Starting phenix.real_space_refine
on Wed Sep 17 20:25:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j7a_61199/09_2025/9j7a_61199.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j7a_61199/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j7a_61199/09_2025/9j7a_61199.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j7a_61199/09_2025/9j7a_61199.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j7a_61199/09_2025/9j7a_61199.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j7a_61199/09_2025/9j7a_61199.map"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.29, per 1000 atoms: 0.21
  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: 0.99
  Conformation dependent library (CDL) restraints added in 372.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.35
  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: 1.50

  Time building geometry restraints manager: 1.29 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:             22.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     10.490
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.990
-------------------------------------------------------------------------------
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 : 8.46
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.81 (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
 ARG   0.005   0.000   ARG A 379 
 TYR   0.018   0.001   TYR D 542 
 PHE   0.021   0.001   PHE A 388 
 TRP   0.009   0.001   TRP A 367 
 HIS   0.005   0.001   HIS A 537 

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

*********************** 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  : 0.448 
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: 0.8750 (t80) cc_final: 0.8480 (t80)
REVERT: A   41 GLN cc_start: 0.8809 (pp30) cc_final: 0.8515 (pp30)
REVERT: A   58 HIS cc_start: 0.7541 (m90) cc_final: 0.7242 (m90)
REVERT: A   60 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8679 (mtpp)
REVERT: A   75 GLN cc_start: 0.7011 (mp10) cc_final: 0.6724 (mp10)
REVERT: A  100 HIS cc_start: 0.6061 (m-70) cc_final: 0.5824 (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: 0.8043 (mmm-85)
REVERT: A  175 GLU cc_start: 0.8864 (mt-10) cc_final: 0.8443 (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: 0.8922 (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   76 LEU cc_start: 0.9110 (mp) cc_final: 0.8735 (mp)
REVERT: B   92 HIS cc_start: 0.8378 (m90) cc_final: 0.7408 (m90)
REVERT: B  118 VAL cc_start: 0.8706 (t) cc_final: 0.8483 (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: 0.9133 (pttt)
REVERT: D  147 ILE cc_start: 0.8170 (pt) cc_final: 0.7886 (mm)
REVERT: D  228 GLU cc_start: 0.8225 (tt0) cc_final: 0.7921 (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: 0.7743 (m90)
REVERT: D  321 ARG cc_start: 0.8326 (ptt180) cc_final: 0.7988 (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: 0.1039
  time to fit residues: 51.2964
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  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.133920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.108906 restraints weight = 35223.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.110613 restraints weight = 20245.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.111501 restraints weight = 14425.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.111688 restraints weight = 12660.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.111889 restraints weight = 11966.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11225  Z= 0.173
  Angle     :  0.650  12.276  15224  Z= 0.335
  Chirality :  0.041   0.187   1767
  Planarity :  0.005   0.063   1983
  Dihedral  :  4.495  20.922   1523
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  5.54 %
    Favored  : 94.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.23), residues: 1381
  helix:  0.63 (0.16), residues: 941
  sheet:  None (None), residues: 0
  loop : -1.33 (0.31), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 171 
 TYR   0.017   0.001   TYR A 445 
 PHE   0.022   0.002   PHE A 388 
 TRP   0.008   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 325 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 (11225)
  covalent geometry    : angle       0.65035 (15224)
  hydrogen bonds       : bond        0.04721 (  630)
  hydrogen bonds       : angle       4.98605 ( 1863)

