Starting phenix.real_space_refine
on Tue Jun 10 00:09:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j7a_61199/06_2025/9j7a_61199.cif"
  }
  resolution = 4.13
  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=   0.009
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      62      5.16       5
     C    6939      2.51       5
     N    1954      2.21       5
     O    2081      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11036
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4932
          Classifications: {'peptide': 627}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611}
    Chain: "B"
      Number of atoms: 572
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 572
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 6, 'TRANS': 66}
    Chain: "C"
      Number of atoms: 490
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 62, 490
          Classifications: {'peptide': 62}
          Link IDs: {'PTRANS': 5, 'TRANS': 56}
    Chain: "F"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 55
          Classifications: {'peptide': 11}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'TRANS': 10}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'UNK:plan-1': 11}
          Unresolved non-hydrogen planarities: 11
    Chain: "D"
      Number of atoms: 4932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 627, 4932
          Classifications: {'peptide': 627}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 611}
    Chain: "E"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 55
          Classifications: {'peptide': 11}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'TRANS': 10}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'UNK:plan-1': 11}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 12.64, per 1000 atoms: 1.15
  Number of scatterers: 11036
  At special positions: 0
  Unit cell: (116.44, 127.1, 158.26, 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      62     16.00
     O    2081      8.00
     N    1954      7.00
     C    6939      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: 2.86
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2678

  Finding SS restraints...
    Secondary structure from input PDB file:
      81 helices and 1 sheets defined
      71.6% alpha, 0.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 14
    Processing helix  chain 'A' and resid 16 through 23
    Processing helix  chain 'A' and resid 28 through 37
    Processing helix  chain 'A' and resid 41 through 45
    Processing helix  chain 'A' and resid 48 through 57
      removed outlier: 3.851A  pdb=" N   GLY A  57 " --> pdb=" O   ALA A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 67
    Processing helix  chain 'A' and resid 90 through 99
    Processing helix  chain 'A' and resid 100 through 111
      removed outlier: 3.641A  pdb=" N   GLY A 111 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 132
    Processing helix  chain 'A' and resid 133 through 143
    Processing helix  chain 'A' and resid 156 through 164
      removed outlier: 3.558A  pdb=" N   LYS A 164 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 176
    Processing helix  chain 'A' and resid 199 through 209
    Processing helix  chain 'A' and resid 221 through 229
    Processing helix  chain 'A' and resid 231 through 240
    Processing helix  chain 'A' and resid 245 through 262
      removed outlier: 3.614A  pdb=" N   ARG A 249 " --> pdb=" O   ASP A 245 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ASN A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 284
    Processing helix  chain 'A' and resid 299 through 303
    Processing helix  chain 'A' and resid 310 through 317
    Processing helix  chain 'A' and resid 320 through 337
    Processing helix  chain 'A' and resid 340 through 342
      No H-bonds generated for 'chain 'A' and resid 340 through 342'
    Processing helix  chain 'A' and resid 343 through 357
      removed outlier: 4.382A  pdb=" N   ILE A 347 " --> pdb=" O   VAL A 343 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   ILE A 348 " --> pdb=" O   SER A 344 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   TYR A 349 " --> pdb=" O   HIS A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 377
      removed outlier: 3.531A  pdb=" N   CYS A 363 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A 365 " --> pdb=" O   GLU A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 398
    Processing helix  chain 'A' and resid 403 through 428
    Processing helix  chain 'A' and resid 432 through 456
    Processing helix  chain 'A' and resid 461 through 478
    Processing helix  chain 'A' and resid 486 through 493
    Processing helix  chain 'A' and resid 501 through 506
    Processing helix  chain 'A' and resid 511 through 521
    Processing helix  chain 'A' and resid 534 through 540
    Processing helix  chain 'A' and resid 545 through 547
      No H-bonds generated for 'chain 'A' and resid 545 through 547'
    Processing helix  chain 'A' and resid 548 through 562
    Processing helix  chain 'A' and resid 582 through 593
    Processing helix  chain 'A' and resid 596 through 608
      removed outlier: 4.399A  pdb=" N   ALA A 602 " --> pdb=" O   LYS A 598 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   ALA A 607 " --> pdb=" O   ARG A 603 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ASN A 608 " --> pdb=" O   ALA A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 627
    Processing helix  chain 'B' and resid 63 through 84
      removed outlier: 3.682A  pdb=" N   GLN B  67 " --> pdb=" O   ALA B  63 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   PHE B  70 " --> pdb=" O   VAL B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 85 through 101
      removed outlier: 3.677A  pdb=" N   GLY B  89 " --> pdb=" O   GLU B  85 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLY B 101 " --> pdb=" O   ILE B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 110
      removed outlier: 3.609A  pdb=" N   GLN B 108 " --> pdb=" O   GLN B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 113
      No H-bonds generated for 'chain 'B' and resid 111 through 113'
    Processing helix  chain 'B' and resid 115 through 125
    Processing helix  chain 'C' and resid 68 through 83
      removed outlier: 3.585A  pdb=" N   ILE C  74 " --> pdb=" O   PHE C  70 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   LEU C  81 " --> pdb=" O   GLY C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 85 through 100
