Starting phenix.real_space_refine
on Sun Jun  8 07:34:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7whn_32505/06_2025/7whn_32505.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      39      5.16       5
     C    5816      2.51       5
     N    1629      2.21       5
     O    1800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9284
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1170, 9284
          Classifications: {'peptide': 1170}
          Link IDs: {'PCIS': 4, 'PTRANS': 38, 'TRANS': 1127}
  Time building chain proxies: 5.83, per 1000 atoms: 0.63
  Number of scatterers: 9284
  At special positions: 0
  Unit cell: (92.394, 98.766, 210.276, 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      39     16.00
     O    1800      8.00
     N    1629      7.00
     C    5816      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2208

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 9 sheets defined
      35.3% alpha, 21.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  Creating SS restraints...
    Processing helix  chain 'A' and resid 28 through 53
    Processing helix  chain 'A' and resid 58 through 74
    Processing helix  chain 'A' and resid 86 through 97
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 306 through 338
      removed outlier: 3.910A  pdb=" N   HIS A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   SER A 338 " --> pdb=" O   SER A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 372
      removed outlier: 3.806A  pdb=" N   ARG A 353 " --> pdb=" O   ASP A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 373 through 377
    Processing helix  chain 'A' and resid 652 through 658
    Processing helix  chain 'A' and resid 682 through 688
      removed outlier: 3.688A  pdb=" N   ASN A 688 " --> pdb=" O   TYR A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 754
    Processing helix  chain 'A' and resid 756 through 772
      removed outlier: 4.306A  pdb=" N   GLY A 770 " --> pdb=" O   SER A 766 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ARG A 771 " --> pdb=" O   GLN A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 774 through 777
      removed outlier: 3.627A  pdb=" N   LEU A 777 " --> pdb=" O   ASP A 774 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 774 through 777'
    Processing helix  chain 'A' and resid 778 through 796
      removed outlier: 3.611A  pdb=" N   SER A 796 " --> pdb=" O   MET A 792 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 800 through 815
      removed outlier: 3.690A  pdb=" N   ILE A 804 " --> pdb=" O   GLU A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 820 through 835
    Processing helix  chain 'A' and resid 835 through 850
      removed outlier: 3.578A  pdb=" N   THR A 839 " --> pdb=" O   ALA A 835 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 861
      removed outlier: 4.090A  pdb=" N   GLY A 861 " --> pdb=" O   THR A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 867 through 885
    Processing helix  chain 'A' and resid 887 through 891
    Processing helix  chain 'A' and resid 897 through 901
    Processing helix  chain 'A' and resid 904 through 909
    Processing helix  chain 'A' and resid 909 through 923
      removed outlier: 3.606A  pdb=" N   PHE A 922 " --> pdb=" O   MET A 918 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 938
      removed outlier: 3.873A  pdb=" N   ARG A 938 " --> pdb=" O   ASP A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 994
    Processing helix  chain 'A' and resid 1036 through 1040
    Processing helix  chain 'A' and resid 1074 through 1087
    Processing helix  chain 'A' and resid 1094 through 1107
      removed outlier: 3.528A  pdb=" N   VAL A1106 " --> pdb=" O   ILE A1102 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   ASP A1107 " --> pdb=" O   SER A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1136
      removed outlier: 3.593A  pdb=" N   LEU A1133 " --> pdb=" O   MET A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1146
    Processing helix  chain 'A' and resid 1148 through 1161
      removed outlier: 4.119A  pdb=" N   PHE A1152 " --> pdb=" O   ASN A1148 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   VAL A1153 " --> pdb=" O   CYS A1149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1194
      removed outlier: 4.322A  pdb=" N   ALA A1174 " --> pdb=" O   ASP A1170 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 85
      removed outlier: 3.949A  pdb=" N   ASN A 105 " --> pdb=" O   GLU A 295 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   VAL A 106 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   GLU A 231 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU A 263 " --> pdb=" O   GLU A 231 " (cutoff:3.500A)
      removed outlier: 6.203A  pdb=" N   LEU A 233 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 171 through 181
