
 TRP   0.007   0.001   TRP A 216 
 HIS   0.005   0.001   HIS A 586 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9943)
  covalent geometry    : angle       0.52643 (13445)
  hydrogen bonds       : bond        0.04609 (  442)
  hydrogen bonds       : angle       4.80564 ( 1263)

*********************** 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  : 0.264 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9378 (tpp) cc_final: 0.9004 (tpp)
REVERT: A  437 MET cc_start: 0.9052 (mmm) cc_final: 0.8616 (mmm)
REVERT: A  512 MET cc_start: 0.8353 (ttm) cc_final: 0.7735 (tmm)
REVERT: A  517 MET cc_start: 0.7805 (mtp) cc_final: 0.7239 (mpp)
REVERT: A  584 MET cc_start: 0.8832 (ttm) cc_final: 0.8443 (tmm)
REVERT: A  638 MET cc_start: 0.8447 (mmp) cc_final: 0.8175 (mmm)
REVERT: A  948 ASP cc_start: 0.8866 (m-30) cc_final: 0.8627 (m-30)
REVERT: A 1072 MET cc_start: 0.9227 (mtm) cc_final: 0.8944 (mtm)
REVERT: A 1109 MET cc_start: 0.9540 (ttm) cc_final: 0.9238 (tmm)
  outliers start: 7
  outliers final: 2
  residues processed: 46
  average time/residue: 0.0944
  time to fit residues: 6.3904
Evaluate side-chains
  36 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 34
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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 25 optimal weight:    3.9990
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 10 optimal weight:    9.9990
   chunk 27 optimal weight:    0.6980
   chunk 115 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0980
   chunk 78 optimal weight:   10.0000
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 409 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.050818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.035614 restraints weight = 66718.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.036932 restraints weight = 39999.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.037801 restraints weight = 29626.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.038337 restraints weight = 24706.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.2883 r_free = 0.2883 target = 0.038534 restraints weight = 22149.446|
|-----------------------------------------------------------------------------|
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1486

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= 0.122
  Angle     :  0.480   6.695  13445  Z= 0.255
  Chirality :  0.038   0.141   1444
  Planarity :  0.003   0.034   1749
  Dihedral  :  3.703  17.601   1320
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.17 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.25), residues: 1203
  helix:  2.50 (0.22), residues: 581
  sheet: -0.54 (0.68), residues: 60
  loop : -0.80 (0.26), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1127 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.010   0.001   PHE A 174 
 TRP   0.006   0.001   TRP A 401 
 HIS   0.004   0.001   HIS A1166 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 9943)
  covalent geometry    : angle       0.48005 (13445)
  hydrogen bonds       : bond        0.03890 (  442)
  hydrogen bonds       : angle       4.38052 ( 1263)

*********************** 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  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9451 (tpp) cc_final: 0.9086 (tpp)
REVERT: A  406 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.7363 (t80)
REVERT: A  437 MET cc_start: 0.9150 (mmm) cc_final: 0.8747 (mmm)
REVERT: A  512 MET cc_start: 0.8471 (ttm) cc_final: 0.7802 (tmm)
REVERT: A  517 MET cc_start: 0.7553 (mtp) cc_final: 0.7055 (mpp)
REVERT: A  584 MET cc_start: 0.8814 (ttm) cc_final: 0.8372 (tmm)
REVERT: A  638 MET cc_start: 0.8491 (mmp) cc_final: 0.8194 (mmm)
REVERT: A  962 MET cc_start: 0.8764 (tpp) cc_final: 0.8560 (tpp)
REVERT: A 1072 MET cc_start: 0.9224 (mtm) cc_final: 0.8899 (mtm)
REVERT: A 1109 MET cc_start: 0.9508 (ttm) cc_final: 0.9245 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 43
  average time/residue: 0.0741
  time to fit residues: 4.8966
Evaluate side-chains
  43 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
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 2 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 25 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    3.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 150 GLN
A 325 ASN
A 409 HIS
A 976 HIS
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.048855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.033471 restraints weight = 67589.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.034745 restraints weight = 40391.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.035568 restraints weight = 29849.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2785 r_free = 0.2785 target = 0.036071 restraints weight = 24861.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.036367 restraints weight = 22290.684|
|-----------------------------------------------------------------------------|
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8577
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048   9943  Z= 0.263
  Angle     :  0.615  11.740  13445  Z= 0.321
  Chirality :  0.042   0.362   1444
  Planarity :  0.004   0.035   1749
  Dihedral  :  4.008  21.096   1320
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.15 %
    Favored  : 94.85 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.23 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1203
  helix:  2.07 (0.22), residues: 590
  sheet: -0.87 (0.66), residues: 60
  loop : -1.00 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  65 
 TYR   0.019   0.002   TYR A  86 
 PHE   0.011   0.002   PHE A 886 
 TRP   0.010   0.001   TRP A 726 
 HIS   0.017   0.002   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00571 ( 9943)
  covalent geometry    : angle       0.61519 (13445)
  hydrogen bonds       : bond        0.04434 (  442)
  hydrogen bonds       : angle       4.70094 ( 1263)