      removed outlier: 3.926A  pdb=" N   ASN C  95 " --> pdb=" O   ASP C  91 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   ALA C  96 " --> pdb=" O   HIS C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 4.181A  pdb=" N   GLN C 108 " --> pdb=" O   GLN C 104 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   VAL C 109 " --> pdb=" O   GLN C 105 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   GLN C 112 " --> pdb=" O   GLN C 108 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   THR C 113 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   LEU C 114 " --> pdb=" O   LEU C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 126
      removed outlier: 3.618A  pdb=" N   MET C 121 " --> pdb=" O   PRO C 117 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LYS C 125 " --> pdb=" O   MET C 121 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   LEU C 126 " --> pdb=" O   LEU C 122 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3 through 11
      removed outlier: 3.665A  pdb=" N   UNK F   9 " --> pdb=" O   UNK F   5 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   UNK F  10 " --> pdb=" O   UNK F   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 14
    Processing helix  chain 'D' and resid 16 through 26
      removed outlier: 4.043A  pdb=" N   LEU D  20 " --> pdb=" O   LYS D  16 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ASN D  26 " --> pdb=" O   ALA D  22 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 36
    Processing helix  chain 'D' and resid 48 through 57
    Processing helix  chain 'D' and resid 58 through 69
      removed outlier: 3.796A  pdb=" N   VAL D  62 " --> pdb=" O   HIS D  58 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 99
    Processing helix  chain 'D' and resid 100 through 111
      removed outlier: 3.512A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 132
    Processing helix  chain 'D' and resid 133 through 143
    Processing helix  chain 'D' and resid 156 through 164
      removed outlier: 3.504A  pdb=" N   ILE D 160 " --> pdb=" O   THR D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 166 through 176
    Processing helix  chain 'D' and resid 189 through 198
    Processing helix  chain 'D' and resid 199 through 209
    Processing helix  chain 'D' and resid 221 through 229
    Processing helix  chain 'D' and resid 231 through 240
      removed outlier: 4.053A  pdb=" N   VAL D 235 " --> pdb=" O   LYS D 231 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   GLU D 236 " --> pdb=" O   ALA D 232 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 245 through 262
      removed outlier: 3.552A  pdb=" N   GLU D 251 " --> pdb=" O   ARG D 247 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ASN D 262 " --> pdb=" O   ALA D 258 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 268 through 285
    Processing helix  chain 'D' and resid 299 through 303
      removed outlier: 3.540A  pdb=" N   GLY D 303 " --> pdb=" O   HIS D 300 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 310 through 317
      removed outlier: 4.035A  pdb=" N   LEU D 314 " --> pdb=" O   ASN D 310 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 320 through 337
    Processing helix  chain 'D' and resid 344 through 357
    Processing helix  chain 'D' and resid 359 through 377
    Processing helix  chain 'D' and resid 381 through 398
      removed outlier: 3.567A  pdb=" N   LEU D 385 " --> pdb=" O   THR D 381 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 403 through 428
    Processing helix  chain 'D' and resid 432 through 457
    Processing helix  chain 'D' and resid 460 through 478
    Processing helix  chain 'D' and resid 486 through 493
    Processing helix  chain 'D' and resid 502 through 507
      removed outlier: 3.849A  pdb=" N   VAL D 506 " --> pdb=" O   HIS D 502 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 511 through 522
    Processing helix  chain 'D' and resid 534 through 541
      removed outlier: 3.666A  pdb=" N   ILE D 539 " --> pdb=" O   ALA D 535 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   GLN D 541 " --> pdb=" O   HIS D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 548 through 563
    Processing helix  chain 'D' and resid 582 through 593
      removed outlier: 3.665A  pdb=" N   GLU D 586 " --> pdb=" O   THR D 582 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   GLN D 592 " --> pdb=" O   LEU D 588 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 596 through 608
      removed outlier: 3.610A  pdb=" N   ARG D 606 " --> pdb=" O   ALA D 602 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 617 through 627
      removed outlier: 3.672A  pdb=" N   HIS D 627 " --> pdb=" O   PHE D 623 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 2 through 10
    Processing sheet with id=AA1, first strand: chain 'D' and resid 77 through 81
      removed outlier: 6.260A  pdb=" N   GLY D  77 " --> pdb=" O   GLY D  88 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY D  88 " --> pdb=" O   GLY D  77 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL D  79 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)

    630 hydrogen bonds defined for protein.
    1863 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: 3.22

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3769
        1.34 -     1.46: 2077
        1.46 -     1.58: 5291
        1.58 -     1.70: 0
        1.70 -     1.81: 88
  Bond restraints: 11225
  Sorted by residual:
  bond pdb=" C   PRO B 116 "
       pdb=" N   PRO B 117 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.019 1.28e-02 6.10e+03 2.10e+00
  bond pdb=" C   PRO C 116 "
       pdb=" N   PRO C 117 "
    ideal  model  delta    sigma   weight residual
    1.335  1.350 -0.014 1.36e-02 5.41e+03 1.14e+00
  bond pdb=" N   ARG A  80 "
       pdb=" CA  ARG A  80 "
    ideal  model  delta    sigma   weight residual
    1.462  1.477 -0.015 1.54e-02 4.22e+03 9.01e-01
  bond pdb=" CA  THR B 113 "
       pdb=" C   THR B 113 "
    ideal  model  delta    sigma   weight residual
    1.522  1.536 -0.014 1.52e-02 4.33e+03 8.93e-01
  bond pdb=" CG  LEU A 519 "
       pdb=" CD2 LEU A 519 "
    ideal  model  delta    sigma   weight residual
    1.521  1.491  0.030 3.30e-02 9.18e+02 8.31e-01
  ... (remaining 11220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 14976
        2.15 -     4.29: 193
        4.29 -     6.44: 43
        6.44 -     8.59: 10
        8.59 -    10.74: 2
  Bond angle restraints: 15224
  Sorted by residual:
  angle pdb=" N   SER A  40 "
        pdb=" CA  SER A  40 "
        pdb=" C   SER A  40 "
      ideal   model   delta    sigma   weight residual
     111.90  117.23   -5.33 1.32e+00 5.74e-01 1.63e+01
  angle pdb=" N   ARG D 309 "
        pdb=" CA  ARG D 309 "
        pdb=" C   ARG D 309 "
      ideal   model   delta    sigma   weight residual
     114.56  109.46    5.10 1.27e+00 6.20e-01 1.61e+01
  angle pdb=" C   LEU A  65 "
        pdb=" N   LEU A  66 "
        pdb=" CA  LEU A  66 "
      ideal   model   delta    sigma   weight residual
     121.98  116.76    5.22 1.53e+00 4.27e-01 1.16e+01
  angle pdb=" N   PRO B 116 "
        pdb=" CA  PRO B 116 "