      removed outlier: 6.455A  pdb=" N   ASP A 155 " --> pdb=" O   TYR A 149 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   TYR A 149 " --> pdb=" O   ASP A 155 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   GLU A 157 " --> pdb=" O   LEU A 147 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   GLN A 124 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
      removed outlier: 6.695A  pdb=" N   ARG A 125 " --> pdb=" O   ILE A 284 " (cutoff:3.500A)
      removed outlier: 4.513A  pdb=" N   ILE A 284 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   PHE A 127 " --> pdb=" O   GLU A 282 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 213 through 214
      removed outlier: 4.133A  pdb=" N   ASN A1053 " --> pdb=" O   ILE A1062 " (cutoff:3.500A)
      removed outlier: 7.073A  pdb=" N   ILE A1062 " --> pdb=" O   ASN A1053 " (cutoff:3.500A)
      removed outlier: 6.763A  pdb=" N   LEU A 300 " --> pdb=" O   ILE A1063 " (cutoff:3.500A)
      removed outlier: 8.134A  pdb=" N   ARG A1065 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214
      removed outlier: 6.731A  pdb=" N   SER A1016 " --> pdb=" O   GLU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 384
      removed outlier: 4.160A  pdb=" N   LEU A 379 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 736 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE A 394 " --> pdb=" O   LEU A 726 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   PHE A 728 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLY A 392 " --> pdb=" O   PHE A 728 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 730 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   GLY A 732 " --> pdb=" O   ASP A 388 " (cutoff:3.500A)
      removed outlier: 4.840A  pdb=" N   ASP A 388 " --> pdb=" O   GLY A 732 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 384
      removed outlier: 4.160A  pdb=" N   LEU A 379 " --> pdb=" O   TYR A 740 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ALA A 736 " --> pdb=" O   ALA A 383 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ARG A 729 " --> pdb=" O   GLU A 567 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   GLU A 567 " --> pdb=" O   ARG A 729 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   HIS A 731 " --> pdb=" O   SER A 565 " (cutoff:3.500A)
      removed outlier: 4.781A  pdb=" N   SER A 565 " --> pdb=" O   HIS A 731 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASN A 733 " --> pdb=" O   ARG A 563 " (cutoff:3.500A)
      removed outlier: 4.110A  pdb=" N   ARG A 737 " --> pdb=" O   ASP A 559 " (cutoff:3.500A)
      removed outlier: 5.747A  pdb=" N   ASP A 559 " --> pdb=" O   ARG A 737 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 407 through 408
      removed outlier: 3.613A  pdb=" N   TYR A 407 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ILE A 439 " --> pdb=" O   PHE A 676 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   LYS A 441 " --> pdb=" O   VAL A 678 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 451 through 453
      removed outlier: 3.819A  pdb=" N   PHE A 468 " --> pdb=" O   HIS A 452 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG A 467 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 4.920A  pdb=" N   GLU A 545 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 7.227A  pdb=" N   SER A 469 " --> pdb=" O   VAL A 543 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   VAL A 543 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   GLU A 545 " --> pdb=" O   ILE A 602 " (cutoff:3.500A)
      removed outlier: 6.246A  pdb=" N   ILE A 602 " --> pdb=" O   GLU A 545 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   LEU A 547 " --> pdb=" O   CYS A 600 " (cutoff:3.500A)
      removed outlier: 7.748A  pdb=" N   CYS A 600 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   GLY A 549 " --> pdb=" O   LEU A 598 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU A 598 " --> pdb=" O   GLY A 549 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 864 through 865
      removed outlier: 6.633A  pdb=" N   ASN A 864 " --> pdb=" O   GLU A1119 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    404 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.43

  Time building geometry restraints manager: 2.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2732
        1.33 -     1.45: 1440
        1.45 -     1.57: 5209
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 9455
  Sorted by residual:
  bond pdb=" CB  ASN A1030 "
       pdb=" CG  ASN A1030 "
    ideal  model  delta    sigma   weight residual
    1.516  1.472  0.044 2.50e-02 1.60e+03 3.11e+00
  bond pdb=" C   GLU A 679 "
       pdb=" N   LEU A 680 "
    ideal  model  delta    sigma   weight residual
    1.325  1.345 -0.020 1.25e-02 6.40e+03 2.67e+00
  bond pdb=" CG  GLN A1179 "
       pdb=" CD  GLN A1179 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.42e+00
  bond pdb=" CB  ASP A 182 "
       pdb=" CG  ASP A 182 "
    ideal  model  delta    sigma   weight residual
    1.516  1.477  0.039 2.50e-02 1.60e+03 2.38e+00
  bond pdb=" CB  ASP A 756 "
       pdb=" CG  ASP A 756 "