*********************** 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
  48 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 36
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8096 (mmm) cc_final: 0.7753 (mmm)
REVERT: A   98 MET cc_start: 0.9451 (tpp) cc_final: 0.9059 (tpp)
REVERT: A  277 MET cc_start: 0.8969 (mpp) cc_final: 0.8646 (mpp)
REVERT: A  406 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7511 (t80)
REVERT: A  409 HIS cc_start: 0.7793 (OUTLIER) cc_final: 0.7496 (m90)
REVERT: A  437 MET cc_start: 0.9056 (mmm) cc_final: 0.8616 (mmm)
REVERT: A  512 MET cc_start: 0.8581 (ttm) cc_final: 0.7838 (tmm)
REVERT: A  517 MET cc_start: 0.7782 (mtp) cc_final: 0.7201 (mpp)
REVERT: A  584 MET cc_start: 0.8866 (ttm) cc_final: 0.8210 (tmm)
REVERT: A  638 MET cc_start: 0.8660 (mmp) cc_final: 0.8299 (mmm)
REVERT: A 1072 MET cc_start: 0.9257 (mtm) cc_final: 0.8908 (mtm)
REVERT: A 1109 MET cc_start: 0.9523 (ttm) cc_final: 0.9267 (tmm)
  outliers start: 12
  outliers final: 8
  residues processed: 45
  average time/residue: 0.0814
  time to fit residues: 5.8266
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  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 LYS
Chi-restraints excluded: chain A residue   21 VAL
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
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 99 optimal weight:    4.9990
   chunk 111 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 39 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 95 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 409 HIS
** 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 = 0.3236 r_free = 0.3236 target = 0.049344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.033962 restraints weight = 66516.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.035250 restraints weight = 39466.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.036107 restraints weight = 29092.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036625 restraints weight = 24157.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2817 r_free = 0.2817 target = 0.036974 restraints weight = 21570.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9943  Z= 0.155
  Angle     :  0.526  13.302  13445  Z= 0.274
  Chirality :  0.039   0.252   1444
  Planarity :  0.003   0.034   1749
  Dihedral  :  3.935  19.897   1320
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.80 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.06 (0.25), residues: 1203
  helix:  2.30 (0.22), residues: 582
  sheet: -1.22 (0.61), residues: 70
  loop : -0.82 (0.27), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 372 
 TYR   0.020   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A1021 
 TRP   0.006   0.001   TRP A 862 
 HIS   0.006   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9943)
  covalent geometry    : angle       0.52578 (13445)
  hydrogen bonds       : bond        0.04075 (  442)
  hydrogen bonds       : angle       4.40437 ( 1263)