        pdb=" C   PRO B 116 "
      ideal   model   delta    sigma   weight residual
     110.70  114.49   -3.79 1.22e+00 6.72e-01 9.66e+00
  angle pdb=" CA  LEU A 519 "
        pdb=" CB  LEU A 519 "
        pdb=" CG  LEU A 519 "
      ideal   model   delta    sigma   weight residual
     116.30  127.04  -10.74 3.50e+00 8.16e-02 9.41e+00
  ... (remaining 15219 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.14: 6045
       17.14 -    34.27: 594
       34.27 -    51.41: 128
       51.41 -    68.55: 25
       68.55 -    85.68: 14
  Dihedral angle restraints: 6806
    sinusoidal: 2675
      harmonic: 4131
  Sorted by residual:
  dihedral pdb=" CA  VAL A  39 "
           pdb=" C   VAL A  39 "
           pdb=" N   SER A  40 "
           pdb=" CA  SER A  40 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.69   23.31     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  LYS A 598 "
           pdb=" C   LYS A 598 "
           pdb=" N   CYS A 599 "
           pdb=" CA  CYS A 599 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.64   18.36     0      5.00e+00 4.00e-02 1.35e+01
  dihedral pdb=" CG  ARG D  55 "
           pdb=" CD  ARG D  55 "
           pdb=" NE  ARG D  55 "
           pdb=" CZ  ARG D  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -137.55  -42.45     2      1.50e+01 4.44e-03 9.72e+00
  ... (remaining 6803 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1283
       0.041 -    0.082: 384
       0.082 -    0.123: 78
       0.123 -    0.163: 18
       0.163 -    0.204: 4
  Chirality restraints: 1767
  Sorted by residual:
  chirality pdb=" CB  VAL A 492 "
            pdb=" CA  VAL A 492 "
            pdb=" CG1 VAL A 492 "
            pdb=" CG2 VAL A 492 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  LEU A  66 "
            pdb=" N   LEU A  66 "
            pdb=" C   LEU A  66 "
            pdb=" CB  LEU A  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.00e+00
  chirality pdb=" CA  ILE D 616 "
            pdb=" N   ILE D 616 "
            pdb=" C   ILE D 616 "
            pdb=" CB  ILE D 616 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.61   -0.17 2.00e-01 2.50e+01 7.52e-01
  ... (remaining 1764 not shown)

  Planarity restraints: 1983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  48 "    0.049 5.00e-02 4.00e+02   7.36e-02 8.66e+00
        pdb=" N   PRO A  49 "   -0.127 5.00e-02 4.00e+02
        pdb=" CA  PRO A  49 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A  49 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D 616 "   -0.048 5.00e-02 4.00e+02   7.23e-02 8.37e+00
        pdb=" N   PRO D 617 "    0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO D 617 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO D 617 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 404 "   -0.042 5.00e-02 4.00e+02   6.39e-02 6.54e+00
        pdb=" N   PRO D 405 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO D 405 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO D 405 "   -0.036 5.00e-02 4.00e+02
  ... (remaining 1980 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 2260
        2.78 -     3.31: 11763
        3.31 -     3.84: 19246
        3.84 -     4.37: 21902
        4.37 -     4.90: 35475
  Nonbonded interactions: 90646
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 580 "
            pdb=" OG  SER A 585 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" OG  SER A  40 "
            pdb=" OE1 GLN A  42 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   THR A  73 "
            pdb=" OG1 THR A  90 "
     model   vdw
     2.283 3.040
  nonbonded pdb=" OH  TYR A 449 "
            pdb=" O   PRO A 497 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" NH2 ARG D 332 "
            pdb=" OD2 ASP D 342 "
     model   vdw
     2.299 3.120
  ... (remaining 90641 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'D'
}
ncs_group {
  reference = chain 'E'
  selection = chain 'F'
}

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:             16.130
  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:          0.530
  Check model and map are aligned:         0.080
  Set scattering table:                    0.120
  Process input model:                     33.810
  Find NCS groups from input model:        0.330
  Set up NCS constraints:                  0.060
  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:2.950
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
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      :  0.003   0.033  11225  Z= 0.143
  Angle     :  0.663  10.736  15224  Z= 0.342
  Chirality :  0.042   0.204   1767
  Planarity :  0.005   0.074   1983
  Dihedral  : 14.848  85.683   4128
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.76 %
    Favored  : 99.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.81 (0.21), residues: 1381
  helix: -0.02 (0.16), residues: 901
  sheet:  None (None), residues: 0
  loop : -1.38 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 367 
 HIS   0.005   0.001   HIS A 537 
 PHE   0.021   0.001   PHE A 388 
 TYR   0.018   0.001   TYR D 542 
 ARG   0.005   0.000   ARG A 379 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19823 (  630)
  hydrogen bonds       : angle       6.55585 ( 1863)
  covalent geometry    : bond        0.00305 (11225)
  covalent geometry    : angle       0.66323 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  349 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 348
  time to evaluate  : 1.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8750 (t80) cc_final: 0.8482 (t80)
REVERT: A   41 GLN cc_start: 0.8809 (pp30) cc_final: 0.8514 (pp30)
REVERT: A   58 HIS cc_start: 0.7541 (m90) cc_final: 0.7239 (m90)
REVERT: A   60 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8683 (mtpp)
REVERT: A   75 GLN cc_start: 0.7011 (mp10) cc_final: 0.6723 (mp10)
REVERT: A  100 HIS cc_start: 0.6061 (m-70) cc_final: 0.5823 (m-70)
REVERT: A  131 ASP cc_start: 0.9119 (t70) cc_final: 0.8837 (t0)
REVERT: A  133 ARG cc_start: 0.8529 (mmm-85) cc_final: 0.8044 (mmm-85)
REVERT: A  175 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8442 (mt-10)
REVERT: A  205 GLU cc_start: 0.9085 (mm-30) cc_final: 0.8830 (tp30)
REVERT: A  231 LYS cc_start: 0.8579 (mmtp) cc_final: 0.8317 (mmtm)
REVERT: A  239 LEU cc_start: 0.9261 (tt) cc_final: 0.8961 (mt)
REVERT: A  356 ASP cc_start: 0.8958 (m-30) cc_final: 0.8072 (t70)
REVERT: A  395 MET cc_start: 0.8677 (ttm) cc_final: 0.8445 (ttm)
REVERT: A  397 HIS cc_start: 0.8001 (t-170) cc_final: 0.7770 (t70)
REVERT: A  483 GLU cc_start: 0.9157 (mp0) cc_final: 0.8921 (mp0)
REVERT: A  507 CYS cc_start: 0.7624 (m) cc_final: 0.7268 (m)
REVERT: A  541 GLN cc_start: 0.8608 (mt0) cc_final: 0.7559 (tm-30)
REVERT: A  567 ASP cc_start: 0.7813 (t70) cc_final: 0.7540 (t70)