    ideal  model  delta    sigma   weight residual
    1.516  1.478  0.038 2.50e-02 1.60e+03 2.34e+00
  ... (remaining 9450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 12083
        1.59 -     3.17: 656
        3.17 -     4.76: 75
        4.76 -     6.34: 12
        6.34 -     7.93: 2
  Bond angle restraints: 12828
  Sorted by residual:
  angle pdb=" N   GLY A 815 "
        pdb=" CA  GLY A 815 "
        pdb=" C   GLY A 815 "
      ideal   model   delta    sigma   weight residual
     114.92  120.28   -5.36 1.30e+00 5.92e-01 1.70e+01
  angle pdb=" CA  LEU A 777 "
        pdb=" C   LEU A 777 "
        pdb=" N   ASN A 778 "
      ideal   model   delta    sigma   weight residual
     118.27  112.71    5.56 1.59e+00 3.96e-01 1.22e+01
  angle pdb=" C   LEU A 240 "
        pdb=" N   HIS A 241 "
        pdb=" CA  HIS A 241 "
      ideal   model   delta    sigma   weight residual
     122.21  117.99    4.22 1.48e+00 4.57e-01 8.11e+00
  angle pdb=" N   VAL A 532 "
        pdb=" CA  VAL A 532 "
        pdb=" C   VAL A 532 "
      ideal   model   delta    sigma   weight residual
     107.71  111.90   -4.19 1.58e+00 4.01e-01 7.02e+00
  angle pdb=" N   ASP A 629 "
        pdb=" CA  ASP A 629 "
        pdb=" C   ASP A 629 "
      ideal   model   delta    sigma   weight residual
     111.36  114.08   -2.72 1.09e+00 8.42e-01 6.24e+00
  ... (remaining 12823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.96: 5139
       16.96 -    33.91: 489
       33.91 -    50.86: 77
       50.86 -    67.82: 18
       67.82 -    84.77: 7
  Dihedral angle restraints: 5730
    sinusoidal: 2307
      harmonic: 3423
  Sorted by residual:
  dihedral pdb=" CA  ILE A 730 "
           pdb=" C   ILE A 730 "
           pdb=" N   HIS A 731 "
           pdb=" CA  HIS A 731 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.63   23.37     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  GLN A 755 "
           pdb=" C   GLN A 755 "
           pdb=" N   ASP A 756 "
           pdb=" CA  ASP A 756 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.28  -20.72     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  HIS A 136 "
           pdb=" C   HIS A 136 "
           pdb=" N   PHE A 137 "
           pdb=" CA  PHE A 137 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.34  -19.66     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 5727 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 831
       0.040 -    0.081: 448
       0.081 -    0.121: 151
       0.121 -    0.162: 32
       0.162 -    0.202: 2
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CB  THR A1007 "
            pdb=" CA  THR A1007 "
            pdb=" OG1 THR A1007 "
            pdb=" CG2 THR A1007 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.35    0.20 2.00e-01 2.50e+01 1.02e+00
  chirality pdb=" CG  LEU A 240 "
            pdb=" CB  LEU A 240 "
            pdb=" CD1 LEU A 240 "
            pdb=" CD2 LEU A 240 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.76e-01
  chirality pdb=" CB  ILE A1063 "
            pdb=" CA  ILE A1063 "
            pdb=" CG1 ILE A1063 "
            pdb=" CG2 ILE A1063 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.16e-01
  ... (remaining 1461 not shown)

  Planarity restraints: 1674
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 952 "   -0.053 5.00e-02 4.00e+02   8.08e-02 1.04e+01
        pdb=" N   PRO A 953 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 953 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 953 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 234 "   -0.011 2.00e-02 2.50e+03   1.26e-02 3.19e+00
        pdb=" CG  TYR A 234 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 234 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 234 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 234 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 234 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 234 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 234 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 600 "    0.029 5.00e-02 4.00e+02   4.42e-02 3.13e+00
        pdb=" N   PRO A 601 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 601 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 601 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1671 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 280
        2.70 -     3.25: 8660
        3.25 -     3.80: 13899
        3.80 -     4.35: 17952
        4.35 -     4.90: 30950
  Nonbonded interactions: 71741
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 176 "
            pdb=" OG  SER A 237 "
     model   vdw
     2.147 3.040
  nonbonded pdb=" O   SER A 614 "
            pdb=" NH2 ARG A 698 "
     model   vdw
     2.207 3.120
  nonbonded pdb=" O   ILE A 546 "
            pdb=" OG1 THR A 599 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" NE2 GLN A  94 "
            pdb=" O   LEU A 276 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" O   ARG A 721 "