*********************** 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: 12
    poor density    : 36
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.8024 (mmm) cc_final: 0.7752 (mmm)
REVERT: A   98 MET cc_start: 0.9412 (tpp) cc_final: 0.9029 (tpp)
REVERT: A  437 MET cc_start: 0.9139 (mmm) cc_final: 0.8725 (mmm)
REVERT: A  512 MET cc_start: 0.8539 (ttm) cc_final: 0.7973 (tmm)
REVERT: A  517 MET cc_start: 0.7727 (mtp) cc_final: 0.6776 (mtp)
REVERT: A  584 MET cc_start: 0.8830 (ttm) cc_final: 0.8190 (tmm)
REVERT: A  638 MET cc_start: 0.8582 (mmp) cc_final: 0.8221 (mmm)
REVERT: A  962 MET cc_start: 0.8726 (tpp) cc_final: 0.8451 (ttm)
REVERT: A 1072 MET cc_start: 0.9248 (mtm) cc_final: 0.8928 (mtm)
REVERT: A 1109 MET cc_start: 0.9511 (ttm) cc_final: 0.9228 (tmm)
  outliers start: 12
  outliers final: 9
  residues processed: 46
  average time/residue: 0.0679
  time to fit residues: 4.9321
Evaluate side-chains
  45 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
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  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  741 ILE
Chi-restraints excluded: chain A residue  752 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 117 optimal weight:   10.0000
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    5.9990
   chunk 93 optimal weight:    0.8980
   chunk 88 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   chunk 115 optimal weight:    6.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 409 HIS
A 481 GLN
** 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 = 0.3263 r_free = 0.3263 target = 0.050214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.034831 restraints weight = 65166.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.036173 restraints weight = 38034.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2824 r_free = 0.2824 target = 0.037048 restraints weight = 27724.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037601 restraints weight = 22924.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.037958 restraints weight = 20355.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1980

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= 0.098
  Angle     :  0.489  14.263  13445  Z= 0.253
  Chirality :  0.038   0.219   1444
  Planarity :  0.003   0.031   1749
  Dihedral  :  3.783  19.753   1320
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.30 (0.25), residues: 1203
  helix:  2.52 (0.22), residues: 582
  sheet: -0.75 (0.66), residues: 60
  loop : -0.79 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 469 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.013   0.001   PHE A 406 
 TRP   0.006   0.001   TRP A 496 
 HIS   0.008   0.001   HIS A 409 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 ( 9943)
  covalent geometry    : angle       0.48923 (13445)
  hydrogen bonds       : bond        0.03593 (  442)
  hydrogen bonds       : angle       4.12771 ( 1263)

*********************** 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
  46 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 36
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8842 (p)
REVERT: A   98 MET cc_start: 0.9388 (tpp) cc_final: 0.9053 (tpp)
REVERT: A  277 MET cc_start: 0.8945 (mpp) cc_final: 0.8624 (mpp)
REVERT: A  415 MET cc_start: 0.6998 (mmp) cc_final: 0.6713 (mmp)
REVERT: A  437 MET cc_start: 0.9157 (mmm) cc_final: 0.8730 (mmm)
REVERT: A  512 MET cc_start: 0.8449 (ttm) cc_final: 0.7759 (tmm)
REVERT: A  517 MET cc_start: 0.7642 (mtp) cc_final: 0.7066 (mpp)
REVERT: A  584 MET cc_start: 0.8822 (ttm) cc_final: 0.8215 (tmm)
REVERT: A  638 MET cc_start: 0.8537 (mmp) cc_final: 0.8189 (mmm)
REVERT: A  962 MET cc_start: 0.8651 (tpp) cc_final: 0.8360 (ttm)
REVERT: A 1072 MET cc_start: 0.9246 (mtm) cc_final: 0.8942 (mtm)
REVERT: A 1109 MET cc_start: 0.9492 (ttm) cc_final: 0.9205 (tmm)
  outliers start: 10
  outliers final: 6
  residues processed: 44
  average time/residue: 0.0700
  time to fit residues: 5.0875
Evaluate side-chains
  43 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 36
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
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  367 MET
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 115 optimal weight:    0.9990
   chunk 101 optimal weight:    0.4980
   chunk 81 optimal weight:    3.9990
   chunk 86 optimal weight:    4.9990
   chunk 78 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 1 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   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 409 HIS
A 481 GLN
** 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 = 0.3270 r_free = 0.3270 target = 0.050468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.035144 restraints weight = 64950.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.036503 restraints weight = 38073.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.037381 restraints weight = 27806.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.037938 restraints weight = 22921.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038197 restraints weight = 20364.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.2049