REVERT: A  574 LYS cc_start: 0.9199 (mttp) cc_final: 0.8871 (mtmt)
REVERT: B   70 PHE cc_start: 0.7663 (t80) cc_final: 0.7461 (t80)
REVERT: B   76 LEU cc_start: 0.9110 (mp) cc_final: 0.8730 (mp)
REVERT: B   92 HIS cc_start: 0.8378 (m90) cc_final: 0.7407 (m90)
REVERT: B  118 VAL cc_start: 0.8706 (t) cc_final: 0.8482 (t)
REVERT: C   76 LEU cc_start: 0.7938 (mt) cc_final: 0.7417 (mt)
REVERT: D  105 LYS cc_start: 0.9348 (pttp) cc_final: 0.9132 (pttt)
REVERT: D  147 ILE cc_start: 0.8170 (pt) cc_final: 0.7858 (mm)
REVERT: D  173 LEU cc_start: 0.9106 (tp) cc_final: 0.8529 (tp)
REVERT: D  228 GLU cc_start: 0.8225 (tt0) cc_final: 0.7908 (tt0)
REVERT: D  273 TYR cc_start: 0.8149 (t80) cc_final: 0.7561 (t80)
REVERT: D  274 HIS cc_start: 0.8173 (m90) cc_final: 0.7731 (m90)
REVERT: D  321 ARG cc_start: 0.8326 (ptt180) cc_final: 0.7989 (ptm-80)
REVERT: D  322 ASP cc_start: 0.9082 (p0) cc_final: 0.8694 (p0)
REVERT: D  394 GLN cc_start: 0.9178 (tt0) cc_final: 0.8632 (tp40)
REVERT: D  572 GLN cc_start: 0.9006 (mp10) cc_final: 0.8784 (mp10)
REVERT: D  621 GLU cc_start: 0.8423 (mm-30) cc_final: 0.8027 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 348
  average time/residue: 0.2234
  time to fit residues: 108.8912
Evaluate side-chains
  234 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 58 optimal weight:    0.3980
   chunk 35 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 81 optimal weight:    0.9980
   chunk 126 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 345 HIS
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 592 GLN
D 380 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.133455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.108464 restraints weight = 34972.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.109959 restraints weight = 20865.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110617 restraints weight = 15119.895|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  11225  Z= 0.196
  Angle     :  0.661  11.546  15224  Z= 0.342
  Chirality :  0.041   0.215   1767
  Planarity :  0.005   0.063   1983
  Dihedral  :  4.506  20.755   1523
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.79 %
    Favored  : 93.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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: -0.01 (0.23), residues: 1381
  helix:  0.65 (0.16), residues: 941
  sheet:  None (None), residues: 0
  loop : -1.34 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 325 
 PHE   0.022   0.002   PHE A 388 
 TYR   0.016   0.001   TYR A 445 
 ARG   0.007   0.001   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04892 (  630)
  hydrogen bonds       : angle       5.03563 ( 1863)
  covalent geometry    : bond        0.00424 (11225)
  covalent geometry    : angle       0.66119 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 280
  time to evaluate  : 1.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8750 (mt) cc_final: 0.8333 (mt)
REVERT: A   41 GLN cc_start: 0.8669 (pp30) cc_final: 0.8421 (pp30)
REVERT: A   55 ARG cc_start: 0.8974 (tpp-160) cc_final: 0.8704 (tpp80)
REVERT: A   58 HIS cc_start: 0.7759 (m90) cc_final: 0.7228 (m-70)
REVERT: A   60 LYS cc_start: 0.9046 (mmmm) cc_final: 0.8788 (mtpp)
REVERT: A   75 GLN cc_start: 0.6777 (mp10) cc_final: 0.6564 (mp10)
REVERT: A  131 ASP cc_start: 0.9033 (t70) cc_final: 0.8814 (t0)
REVERT: A  133 ARG cc_start: 0.8502 (mmm-85) cc_final: 0.8268 (mmm-85)
REVERT: A  175 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8527 (mt-10)
REVERT: A  239 LEU cc_start: 0.9182 (tt) cc_final: 0.8977 (mt)
REVERT: A  422 MET cc_start: 0.8206 (ttm) cc_final: 0.7915 (ttt)
REVERT: A  507 CYS cc_start: 0.7913 (m) cc_final: 0.7507 (m)
REVERT: A  541 GLN cc_start: 0.8547 (mt0) cc_final: 0.7396 (tm-30)
REVERT: A  561 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8214 (tm-30)
REVERT: A  567 ASP cc_start: 0.7579 (t70) cc_final: 0.7366 (t0)
REVERT: A  579 LYS cc_start: 0.7377 (mttm) cc_final: 0.7118 (mttt)
REVERT: A  620 LEU cc_start: 0.8624 (mm) cc_final: 0.8324 (mm)
REVERT: B   92 HIS cc_start: 0.8660 (m90) cc_final: 0.7930 (m90)
REVERT: B  118 VAL cc_start: 0.9065 (t) cc_final: 0.8765 (t)
REVERT: C   76 LEU cc_start: 0.8217 (mt) cc_final: 0.7871 (mt)
REVERT: C   92 HIS cc_start: 0.8931 (t70) cc_final: 0.8598 (t70)
REVERT: D  147 ILE cc_start: 0.8418 (pt) cc_final: 0.8058 (mm)
REVERT: D  271 LYS cc_start: 0.9158 (mmtt) cc_final: 0.8958 (mmpt)
REVERT: D  273 TYR cc_start: 0.8119 (t80) cc_final: 0.7782 (t80)
REVERT: D  321 ARG cc_start: 0.8451 (ptt180) cc_final: 0.8214 (ptt90)
REVERT: D  340 ASN cc_start: 0.8724 (t0) cc_final: 0.8439 (t0)
REVERT: D  394 GLN cc_start: 0.9266 (tt0) cc_final: 0.8834 (tp40)
REVERT: D  538 ILE cc_start: 0.9606 (mt) cc_final: 0.9397 (tp)
REVERT: D  621 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8010 (mm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 280
  average time/residue: 0.2266
  time to fit residues: 91.3115
Evaluate side-chains
  227 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 1.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 75 optimal weight:    6.9990
   chunk 108 optimal weight:    1.9990
   chunk 134 optimal weight:    1.9990
   chunk 113 optimal weight:    0.9990
   chunk 81 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 86 optimal weight:    0.8980
   chunk 112 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 397 HIS
** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.131787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.106835 restraints weight = 35240.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.108650 restraints weight = 21010.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.109023 restraints weight = 15804.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11225  Z= 0.161
  Angle     :  0.619   9.196  15224  Z= 0.321
  Chirality :  0.040   0.179   1767
  Planarity :  0.005   0.060   1983
  Dihedral  :  4.455  21.596   1523
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 14.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.09 (0.23), residues: 1381
  helix:  0.76 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop : -1.40 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 372 
 PHE   0.020   0.002   PHE A 549 
 TYR   0.013   0.001   TYR A 445 
 ARG   0.007   0.000   ARG D 264 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  630)
  hydrogen bonds       : angle       4.81018 ( 1863)
  covalent geometry    : bond        0.00350 (11225)
  covalent geometry    : angle       0.61891 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 273
  time to evaluate  : 1.168 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8737 (mt) cc_final: 0.8337 (mt)
REVERT: A   41 GLN cc_start: 0.8627 (pp30) cc_final: 0.8395 (pp30)
REVERT: A   58 HIS cc_start: 0.7805 (m90) cc_final: 0.7299 (m-70)