            pdb=" N   THR A 725 "
     model   vdw
     2.270 3.120
  ... (remaining 71736 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 individual isotropic
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:             2.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.330
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
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      :  0.009   0.057   9455  Z= 0.368
  Angle     :  0.800   7.926  12828  Z= 0.470
  Chirality :  0.053   0.202   1464
  Planarity :  0.005   0.081   1674
  Dihedral  : 13.811  84.774   3522
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.54 %
    Favored  : 95.46 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.10 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.22), residues: 1168
  helix:  0.45 (0.26), residues: 373
  sheet: -0.68 (0.32), residues: 241
  loop : -1.87 (0.22), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A1099 
 HIS   0.007   0.002   HIS A 317 
 PHE   0.027   0.003   PHE A1140 
 TYR   0.031   0.003   TYR A 234 
 ARG   0.014   0.001   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18674 (  399)
  hydrogen bonds       : angle       7.32140 ( 1164)
  covalent geometry    : bond        0.00877 ( 9455)
  covalent geometry    : angle       0.80034 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 1.089 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8279 (t0) cc_final: 0.7943 (t0)
REVERT: A  763 ASP cc_start: 0.7673 (m-30) cc_final: 0.6880 (m-30)
REVERT: A  768 GLU cc_start: 0.8162 (tp30) cc_final: 0.7191 (mt-10)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.2881
  time to fit residues: 39.9364
Evaluate side-chains
  94 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 88 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 59 optimal weight:   20.0000
   chunk 47 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   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 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A 993 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1167 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.185638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.125445 restraints weight = 10194.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.79
r_work: 0.2975 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9455  Z= 0.126
  Angle     :  0.522   5.910  12828  Z= 0.283
  Chirality :  0.044   0.148   1464
  Planarity :  0.004   0.063   1674
  Dihedral  :  4.889  17.811   1298
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.20 %
    Favored  : 94.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1168
  helix:  1.56 (0.27), residues: 377
  sheet: -0.36 (0.34), residues: 210
  loop : -1.60 (0.22), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 317 
 PHE   0.014   0.001   PHE A 128 
 TYR   0.016   0.001   TYR A1050 
 ARG   0.004   0.000   ARG A 381 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04792 (  399)
  hydrogen bonds       : angle       5.16543 ( 1164)
  covalent geometry    : bond        0.00284 ( 9455)
  covalent geometry    : angle       0.52188 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 113
  time to evaluate  : 1.148 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8206 (t0) cc_final: 0.7984 (t70)
REVERT: A  282 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7934 (mm-30)
REVERT: A  763 ASP cc_start: 0.8031 (m-30) cc_final: 0.7243 (m-30)
REVERT: A  872 SER cc_start: 0.9036 (t) cc_final: 0.8674 (p)
  outliers start: 3
  outliers final: 3
  residues processed: 113
  average time/residue: 0.2646
  time to fit residues: 40.8104
Evaluate side-chains
  107 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  934 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 99 optimal weight:    4.9990
   chunk 109 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    6.9990
   chunk 68 optimal weight:   20.0000
   chunk 60 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 HIS
A 767 GLN
A 993 ASN
** A1030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1139 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.183441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.123700 restraints weight = 10373.299|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 1.88
r_work: 0.2940 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2829 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.1168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9455  Z= 0.176
  Angle     :  0.538   5.767  12828  Z= 0.289
  Chirality :  0.045   0.145   1464
  Planarity :  0.004   0.058   1674
  Dihedral  :  4.808  17.155   1298
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  7.31 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.24), residues: 1168
  helix:  1.59 (0.27), residues: 383
  sheet: -0.29 (0.32), residues: 239
  loop : -1.53 (0.24), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A1099 
 HIS   0.005   0.001   HIS A 317 
 PHE   0.017   0.002   PHE A1003 