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= 0.092
  Angle     :  0.482  14.225  13445  Z= 0.246
  Chirality :  0.038   0.196   1444
  Planarity :  0.002   0.030   1749
  Dihedral  :  3.649  19.580   1320
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  8.77 %
    Favored  : 90.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.25), residues: 1203
  helix:  2.53 (0.22), residues: 587
  sheet: -0.55 (0.67), residues: 55
  loop : -0.79 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 469 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A1021 
 TRP   0.005   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 9943)
  covalent geometry    : angle       0.48213 (13445)
  hydrogen bonds       : bond        0.03272 (  442)
  hydrogen bonds       : angle       4.00474 ( 1263)

*********************** 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  : 0.374 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8826 (p)
REVERT: A   98 MET cc_start: 0.9361 (tpp) cc_final: 0.9034 (tpp)
REVERT: A  277 MET cc_start: 0.8974 (mpp) cc_final: 0.8643 (mpp)
REVERT: A  415 MET cc_start: 0.7245 (mmp) cc_final: 0.6826 (mmp)
REVERT: A  437 MET cc_start: 0.9151 (mmm) cc_final: 0.8738 (mmm)
REVERT: A  512 MET cc_start: 0.8423 (ttm) cc_final: 0.7728 (tmm)
REVERT: A  517 MET cc_start: 0.7628 (mtp) cc_final: 0.7062 (mpp)
REVERT: A  584 MET cc_start: 0.8837 (ttm) cc_final: 0.8214 (tmm)
REVERT: A  638 MET cc_start: 0.8525 (mmp) cc_final: 0.8182 (mmm)
REVERT: A  755 MET cc_start: 0.8256 (mmm) cc_final: 0.7790 (mmm)
REVERT: A  962 MET cc_start: 0.8646 (tpp) cc_final: 0.8364 (ttm)
REVERT: A 1072 MET cc_start: 0.9231 (mtm) cc_final: 0.8937 (mtm)
REVERT: A 1109 MET cc_start: 0.9479 (ttm) cc_final: 0.9152 (tmm)
  outliers start: 10
  outliers final: 4
  residues processed: 44
  average time/residue: 0.0782
  time to fit residues: 5.4367
Evaluate side-chains
  41 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 36
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  705 ASP
Chi-restraints excluded: chain A residue  717 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 106 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 41 optimal weight:    0.0870
   chunk 105 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   overall best weight:    0.6560

-------------------------------------------------------------------------------
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 = 0.3278 r_free = 0.3278 target = 0.050738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.035328 restraints weight = 65468.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.036718 restraints weight = 38433.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037615 restraints weight = 28050.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038214 restraints weight = 23072.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038577 restraints weight = 20399.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.2853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2114

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= 0.091
  Angle     :  0.510  17.094  13445  Z= 0.256
  Chirality :  0.039   0.251   1444
  Planarity :  0.002   0.030   1749
  Dihedral  :  3.585  19.345   1320
  Min Nonbonded Distance : 2.631

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.15 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.25), residues: 1203
  helix:  2.54 (0.22), residues: 587
  sheet: -0.45 (0.68), residues: 55
  loop : -0.79 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 469 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A1021 
 TRP   0.006   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00194 ( 9943)
  covalent geometry    : angle       0.51039 (13445)
  hydrogen bonds       : bond        0.03224 (  442)
  hydrogen bonds       : angle       3.98799 ( 1263)