REVERT: A   60 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8705 (mtpp)
REVERT: A  138 LYS cc_start: 0.9346 (tppp) cc_final: 0.9122 (tppt)
REVERT: A  171 ARG cc_start: 0.8307 (ptp90) cc_final: 0.7721 (ptp90)
REVERT: A  176 GLN cc_start: 0.7844 (mm110) cc_final: 0.7257 (mp10)
REVERT: A  231 LYS cc_start: 0.8936 (mmtp) cc_final: 0.8567 (mmtm)
REVERT: A  268 ASP cc_start: 0.8402 (t0) cc_final: 0.8151 (t0)
REVERT: A  422 MET cc_start: 0.8204 (ttm) cc_final: 0.7914 (ttt)
REVERT: A  439 ASN cc_start: 0.8178 (t0) cc_final: 0.7972 (t0)
REVERT: A  507 CYS cc_start: 0.7969 (m) cc_final: 0.7548 (m)
REVERT: A  515 THR cc_start: 0.9518 (p) cc_final: 0.9303 (t)
REVERT: A  541 GLN cc_start: 0.8424 (mt0) cc_final: 0.7473 (tm-30)
REVERT: A  561 GLU cc_start: 0.8497 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A  567 ASP cc_start: 0.7450 (t70) cc_final: 0.7177 (t0)
REVERT: A  620 LEU cc_start: 0.8629 (mm) cc_final: 0.8299 (mm)
REVERT: B   91 ASP cc_start: 0.8800 (t70) cc_final: 0.8577 (t70)
REVERT: B   92 HIS cc_start: 0.8705 (m90) cc_final: 0.7888 (m90)
REVERT: B  118 VAL cc_start: 0.9047 (t) cc_final: 0.8637 (t)
REVERT: C   76 LEU cc_start: 0.8182 (mt) cc_final: 0.7817 (mt)
REVERT: C   92 HIS cc_start: 0.8908 (t70) cc_final: 0.8609 (t70)
REVERT: D  135 ASP cc_start: 0.9180 (p0) cc_final: 0.8923 (p0)
REVERT: D  147 ILE cc_start: 0.8462 (pt) cc_final: 0.8115 (mm)
REVERT: D  273 TYR cc_start: 0.8090 (t80) cc_final: 0.7755 (t80)
REVERT: D  319 GLN cc_start: 0.7769 (pm20) cc_final: 0.7537 (pm20)
REVERT: D  340 ASN cc_start: 0.8575 (t0) cc_final: 0.8251 (t0)
REVERT: D  394 GLN cc_start: 0.9263 (tt0) cc_final: 0.8835 (tp40)
REVERT: D  538 ILE cc_start: 0.9599 (mt) cc_final: 0.9379 (mm)
REVERT: D  621 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7928 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 273
  average time/residue: 0.2244
  time to fit residues: 87.4556
Evaluate side-chains
  214 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 93 optimal weight:    1.9990
   chunk 72 optimal weight:    4.9990
   chunk 81 optimal weight:    7.9990
   chunk 76 optimal weight:   10.0000
   chunk 46 optimal weight:    0.7980
   chunk 22 optimal weight:    0.5980
   chunk 130 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 32 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0770
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 553 HIS
D 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.121549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098238 restraints weight = 35502.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.099631 restraints weight = 20152.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100222 restraints weight = 14232.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3425
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11225  Z= 0.140
  Angle     :  0.607   7.370  15224  Z= 0.313
  Chirality :  0.039   0.180   1767
  Planarity :  0.005   0.062   1983
  Dihedral  :  4.446  20.885   1523
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  4.45 %
    Favored  : 95.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.24 (0.23), residues: 1381
  helix:  0.91 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop : -1.43 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 372 
 PHE   0.023   0.002   PHE A 549 
 TYR   0.015   0.001   TYR A  38 
 ARG   0.005   0.000   ARG A 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  630)
  hydrogen bonds       : angle       4.65381 ( 1863)
  covalent geometry    : bond        0.00309 (11225)
  covalent geometry    : angle       0.60691 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8715 (mt) cc_final: 0.8305 (mt)
REVERT: A   34 TYR cc_start: 0.8612 (t80) cc_final: 0.7930 (t80)
REVERT: A   41 GLN cc_start: 0.8567 (pp30) cc_final: 0.8347 (pp30)
REVERT: A   58 HIS cc_start: 0.7766 (m90) cc_final: 0.7297 (m-70)
REVERT: A   60 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8693 (mtpp)
REVERT: A  138 LYS cc_start: 0.9386 (tppp) cc_final: 0.9163 (tppt)
REVERT: A  176 GLN cc_start: 0.7829 (mm110) cc_final: 0.7186 (mp10)
REVERT: A  231 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8605 (mmtm)
REVERT: A  507 CYS cc_start: 0.7970 (m) cc_final: 0.7547 (m)
REVERT: A  541 GLN cc_start: 0.8273 (mt0) cc_final: 0.7348 (tm-30)
REVERT: A  561 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8169 (tm-30)
REVERT: A  567 ASP cc_start: 0.7336 (t70) cc_final: 0.7090 (t0)
REVERT: A  620 LEU cc_start: 0.8598 (mm) cc_final: 0.8246 (mm)
REVERT: B   92 HIS cc_start: 0.8660 (m90) cc_final: 0.7863 (m90)
REVERT: B  118 VAL cc_start: 0.9035 (t) cc_final: 0.8708 (t)
REVERT: C   76 LEU cc_start: 0.8134 (mt) cc_final: 0.7773 (mt)
REVERT: C   92 HIS cc_start: 0.8879 (t70) cc_final: 0.8659 (t70)
REVERT: D  135 ASP cc_start: 0.9095 (p0) cc_final: 0.8842 (p0)
REVERT: D  147 ILE cc_start: 0.8426 (pt) cc_final: 0.8077 (mm)
REVERT: D  273 TYR cc_start: 0.8138 (t80) cc_final: 0.7727 (t80)
REVERT: D  394 GLN cc_start: 0.9294 (tt0) cc_final: 0.8878 (tp40)
REVERT: D  538 ILE cc_start: 0.9601 (mt) cc_final: 0.9372 (tp)
REVERT: D  621 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7818 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 276
  average time/residue: 0.2410
  time to fit residues: 96.0324
Evaluate side-chains
  223 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 133 optimal weight:    0.8980
   chunk 39 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 76 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   chunk 9 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 115 optimal weight:    0.5980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
D 380 ASN
D 443 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.132836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108839 restraints weight = 34905.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.109357 restraints weight = 21010.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110236 restraints weight = 15974.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11225  Z= 0.155
  Angle     :  0.620   9.287  15224  Z= 0.320
  Chirality :  0.041   0.334   1767
  Planarity :  0.005   0.059   1983
  Dihedral  :  4.451  22.311   1523
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.30 (0.23), residues: 1381
  helix:  0.97 (0.17), residues: 935
  sheet:  None (None), residues: 0
  loop : -1.40 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 372 
 PHE   0.018   0.002   PHE A 549 
 TYR   0.016   0.001   TYR D 267 
 ARG   0.004   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  630)
  hydrogen bonds       : angle       4.64577 ( 1863)
  covalent geometry    : bond        0.00342 (11225)
  covalent geometry    : angle       0.62044 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8652 (t80) cc_final: 0.7870 (t80)