 TYR   0.015   0.002   TYR A 234 
 ARG   0.003   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05014 (  399)
  hydrogen bonds       : angle       4.93153 ( 1164)
  covalent geometry    : bond        0.00426 ( 9455)
  covalent geometry    : angle       0.53750 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8175 (t0) cc_final: 0.7909 (t70)
REVERT: A  651 MET cc_start: 0.0725 (mpp) cc_final: -0.0347 (tpt)
REVERT: A  763 ASP cc_start: 0.8027 (m-30) cc_final: 0.7193 (m-30)
REVERT: A  872 SER cc_start: 0.9100 (t) cc_final: 0.8685 (p)
  outliers start: 11
  outliers final: 6
  residues processed: 109
  average time/residue: 0.2654
  time to fit residues: 39.2807
Evaluate side-chains
  107 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1122 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0770
   chunk 116 optimal weight:    6.9990
   chunk 52 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 80 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 65 optimal weight:    9.9990
   overall best weight:    1.7942

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.184941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.124232 restraints weight = 10271.924|
|-----------------------------------------------------------------------------|
r_work (start): 0.3206 rms_B_bonded: 1.84
r_work: 0.2958 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1441

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9455  Z= 0.135
  Angle     :  0.488   5.653  12828  Z= 0.263
  Chirality :  0.043   0.143   1464
  Planarity :  0.004   0.055   1674
  Dihedral  :  4.526  15.570   1298
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 4.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  9.34 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.24), residues: 1168
  helix:  1.87 (0.27), residues: 382
  sheet: -0.04 (0.33), residues: 220
  loop : -1.40 (0.23), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.015   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A1050 
 ARG   0.005   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04399 (  399)
  hydrogen bonds       : angle       4.64062 ( 1164)
  covalent geometry    : bond        0.00321 ( 9455)
  covalent geometry    : angle       0.48806 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 1.013 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8103 (t0) cc_final: 0.7719 (t0)
REVERT: A  569 MET cc_start: 0.2509 (mtm) cc_final: 0.2286 (mtt)
REVERT: A  651 MET cc_start: 0.0423 (mpp) cc_final: -0.0436 (tpt)
REVERT: A  763 ASP cc_start: 0.8014 (m-30) cc_final: 0.7217 (m-30)
REVERT: A  872 SER cc_start: 0.9037 (t) cc_final: 0.8682 (p)
REVERT: A 1005 THR cc_start: 0.9086 (m) cc_final: 0.8720 (p)
  outliers start: 14
  outliers final: 8
  residues processed: 117
  average time/residue: 0.2548
  time to fit residues: 40.5941
Evaluate side-chains
  120 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  934 ASP
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1122 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0670
   chunk 57 optimal weight:    6.9990
   chunk 63 optimal weight:   20.0000
   chunk 34 optimal weight:    0.5980
   chunk 66 optimal weight:    5.9990
   chunk 100 optimal weight:    0.2980
   chunk 83 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    1.7922

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.185086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.125366 restraints weight = 10287.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 1.79
r_work: 0.2974 rms_B_bonded: 1.83 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.08 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9455  Z= 0.135
  Angle     :  0.484   5.628  12828  Z= 0.259
  Chirality :  0.043   0.142   1464
  Planarity :  0.004   0.053   1674
  Dihedral  :  4.400  14.677   1298
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  :  9.53 %
    Favored  : 88.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.24), residues: 1168
  helix:  2.11 (0.27), residues: 376
  sheet:  0.08 (0.34), residues: 220
  loop : -1.27 (0.24), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.016   0.001   PHE A1003 
 TYR   0.015   0.001   TYR A1050 
 ARG   0.005   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04307 (  399)
  hydrogen bonds       : angle       4.51434 ( 1164)
  covalent geometry    : bond        0.00321 ( 9455)
  covalent geometry    : angle       0.48374 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 114
  time to evaluate  : 1.091 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8097 (t0) cc_final: 0.7704 (t0)
REVERT: A  283 ASP cc_start: 0.8832 (t70) cc_final: 0.8529 (t0)
REVERT: A  651 MET cc_start: 0.0287 (mpp) cc_final: -0.0297 (tpt)
REVERT: A  754 HIS cc_start: 0.8988 (OUTLIER) cc_final: 0.8203 (p90)
REVERT: A  763 ASP cc_start: 0.7990 (m-30) cc_final: 0.7182 (m-30)
REVERT: A  866 SER cc_start: 0.8530 (t) cc_final: 0.8295 (m)
REVERT: A  872 SER cc_start: 0.9053 (t) cc_final: 0.8688 (p)