*********************** 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
  47 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 38
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8810 (p)
REVERT: A   98 MET cc_start: 0.9396 (tpp) cc_final: 0.9042 (tpp)
REVERT: A  277 MET cc_start: 0.8975 (mpp) cc_final: 0.8649 (mpp)
REVERT: A  415 MET cc_start: 0.7120 (mmp) cc_final: 0.6705 (mmp)
REVERT: A  437 MET cc_start: 0.9156 (mmm) cc_final: 0.8737 (mmm)
REVERT: A  512 MET cc_start: 0.8396 (ttm) cc_final: 0.7718 (tmm)
REVERT: A  517 MET cc_start: 0.7620 (mtp) cc_final: 0.7064 (mpp)
REVERT: A  584 MET cc_start: 0.8834 (ttm) cc_final: 0.8195 (tmm)
REVERT: A  638 MET cc_start: 0.8520 (mmp) cc_final: 0.8186 (mmm)
REVERT: A  696 TRP cc_start: 0.9416 (OUTLIER) cc_final: 0.8735 (p-90)
REVERT: A  755 MET cc_start: 0.8242 (mmm) cc_final: 0.7813 (mmm)
REVERT: A  962 MET cc_start: 0.8638 (tpp) cc_final: 0.8376 (ttm)
REVERT: A 1072 MET cc_start: 0.9225 (mtm) cc_final: 0.8936 (mtm)
REVERT: A 1093 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8940 (mp0)
REVERT: A 1109 MET cc_start: 0.9476 (ttm) cc_final: 0.9146 (tmm)
  outliers start: 9
  outliers final: 5
  residues processed: 45
  average time/residue: 0.0680
  time to fit residues: 5.0533
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  : 0.362 
-------------------------------------------------------------------------------
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  696 TRP
Chi-restraints excluded: chain A residue  705 ASP
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 83 optimal weight:    0.7980
   chunk 108 optimal weight:    0.9980
   chunk 86 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 68 optimal weight:    7.9990
   chunk 119 optimal weight:    0.8980
   chunk 80 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 39 optimal weight:    4.9990
   chunk 87 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.3277 r_free = 0.3277 target = 0.050741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.035373 restraints weight = 65163.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.036751 restraints weight = 38253.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.037643 restraints weight = 27915.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.038210 restraints weight = 23043.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.038569 restraints weight = 20472.228|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8492
moved from start:          0.2180

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9943  Z= 0.094
  Angle     :  0.502  14.836  13445  Z= 0.254
  Chirality :  0.039   0.278   1444
  Planarity :  0.002   0.031   1749
  Dihedral  :  3.561  19.502   1320
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 5.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.25 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.25), residues: 1203
  helix:  2.51 (0.22), residues: 588
  sheet: -0.41 (0.68), residues: 55
  loop : -0.79 (0.26), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 372 
 TYR   0.020   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A1021 
 TRP   0.007   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00205 ( 9943)
  covalent geometry    : angle       0.50183 (13445)
  hydrogen bonds       : bond        0.03171 (  442)
  hydrogen bonds       : angle       3.97827 ( 1263)

*********************** 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
  46 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 38
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.9159 (OUTLIER) cc_final: 0.8802 (p)
REVERT: A   98 MET cc_start: 0.9412 (tpp) cc_final: 0.9063 (tpp)
REVERT: A  277 MET cc_start: 0.8971 (mpp) cc_final: 0.8616 (mpp)
REVERT: A  415 MET cc_start: 0.7003 (mmp) cc_final: 0.6576 (mmp)
REVERT: A  437 MET cc_start: 0.9138 (mmm) cc_final: 0.8706 (mmm)
REVERT: A  512 MET cc_start: 0.8424 (ttm) cc_final: 0.7822 (tmm)
REVERT: A  517 MET cc_start: 0.7632 (mtp) cc_final: 0.7090 (mtp)
REVERT: A  584 MET cc_start: 0.8834 (ttm) cc_final: 0.8193 (tmm)
REVERT: A  638 MET cc_start: 0.8528 (mmp) cc_final: 0.8196 (mmm)
REVERT: A  696 TRP cc_start: 0.9407 (OUTLIER) cc_final: 0.8766 (p-90)
REVERT: A  755 MET cc_start: 0.8237 (mmm) cc_final: 0.7816 (mmm)
REVERT: A  962 MET cc_start: 0.8632 (tpp) cc_final: 0.8379 (ttm)
REVERT: A 1093 GLU cc_start: 0.9163 (mt-10) cc_final: 0.8820 (mp0)
REVERT: A 1109 MET cc_start: 0.9488 (ttm) cc_final: 0.9163 (tmm)
  outliers start: 8
  outliers final: 6
  residues processed: 46
  average time/residue: 0.0676
  time to fit residues: 5.0069
Evaluate side-chains
  45 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  428 THR
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  705 ASP
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 6 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 42 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
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 = 0.3272 r_free = 0.3272 target = 0.050519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2761 r_free = 0.2761 target = 0.035137 restraints weight = 65435.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.036492 restraints weight = 38575.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2837 r_free = 0.2837 target = 0.037391 restraints weight = 28332.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.037948 restraints weight = 23400.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.038198 restraints weight = 20805.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.2213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9943  Z= 0.109
  Angle     :  0.513  15.594  13445  Z= 0.260
  Chirality :  0.039   0.295   1444
  Planarity :  0.002   0.031   1749
  Dihedral  :  3.584  19.875   1320
  Min Nonbonded Distance : 2.625