REVERT: A   58 HIS cc_start: 0.7784 (m90) cc_final: 0.7289 (m-70)
REVERT: A   60 LYS cc_start: 0.9050 (mmmm) cc_final: 0.8665 (mtpp)
REVERT: A  133 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8293 (mmm-85)
REVERT: A  507 CYS cc_start: 0.7872 (m) cc_final: 0.7448 (m)
REVERT: A  541 GLN cc_start: 0.8278 (mt0) cc_final: 0.7310 (tm-30)
REVERT: A  561 GLU cc_start: 0.8499 (tm-30) cc_final: 0.8138 (tm-30)
REVERT: A  620 LEU cc_start: 0.8609 (mm) cc_final: 0.8274 (mm)
REVERT: B   70 PHE cc_start: 0.8643 (t80) cc_final: 0.8427 (t80)
REVERT: B  118 VAL cc_start: 0.9032 (t) cc_final: 0.8716 (t)
REVERT: C   76 LEU cc_start: 0.8104 (mt) cc_final: 0.7813 (mt)
REVERT: D  135 ASP cc_start: 0.9184 (p0) cc_final: 0.8881 (p0)
REVERT: D  147 ILE cc_start: 0.8487 (pt) cc_final: 0.8131 (mm)
REVERT: D  196 GLU cc_start: 0.8696 (tt0) cc_final: 0.8406 (pt0)
REVERT: D  260 PHE cc_start: 0.8922 (m-80) cc_final: 0.8607 (m-80)
REVERT: D  273 TYR cc_start: 0.8109 (t80) cc_final: 0.7728 (t80)
REVERT: D  394 GLN cc_start: 0.9292 (tt0) cc_final: 0.8850 (tp40)
REVERT: D  417 GLU cc_start: 0.8352 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: D  538 ILE cc_start: 0.9578 (mt) cc_final: 0.9344 (tp)
REVERT: D  621 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7742 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 275
  average time/residue: 0.2213
  time to fit residues: 89.0019
Evaluate side-chains
  214 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 1.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 107 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   chunk 131 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 120 optimal weight:    0.5980
   chunk 22 optimal weight:    0.5980
   chunk 45 optimal weight:    0.8980
   chunk 132 optimal weight:    0.9990
   chunk 19 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN
D 533 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.121382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.097231 restraints weight = 35923.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098706 restraints weight = 20557.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.099258 restraints weight = 14634.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11225  Z= 0.158
  Angle     :  0.639   9.372  15224  Z= 0.328
  Chirality :  0.041   0.184   1767
  Planarity :  0.005   0.055   1983
  Dihedral  :  4.534  22.520   1523
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.52 %
    Favored  : 97.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.25 (0.23), residues: 1381
  helix:  0.92 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop : -1.42 (0.31), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A  93 
 HIS   0.007   0.001   HIS D 274 
 PHE   0.026   0.002   PHE C 119 
 TYR   0.020   0.001   TYR A  38 
 ARG   0.004   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  630)
  hydrogen bonds       : angle       4.63149 ( 1863)
  covalent geometry    : bond        0.00350 (11225)
  covalent geometry    : angle       0.63930 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8623 (t80) cc_final: 0.7878 (t80)
REVERT: A   58 HIS cc_start: 0.7747 (m90) cc_final: 0.7244 (m-70)
REVERT: A   60 LYS cc_start: 0.9030 (mmmm) cc_final: 0.8468 (mtpp)
REVERT: A  133 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8077 (mtm-85)
REVERT: A  175 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8213 (mt-10)
REVERT: A  507 CYS cc_start: 0.7854 (m) cc_final: 0.7375 (m)
REVERT: A  541 GLN cc_start: 0.8264 (mt0) cc_final: 0.7330 (tm-30)
REVERT: A  561 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8173 (tm-30)
REVERT: A  620 LEU cc_start: 0.8581 (mm) cc_final: 0.8245 (mm)
REVERT: B   70 PHE cc_start: 0.8627 (t80) cc_final: 0.8358 (t80)
REVERT: B  118 VAL cc_start: 0.9053 (t) cc_final: 0.8756 (t)
REVERT: C   76 LEU cc_start: 0.8182 (mt) cc_final: 0.7904 (mt)
REVERT: D    1 MET cc_start: 0.1973 (mpp) cc_final: 0.1597 (mpp)
REVERT: D  135 ASP cc_start: 0.9097 (p0) cc_final: 0.8780 (p0)
REVERT: D  147 ILE cc_start: 0.8494 (pt) cc_final: 0.8138 (mm)
REVERT: D  260 PHE cc_start: 0.8876 (m-80) cc_final: 0.8537 (m-80)
REVERT: D  273 TYR cc_start: 0.8072 (t80) cc_final: 0.7707 (t80)
REVERT: D  394 GLN cc_start: 0.9261 (tt0) cc_final: 0.8784 (tp40)
REVERT: D  538 ILE cc_start: 0.9606 (mt) cc_final: 0.9333 (mm)
REVERT: D  621 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7811 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.2036
  time to fit residues: 78.0376
Evaluate side-chains
  213 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0070
   chunk 8 optimal weight:    0.0670
   chunk 56 optimal weight:    0.0040
   chunk 10 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   chunk 121 optimal weight:    0.8980
   chunk 126 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.3148

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

Flipped N/Q/H residues before XYZ refinement:
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 375 GLN
D 380 ASN
D 443 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.122939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.098897 restraints weight = 35837.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100385 restraints weight = 20370.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.101402 restraints weight = 14409.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8002
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11225  Z= 0.128
  Angle     :  0.645  13.228  15224  Z= 0.324
  Chirality :  0.040   0.190   1767
  Planarity :  0.005   0.057   1983
  Dihedral  :  4.499  21.805   1523
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.28 (0.23), residues: 1381
  helix:  0.98 (0.17), residues: 934
  sheet:  None (None), residues: 0
  loop : -1.49 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.003   TRP A  93 
 HIS   0.008   0.001   HIS A 110 
 PHE   0.028   0.002   PHE A 549 
 TYR   0.024   0.001   TYR A  38 
 ARG   0.005   0.000   ARG A 171 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03767 (  630)
  hydrogen bonds       : angle       4.52037 ( 1863)
  covalent geometry    : bond        0.00279 (11225)
  covalent geometry    : angle       0.64521 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 1.194 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8642 (t80) cc_final: 0.7913 (t80)
REVERT: A   58 HIS cc_start: 0.7717 (m90) cc_final: 0.7198 (m-70)
REVERT: A   60 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8423 (mtpp)
REVERT: A  133 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8065 (mtm-85)
REVERT: A  314 LEU cc_start: 0.8929 (tt) cc_final: 0.8662 (tt)
REVERT: A  507 CYS cc_start: 0.7851 (m) cc_final: 0.7379 (m)
REVERT: A  541 GLN cc_start: 0.8204 (mt0) cc_final: 0.7274 (tm-30)
REVERT: A  561 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8133 (tm-30)