REVERT: A 1005 THR cc_start: 0.9075 (m) cc_final: 0.8710 (p)
  outliers start: 19
  outliers final: 9
  residues processed: 123
  average time/residue: 0.2578
  time to fit residues: 43.3226
Evaluate side-chains
  123 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  934 ASP
Chi-restraints excluded: chain A residue 1117 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 3 optimal weight:    5.9990
   chunk 12 optimal weight:    7.9990
   chunk 7 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 54 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 97 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.186215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.125427 restraints weight = 10263.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.79
r_work: 0.2974 rms_B_bonded: 1.99 restraints_weight: 0.5000
r_work: 0.2866 rms_B_bonded: 3.36 restraints_weight: 0.2500
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9455  Z= 0.111
  Angle     :  0.459   5.548  12828  Z= 0.246
  Chirality :  0.042   0.139   1464
  Planarity :  0.004   0.051   1674
  Dihedral  :  4.228  14.111   1298
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 4.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.97 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.24), residues: 1168
  helix:  2.36 (0.27), residues: 373
  sheet: -0.07 (0.33), residues: 233
  loop : -1.09 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.015   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A1050 
 ARG   0.005   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  399)
  hydrogen bonds       : angle       4.36287 ( 1164)
  covalent geometry    : bond        0.00259 ( 9455)
  covalent geometry    : angle       0.45910 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  182 ASP cc_start: 0.8062 (t0) cc_final: 0.7673 (t0)
REVERT: A  207 ASP cc_start: 0.7774 (t0) cc_final: 0.7493 (t70)
REVERT: A  283 ASP cc_start: 0.8843 (t70) cc_final: 0.8545 (t0)
REVERT: A  651 MET cc_start: 0.0200 (mpp) cc_final: -0.0350 (tpt)
REVERT: A  754 HIS cc_start: 0.8978 (OUTLIER) cc_final: 0.8226 (p90)
REVERT: A  763 ASP cc_start: 0.7946 (m-30) cc_final: 0.7220 (m-30)
REVERT: A  872 SER cc_start: 0.9027 (t) cc_final: 0.8694 (p)
REVERT: A 1005 THR cc_start: 0.9087 (m) cc_final: 0.8737 (p)
REVERT: A 1039 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7910 (mtpt)
  outliers start: 13
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2569
  time to fit residues: 39.3193
Evaluate side-chains
  116 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 108
  time to evaluate  : 1.013 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1117 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 68 optimal weight:    9.9990
   chunk 54 optimal weight:    0.0870
   chunk 67 optimal weight:    7.9990
   chunk 37 optimal weight:   40.0000
   chunk 98 optimal weight:    6.9990
   chunk 30 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.7962

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

Flipped N/Q/H residues before XYZ refinement:
A 138 GLN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.188392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.127796 restraints weight = 10357.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 1.87
r_work: 0.3002 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.2892 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9455  Z= 0.088
  Angle     :  0.431   5.489  12828  Z= 0.231
  Chirality :  0.042   0.301   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  3.984  13.784   1298
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.03 %
    Favored  : 87.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.63 (0.25), residues: 1168
  helix:  2.60 (0.27), residues: 373
  sheet: -0.17 (0.33), residues: 238
  loop : -0.85 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1099 
 HIS   0.003   0.000   HIS A 317 
 PHE   0.013   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A1050 
 ARG   0.006   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03495 (  399)
  hydrogen bonds       : angle       4.19371 ( 1164)
  covalent geometry    : bond        0.00196 ( 9455)
  covalent geometry    : angle       0.43133 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8184 (mt-10)
REVERT: A  182 ASP cc_start: 0.7986 (t0) cc_final: 0.7608 (t0)
REVERT: A  207 ASP cc_start: 0.7710 (t0) cc_final: 0.7445 (t70)
REVERT: A  219 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7395 (mmt180)
REVERT: A  283 ASP cc_start: 0.8867 (t70) cc_final: 0.8590 (t0)
REVERT: A  651 MET cc_start: 0.0042 (mpp) cc_final: -0.0522 (tpt)
REVERT: A  754 HIS cc_start: 0.8956 (OUTLIER) cc_final: 0.8276 (p90)
REVERT: A  872 SER cc_start: 0.9001 (t) cc_final: 0.8737 (p)
REVERT: A 1005 THR cc_start: 0.9032 (m) cc_final: 0.8761 (p)
REVERT: A 1039 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7845 (mtpt)
  outliers start: 10
  outliers final: 3
  residues processed: 122
  average time/residue: 0.2473