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.15 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.25), residues: 1203
  helix:  2.52 (0.22), residues: 588
  sheet: -0.52 (0.63), residues: 72
  loop : -0.74 (0.26), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 372 
 TYR   0.020   0.001   TYR A  86 
 PHE   0.008   0.001   PHE A1021 
 TRP   0.007   0.001   TRP A 696 
 HIS   0.003   0.001   HIS A 318 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9943)
  covalent geometry    : angle       0.51341 (13445)
  hydrogen bonds       : bond        0.03222 (  442)
  hydrogen bonds       : angle       3.99254 ( 1263)

********************** 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
  45 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 36
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   50 VAL cc_start: 0.9161 (OUTLIER) cc_final: 0.8803 (p)
REVERT: A   98 MET cc_start: 0.9394 (tpp) cc_final: 0.9046 (tpp)
REVERT: A  277 MET cc_start: 0.8965 (mpp) cc_final: 0.8614 (mpp)
REVERT: A  415 MET cc_start: 0.7005 (mmp) cc_final: 0.6610 (mmp)
REVERT: A  437 MET cc_start: 0.9122 (mmm) cc_final: 0.8708 (mmm)
REVERT: A  512 MET cc_start: 0.8457 (ttm) cc_final: 0.7739 (tmm)
REVERT: A  517 MET cc_start: 0.7653 (mtp) cc_final: 0.7089 (mpp)
REVERT: A  584 MET cc_start: 0.8836 (ttm) cc_final: 0.8188 (tmm)
REVERT: A  638 MET cc_start: 0.8543 (mmp) cc_final: 0.8207 (mmm)
REVERT: A  696 TRP cc_start: 0.9416 (OUTLIER) cc_final: 0.8777 (p-90)
REVERT: A  755 MET cc_start: 0.8242 (mmm) cc_final: 0.7822 (mmm)
REVERT: A  962 MET cc_start: 0.8652 (tpp) cc_final: 0.8419 (ttm)
REVERT: A 1109 MET cc_start: 0.9489 (ttm) cc_final: 0.9165 (tmm)
  outliers start: 9
  outliers final: 6
  residues processed: 45
  average time/residue: 0.0697
  time to fit residues: 5.0027
Evaluate side-chains
  44 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 36
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
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  428 THR
Chi-restraints excluded: chain A residue  696 TRP
Chi-restraints excluded: chain A residue  705 ASP
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 66 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   chunk 89 optimal weight:    6.9990
   chunk 23 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 118 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0370
   chunk 17 optimal weight:    0.9980
   overall best weight:    0.9060

-------------------------------------------------------------------------------
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 = 0.3281 r_free = 0.3281 target = 0.050858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.035558 restraints weight = 64860.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.036908 restraints weight = 38188.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037800 restraints weight = 27956.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.038330 restraints weight = 23101.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.038710 restraints weight = 20604.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8495
moved from start:          0.2274

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= 0.097
  Angle     :  0.512  15.700  13445  Z= 0.263
  Chirality :  0.039   0.296   1444
  Planarity :  0.002   0.031   1749
  Dihedral  :  3.559  19.343   1320
  Min Nonbonded Distance : 2.629

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  9.25 %
    Favored  : 89.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.25), residues: 1203
  helix:  2.49 (0.22), residues: 589
  sheet: -0.39 (0.64), residues: 67
  loop : -0.73 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  65 
 TYR   0.021   0.001   TYR A  86 
 PHE   0.009   0.001   PHE A1021 
 TRP   0.007   0.001   TRP A 696 
 HIS   0.004   0.001   HIS A 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 9943)
  covalent geometry    : angle       0.51177 (13445)
  hydrogen bonds       : bond        0.03174 (  442)
  hydrogen bonds       : angle       3.95683 ( 1263)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1471.31 seconds
wall clock time: 26 minutes 9.78 seconds (1569.78 seconds total)