REVERT: A  620 LEU cc_start: 0.8555 (mm) cc_final: 0.8218 (mm)
REVERT: B   70 PHE cc_start: 0.8605 (t80) cc_final: 0.8328 (t80)
REVERT: B  118 VAL cc_start: 0.9007 (t) cc_final: 0.8699 (t)
REVERT: D    1 MET cc_start: 0.1915 (mpp) cc_final: 0.1493 (mpp)
REVERT: D  125 LEU cc_start: 0.9624 (tt) cc_final: 0.9417 (tt)
REVERT: D  135 ASP cc_start: 0.9079 (p0) cc_final: 0.8742 (p0)
REVERT: D  147 ILE cc_start: 0.8469 (pt) cc_final: 0.8120 (mm)
REVERT: D  250 ILE cc_start: 0.9411 (mm) cc_final: 0.9086 (mm)
REVERT: D  260 PHE cc_start: 0.8821 (m-80) cc_final: 0.8460 (m-80)
REVERT: D  273 TYR cc_start: 0.8024 (t80) cc_final: 0.7619 (t80)
REVERT: D  394 GLN cc_start: 0.9247 (tt0) cc_final: 0.8822 (tp40)
REVERT: D  538 ILE cc_start: 0.9579 (mt) cc_final: 0.9281 (mm)
REVERT: D  586 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7487 (pt0)
REVERT: D  621 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7771 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.2088
  time to fit residues: 81.6702
Evaluate side-chains
  217 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 76 optimal weight:   10.0000
   chunk 22 optimal weight:    0.5980
   chunk 113 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 80 optimal weight:    7.9990
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 3 optimal weight:    4.9990
   chunk 31 optimal weight:    0.4980
   chunk 8 optimal weight:    4.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 151 ASN
D 155 ASN
D 380 ASN
** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.122310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098885 restraints weight = 35672.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.100394 restraints weight = 19876.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.100972 restraints weight = 14006.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.3539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  11225  Z= 0.153
  Angle     :  0.665  13.087  15224  Z= 0.336
  Chirality :  0.040   0.188   1767
  Planarity :  0.005   0.056   1983
  Dihedral  :  4.451  21.767   1523
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.18 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.25 (0.23), residues: 1381
  helix:  0.95 (0.17), residues: 931
  sheet:  None (None), residues: 0
  loop : -1.48 (0.31), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.004   TRP A  93 
 HIS   0.008   0.001   HIS D 274 
 PHE   0.018   0.001   PHE C 119 
 TYR   0.023   0.001   TYR A  38 
 ARG   0.004   0.000   ARG A 350 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  630)
  hydrogen bonds       : angle       4.57669 ( 1863)
  covalent geometry    : bond        0.00345 (11225)
  covalent geometry    : angle       0.66459 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 259
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8624 (t80) cc_final: 0.7895 (t80)
REVERT: A   58 HIS cc_start: 0.7686 (m90) cc_final: 0.7177 (m-70)
REVERT: A   60 LYS cc_start: 0.9008 (mmmm) cc_final: 0.8438 (mtpp)
REVERT: A   75 GLN cc_start: 0.6736 (mp10) cc_final: 0.6462 (mp10)
REVERT: A  133 ARG cc_start: 0.8558 (mmm-85) cc_final: 0.8064 (mtm-85)
REVERT: A  507 CYS cc_start: 0.7821 (m) cc_final: 0.7369 (m)
REVERT: A  541 GLN cc_start: 0.8263 (mt0) cc_final: 0.7310 (tm-30)
REVERT: A  542 TYR cc_start: 0.7884 (t80) cc_final: 0.7399 (t80)
REVERT: A  561 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8105 (tm-30)
REVERT: A  620 LEU cc_start: 0.8546 (mm) cc_final: 0.8210 (mm)
REVERT: B   70 PHE cc_start: 0.8671 (t80) cc_final: 0.8345 (t80)
REVERT: B  118 VAL cc_start: 0.9008 (t) cc_final: 0.8713 (t)
REVERT: D    1 MET cc_start: 0.1815 (mpp) cc_final: 0.1450 (mpp)
REVERT: D   46 ARG cc_start: 0.8383 (ptm-80) cc_final: 0.8039 (ttp80)
REVERT: D  125 LEU cc_start: 0.9627 (tt) cc_final: 0.9404 (tt)
REVERT: D  134 LEU cc_start: 0.9019 (tp) cc_final: 0.8811 (tp)
REVERT: D  135 ASP cc_start: 0.9061 (p0) cc_final: 0.8784 (p0)
REVERT: D  147 ILE cc_start: 0.8492 (pt) cc_final: 0.8107 (mm)
REVERT: D  260 PHE cc_start: 0.8829 (m-80) cc_final: 0.8440 (m-80)
REVERT: D  273 TYR cc_start: 0.8002 (t80) cc_final: 0.7594 (t80)
REVERT: D  394 GLN cc_start: 0.9222 (tt0) cc_final: 0.8791 (tp40)
REVERT: D  538 ILE cc_start: 0.9572 (mt) cc_final: 0.9306 (mm)
REVERT: D  586 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7522 (pt0)
REVERT: D  621 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7784 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 259
  average time/residue: 0.2058
  time to fit residues: 78.1422
Evaluate side-chains
  216 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9990
   chunk 43 optimal weight:    3.9990
   chunk 118 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 114 optimal weight:    0.2980
   chunk 102 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 56 optimal weight:    0.8980
   chunk 59 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 HIS
** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.122332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.098304 restraints weight = 35776.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.099422 restraints weight = 21063.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.100378 restraints weight = 15448.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11225  Z= 0.153
  Angle     :  0.664  13.381  15224  Z= 0.337
  Chirality :  0.041   0.188   1767
  Planarity :  0.005   0.055   1983
  Dihedral  :  4.477  23.847   1523
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.89 %
    Favored  : 92.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.25 (0.23), residues: 1381
  helix:  0.95 (0.17), residues: 934
  sheet:  None (None), residues: 0
  loop : -1.48 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 209 
 HIS   0.008   0.001   HIS D 274 
 PHE   0.016   0.001   PHE C 119 
 TYR   0.022   0.001   TYR A  38 
 ARG   0.005   0.000   ARG D 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  630)
  hydrogen bonds       : angle       4.57082 ( 1863)
  covalent geometry    : bond        0.00344 (11225)
  covalent geometry    : angle       0.66408 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8649 (t80) cc_final: 0.7917 (t80)
REVERT: A   58 HIS cc_start: 0.7709 (m90) cc_final: 0.7172 (m-70)
REVERT: A   60 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8415 (mtpp)
REVERT: A   75 GLN cc_start: 0.6631 (mp10) cc_final: 0.6400 (mp10)
REVERT: A  133 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8130 (mtm-85)
REVERT: A  395 MET cc_start: 0.8984 (tpp) cc_final: 0.8064 (mmm)
REVERT: A  439 ASN cc_start: 0.8150 (t0) cc_final: 0.7916 (t0)
REVERT: A  507 CYS cc_start: 0.7735 (m) cc_final: 0.7236 (m)
REVERT: A  541 GLN cc_start: 0.8321 (mt0) cc_final: 0.7311 (tm-30)
REVERT: A  542 TYR cc_start: 0.7775 (t80) cc_final: 0.7365 (t80)