  time to fit residues: 41.2384
Evaluate side-chains
  111 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 107
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  754 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 22 optimal weight:    6.9990
   chunk 36 optimal weight:    8.9990
   chunk 79 optimal weight:    4.9990
   chunk 52 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.184970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.125437 restraints weight = 10448.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.82
r_work: 0.2973 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9455  Z= 0.151
  Angle     :  0.485   6.429  12828  Z= 0.258
  Chirality :  0.044   0.222   1464
  Planarity :  0.004   0.050   1674
  Dihedral  :  4.209  14.033   1298
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 11.84 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1168
  helix:  2.39 (0.27), residues: 374
  sheet: -0.02 (0.34), residues: 227
  loop : -0.95 (0.24), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A1099 
 HIS   0.006   0.001   HIS A 317 
 PHE   0.017   0.001   PHE A1003 
 TYR   0.014   0.001   TYR A1050 
 ARG   0.004   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  399)
  hydrogen bonds       : angle       4.34332 ( 1164)
  covalent geometry    : bond        0.00365 ( 9455)
  covalent geometry    : angle       0.48460 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 1.010 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8210 (mt-10)
REVERT: A  182 ASP cc_start: 0.8095 (t0) cc_final: 0.7728 (t0)
REVERT: A  207 ASP cc_start: 0.7745 (t0) cc_final: 0.7467 (t0)
REVERT: A  283 ASP cc_start: 0.8807 (t70) cc_final: 0.8494 (t0)
REVERT: A  651 MET cc_start: 0.0051 (mpp) cc_final: -0.0381 (tpt)
REVERT: A  754 HIS cc_start: 0.8981 (OUTLIER) cc_final: 0.8243 (p90)
REVERT: A  763 ASP cc_start: 0.7941 (m-30) cc_final: 0.7206 (m-30)
REVERT: A  866 SER cc_start: 0.8517 (t) cc_final: 0.8286 (m)
REVERT: A  872 SER cc_start: 0.9063 (t) cc_final: 0.8693 (p)
REVERT: A 1005 THR cc_start: 0.9109 (m) cc_final: 0.8752 (p)
REVERT: A 1039 LYS cc_start: 0.8166 (mtpt) cc_final: 0.7934 (mtpt)
  outliers start: 13
  outliers final: 10
  residues processed: 113
  average time/residue: 0.2568
  time to fit residues: 39.6094
Evaluate side-chains
  119 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  367 MET
Chi-restraints excluded: chain A residue  377 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1117 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 92 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9980
   chunk 72 optimal weight:    5.9990
   chunk 95 optimal weight:    0.3980
   chunk 84 optimal weight:    0.6980
   chunk 101 optimal weight:    5.9990
   chunk 108 optimal weight:    6.9990
   chunk 46 optimal weight:    0.0670
   chunk 110 optimal weight:    1.9990
   chunk 11 optimal weight:    4.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.188652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.128506 restraints weight = 10241.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 1.79
r_work: 0.3016 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.2907 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.2197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9455  Z= 0.084
  Angle     :  0.432   6.617  12828  Z= 0.229
  Chirality :  0.042   0.219   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  3.899  13.489   1298
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.61 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1168
  helix:  2.70 (0.27), residues: 373
  sheet: -0.07 (0.34), residues: 238
  loop : -0.76 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1099 
 HIS   0.003   0.001   HIS A 317 
 PHE   0.013   0.001   PHE A 128 
 TYR   0.013   0.001   TYR A1050 
 ARG   0.007   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03409 (  399)
  hydrogen bonds       : angle       4.13117 ( 1164)
  covalent geometry    : bond        0.00186 ( 9455)
  covalent geometry    : angle       0.43170 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 108
  time to evaluate  : 1.127 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8171 (mt-10)
REVERT: A  182 ASP cc_start: 0.7940 (t0) cc_final: 0.7561 (t0)
REVERT: A  207 ASP cc_start: 0.7731 (t0) cc_final: 0.7471 (t0)
REVERT: A  219 ARG cc_start: 0.8091 (mtm110) cc_final: 0.7409 (mmt180)
REVERT: A  283 ASP cc_start: 0.8872 (t70) cc_final: 0.8619 (t0)
REVERT: A  651 MET cc_start: 0.0016 (mpp) cc_final: -0.0547 (tpt)
REVERT: A  754 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8258 (p90)
REVERT: A  763 ASP cc_start: 0.7949 (m-30) cc_final: 0.7244 (m-30)
REVERT: A  872 SER cc_start: 0.8953 (t) cc_final: 0.8696 (p)
REVERT: A 1005 THR cc_start: 0.9039 (m) cc_final: 0.8772 (p)
REVERT: A 1039 LYS cc_start: 0.8102 (mtpt) cc_final: 0.7859 (mtpt)
  outliers start: 10
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2937
  time to fit residues: 46.2759
Evaluate side-chains