REVERT: A  561 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: A  620 LEU cc_start: 0.8562 (mm) cc_final: 0.8230 (mm)
REVERT: B   70 PHE cc_start: 0.8717 (t80) cc_final: 0.8433 (t80)
REVERT: B  118 VAL cc_start: 0.8995 (t) cc_final: 0.8720 (t)
REVERT: D    1 MET cc_start: 0.1784 (mpp) cc_final: 0.1438 (mpp)
REVERT: D   46 ARG cc_start: 0.8457 (ptm-80) cc_final: 0.8128 (ttp80)
REVERT: D  125 LEU cc_start: 0.9648 (tt) cc_final: 0.9441 (tt)
REVERT: D  147 ILE cc_start: 0.8535 (pt) cc_final: 0.8155 (mm)
REVERT: D  273 TYR cc_start: 0.8008 (t80) cc_final: 0.7662 (t80)
REVERT: D  394 GLN cc_start: 0.9236 (tt0) cc_final: 0.8755 (tp40)
REVERT: D  538 ILE cc_start: 0.9575 (mt) cc_final: 0.9356 (mm)
REVERT: D  586 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7552 (tt0)
REVERT: D  621 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7800 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2226
  time to fit residues: 85.2572
Evaluate side-chains
  215 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 93 optimal weight:    0.1980
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    0.5980
   chunk 72 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   chunk 80 optimal weight:    9.9990
   chunk 58 optimal weight:    0.4980
   chunk 38 optimal weight:    0.5980
   chunk 116 optimal weight:    0.9980
   chunk 117 optimal weight:    0.5980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 HIS
** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.123109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099324 restraints weight = 35706.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.100724 restraints weight = 20525.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.101304 restraints weight = 14627.010|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.3715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11225  Z= 0.135
  Angle     :  0.671  13.720  15224  Z= 0.336
  Chirality :  0.041   0.188   1767
  Planarity :  0.004   0.055   1983
  Dihedral  :  4.494  23.617   1523
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.31 %
    Favored  : 92.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.25 (0.23), residues: 1381
  helix:  0.96 (0.17), residues: 935
  sheet:  None (None), residues: 0
  loop : -1.52 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.003   TRP A 209 
 HIS   0.010   0.001   HIS D 274 
 PHE   0.030   0.002   PHE A 549 
 TYR   0.032   0.001   TYR A  38 
 ARG   0.006   0.000   ARG D 126 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03710 (  630)
  hydrogen bonds       : angle       4.52006 ( 1863)
  covalent geometry    : bond        0.00306 (11225)
  covalent geometry    : angle       0.67058 (15224)

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

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

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2762 Ramachandran restraints generated.
    1381 Oldfield, 0 Emsley, 1381 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8657 (t80) cc_final: 0.7951 (t80)
REVERT: A   58 HIS cc_start: 0.7727 (m90) cc_final: 0.7191 (m-70)
REVERT: A   60 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8406 (mtpp)
REVERT: A  133 ARG cc_start: 0.8598 (mmm-85) cc_final: 0.8057 (mtm-85)
REVERT: A  171 ARG cc_start: 0.8407 (ptp90) cc_final: 0.7843 (ptp90)
REVERT: A  395 MET cc_start: 0.8948 (tpp) cc_final: 0.8045 (mmm)
REVERT: A  439 ASN cc_start: 0.8096 (t0) cc_final: 0.7859 (t0)
REVERT: A  507 CYS cc_start: 0.7687 (m) cc_final: 0.7226 (m)
REVERT: A  541 GLN cc_start: 0.8312 (mt0) cc_final: 0.7289 (tm-30)
REVERT: A  542 TYR cc_start: 0.7795 (t80) cc_final: 0.7439 (t80)
REVERT: A  561 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8114 (tm-30)
REVERT: A  620 LEU cc_start: 0.8553 (mm) cc_final: 0.8291 (mm)
REVERT: B   70 PHE cc_start: 0.8678 (t80) cc_final: 0.8378 (t80)
REVERT: B  118 VAL cc_start: 0.8987 (t) cc_final: 0.8716 (t)
REVERT: C   76 LEU cc_start: 0.8476 (mt) cc_final: 0.8223 (mt)
REVERT: D    1 MET cc_start: 0.1705 (mpp) cc_final: 0.1365 (mpp)
REVERT: D   46 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.7810 (ttp80)
REVERT: D  101 PHE cc_start: 0.8218 (t80) cc_final: 0.7602 (t80)
REVERT: D  105 LYS cc_start: 0.9289 (pttp) cc_final: 0.8932 (pttt)
REVERT: D  125 LEU cc_start: 0.9644 (tt) cc_final: 0.9443 (tt)
REVERT: D  147 ILE cc_start: 0.8520 (pt) cc_final: 0.8163 (mm)
REVERT: D  220 MET cc_start: 0.8641 (ptp) cc_final: 0.7982 (pmm)
REVERT: D  260 PHE cc_start: 0.8918 (m-80) cc_final: 0.8432 (m-80)
REVERT: D  273 TYR cc_start: 0.8025 (t80) cc_final: 0.7661 (t80)
REVERT: D  394 GLN cc_start: 0.9224 (tt0) cc_final: 0.8735 (tp40)
REVERT: D  472 TYR cc_start: 0.8112 (t80) cc_final: 0.7776 (t80)
REVERT: D  538 ILE cc_start: 0.9591 (mt) cc_final: 0.9358 (mm)
REVERT: D  586 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7542 (tt0)
REVERT: D  621 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7806 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2084
  time to fit residues: 78.9474
Evaluate side-chains
  206 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 62 optimal weight:    0.0270
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 107 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0030
   overall best weight:    0.4848

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

Flipped N/Q/H residues before XYZ refinement:
** A  75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 382 HIS
** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.129375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.104798 restraints weight = 35035.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.106284 restraints weight = 20631.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.106861 restraints weight = 14821.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11225  Z= 0.135
  Angle     :  0.664  13.717  15224  Z= 0.337
  Chirality :  0.041   0.200   1767
  Planarity :  0.005   0.082   1983
  Dihedral  :  4.476  22.315   1523
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.08 %
    Favored  : 99.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    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:  0.27 (0.23), residues: 1381
  helix:  0.96 (0.17), residues: 932
  sheet:  None (None), residues: 0
  loop : -1.45 (0.31), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP A 209 
 HIS   0.010   0.001   HIS D 274 
 PHE   0.012   0.001   PHE C 119 
 TYR   0.021   0.001   TYR D 267 
 ARG   0.014   0.000   ARG D 133 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  630)
  hydrogen bonds       : angle       4.52112 ( 1863)
  covalent geometry    : bond        0.00307 (11225)
  covalent geometry    : angle       0.66397 (15224)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4992.94 seconds
wall clock time: 88 minutes 12.00 seconds (5292.00 seconds total)