  115 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   chunk 85 optimal weight:    1.9990
   chunk 104 optimal weight:    8.9990
   chunk 113 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 17 optimal weight:    8.9990
   chunk 69 optimal weight:    0.0570
   chunk 0 optimal weight:   10.0000
   chunk 66 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    3.4106

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

Flipped N/Q/H residues before XYZ refinement:
** A1030 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 = 0.3895 r_free = 0.3895 target = 0.182913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.122704 restraints weight = 10456.974|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 1.89
r_work: 0.2933 rms_B_bonded: 1.94 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 3.27 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   9455  Z= 0.218
  Angle     :  0.550   8.021  12828  Z= 0.291
  Chirality :  0.046   0.213   1464
  Planarity :  0.004   0.050   1674
  Dihedral  :  4.454  16.143   1298
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.61 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.24), residues: 1168
  helix:  2.17 (0.27), residues: 374
  sheet:  0.08 (0.34), residues: 219
  loop : -1.05 (0.24), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1099 
 HIS   0.008   0.001   HIS A 317 
 PHE   0.020   0.002   PHE A1003 
 TYR   0.016   0.002   TYR A1125 
 ARG   0.007   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05146 (  399)
  hydrogen bonds       : angle       4.49151 ( 1164)
  covalent geometry    : bond        0.00535 ( 9455)
  covalent geometry    : angle       0.54989 (12828)

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

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

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2336 Ramachandran restraints generated.
    1168 Oldfield, 0 Emsley, 1168 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A   89 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8231 (mt-10)
REVERT: A  150 ASP cc_start: 0.7797 (t70) cc_final: 0.7434 (t0)
REVERT: A  182 ASP cc_start: 0.8167 (t0) cc_final: 0.7759 (t0)
REVERT: A  207 ASP cc_start: 0.7806 (t0) cc_final: 0.7512 (t0)
REVERT: A  651 MET cc_start: 0.0014 (mpp) cc_final: -0.0431 (tpt)
REVERT: A  754 HIS cc_start: 0.9005 (OUTLIER) cc_final: 0.8308 (p90)
REVERT: A  763 ASP cc_start: 0.7970 (m-30) cc_final: 0.7163 (m-30)
REVERT: A  768 GLU cc_start: 0.8320 (tp30) cc_final: 0.6744 (mt-10)
REVERT: A  866 SER cc_start: 0.8640 (t) cc_final: 0.8387 (m)
  outliers start: 11
  outliers final: 9
  residues processed: 114
  average time/residue: 0.3063
  time to fit residues: 48.2070
Evaluate side-chains
  120 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.018 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ILE
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  609 VAL
Chi-restraints excluded: chain A residue  685 MET
Chi-restraints excluded: chain A residue  704 VAL
Chi-restraints excluded: chain A residue  754 HIS
Chi-restraints excluded: chain A residue  971 GLU
Chi-restraints excluded: chain A residue 1058 ASP
Chi-restraints excluded: chain A residue 1117 SER
Chi-restraints excluded: chain A residue 1153 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 44 optimal weight:    6.9990
   chunk 65 optimal weight:   20.0000
   chunk 115 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 94 optimal weight:    6.9990
   chunk 93 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 438 ASN
** A 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 767 GLN
** A1040 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 = 0.3940 r_free = 0.3940 target = 0.187445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.128431 restraints weight = 10384.857|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 1.90
r_work: 0.3001 rms_B_bonded: 1.93 restraints_weight: 0.5000
r_work: 0.2894 rms_B_bonded: 3.26 restraints_weight: 0.2500
r_work (final): 0.2894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9455  Z= 0.094
  Angle     :  0.444   6.290  12828  Z= 0.236
  Chirality :  0.042   0.208   1464
  Planarity :  0.003   0.049   1674
  Dihedral  :  4.026  14.820   1298
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.80 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.25), residues: 1168
  helix:  2.58 (0.27), residues: 373
  sheet: -0.09 (0.34), residues: 238
  loop : -0.77 (0.25), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1099 
 HIS   0.004   0.001   HIS A 317 
 PHE   0.014   0.001   PHE A 128 
 TYR   0.012   0.001   TYR A1050 
 ARG   0.007   0.000   ARG A 219 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  399)
  hydrogen bonds       : angle       4.20572 ( 1164)
  covalent geometry    : bond        0.00213 ( 9455)
  covalent geometry    : angle       0.44379 (12828)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6250.70 seconds
wall clock time: 108 minutes 20.64 seconds (6500.64 seconds total)