*********************** 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
  286 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 283
  time to evaluate  : 0.448 
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: 0.8743 (mt) cc_final: 0.8385 (mt)
REVERT: A   41 GLN cc_start: 0.8646 (pp30) cc_final: 0.8399 (pp30)
REVERT: A   55 ARG cc_start: 0.8962 (tpp-160) cc_final: 0.8678 (tpp80)
REVERT: A   58 HIS cc_start: 0.7744 (m90) cc_final: 0.7200 (m-70)
REVERT: A   60 LYS cc_start: 0.9048 (mmmm) cc_final: 0.8799 (mtpp)
REVERT: A   75 GLN cc_start: 0.6839 (mp10) cc_final: 0.6616 (mp10)
REVERT: A  133 ARG cc_start: 0.8481 (mmm-85) cc_final: 0.8243 (mmm-85)
REVERT: A  175 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8476 (mt-10)
REVERT: A  231 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8510 (mptt)
REVERT: A  239 LEU cc_start: 0.9168 (tt) cc_final: 0.8958 (mt)
REVERT: A  264 ARG cc_start: 0.7895 (ptt90) cc_final: 0.7610 (ptt-90)
REVERT: A  422 MET cc_start: 0.8154 (ttm) cc_final: 0.7890 (ttt)
REVERT: A  507 CYS cc_start: 0.7925 (m) cc_final: 0.7526 (m)
REVERT: A  541 GLN cc_start: 0.8521 (mt0) cc_final: 0.7389 (tm-30)
REVERT: A  561 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8234 (tm-30)
REVERT: A  579 LYS cc_start: 0.7294 (mttm) cc_final: 0.7040 (mttt)
REVERT: A  620 LEU cc_start: 0.8626 (mm) cc_final: 0.8325 (mm)
REVERT: B   70 PHE cc_start: 0.8677 (t80) cc_final: 0.8411 (t80)
REVERT: B   92 HIS cc_start: 0.8584 (m90) cc_final: 0.7888 (m90)
REVERT: B  118 VAL cc_start: 0.9052 (t) cc_final: 0.8739 (t)
REVERT: C   76 LEU cc_start: 0.8253 (mt) cc_final: 0.7926 (mt)
REVERT: C   92 HIS cc_start: 0.8908 (t70) cc_final: 0.8571 (t70)
REVERT: D  147 ILE cc_start: 0.8339 (pt) cc_final: 0.7970 (mm)
REVERT: D  196 GLU cc_start: 0.8698 (tt0) cc_final: 0.8384 (pt0)
REVERT: D  273 TYR cc_start: 0.8124 (t80) cc_final: 0.7831 (t80)
REVERT: D  321 ARG cc_start: 0.8404 (ptt180) cc_final: 0.8115 (ptt90)
REVERT: D  340 ASN cc_start: 0.8715 (t0) cc_final: 0.8450 (t0)
REVERT: D  394 GLN cc_start: 0.9253 (tt0) cc_final: 0.8848 (tp40)
REVERT: D  538 ILE cc_start: 0.9608 (mt) cc_final: 0.9399 (tp)
REVERT: D  621 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7989 (mm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 283
  average time/residue: 0.0988
  time to fit residues: 40.4898
Evaluate side-chains
  226 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 122 optimal weight:    0.6980
   chunk 6 optimal weight:    0.2980
   chunk 62 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 104 GLN ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.120584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.096323 restraints weight = 36282.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097959 restraints weight = 20802.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098833 restraints weight = 14670.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.099263 restraints weight = 12600.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.099468 restraints weight = 11854.522|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  11225  Z= 0.171
  Angle     :  0.620   9.510  15224  Z= 0.324
  Chirality :  0.041   0.176   1767
  Planarity :  0.005   0.060   1983
  Dihedral  :  4.465  21.505   1523
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.81 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.12 (0.23), residues: 1381
  helix:  0.80 (0.17), residues: 935
  sheet:  None (None), residues: 0
  loop : -1.42 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 264 
 TYR   0.014   0.001   TYR A 472 
 PHE   0.021   0.002   PHE A 388 
 TRP   0.013   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (11225)
  covalent geometry    : angle       0.61994 (15224)
  hydrogen bonds       : bond        0.04269 (  630)
  hydrogen bonds       : angle       4.79107 ( 1863)

*********************** 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
  266 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.8727 (mt) cc_final: 0.8318 (mt)
REVERT: A   41 GLN cc_start: 0.8538 (pp30) cc_final: 0.8299 (pp30)
REVERT: A   58 HIS cc_start: 0.7794 (m90) cc_final: 0.7289 (m-70)
REVERT: A   60 LYS cc_start: 0.9065 (mmmm) cc_final: 0.8531 (mtpp)
REVERT: A   63 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8826 (ttm110)
REVERT: A  138 LYS cc_start: 0.9383 (tppp) cc_final: 0.9023 (tppt)
REVERT: A  175 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: A  231 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8573 (mmtm)
REVERT: A  264 ARG cc_start: 0.7756 (ptt90) cc_final: 0.7475 (ptt-90)
REVERT: A  268 ASP cc_start: 0.8417 (t0) cc_final: 0.8130 (t0)
REVERT: A  422 MET cc_start: 0.8189 (ttm) cc_final: 0.7987 (ttt)
REVERT: A  507 CYS cc_start: 0.7964 (m) cc_final: 0.7539 (m)
REVERT: A  541 GLN cc_start: 0.8403 (mt0) cc_final: 0.7461 (tm-30)
REVERT: A  561 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: A  620 LEU cc_start: 0.8616 (mm) cc_final: 0.8265 (mm)
REVERT: B   70 PHE cc_start: 0.8715 (t80) cc_final: 0.8475 (t80)
REVERT: B  118 VAL cc_start: 0.9038 (t) cc_final: 0.8654 (t)
REVERT: C   76 LEU cc_start: 0.8177 (mt) cc_final: 0.7807 (mt)
REVERT: C   92 HIS cc_start: 0.8879 (t70) cc_final: 0.8614 (t70)
REVERT: D  135 ASP cc_start: 0.9096 (p0) cc_final: 0.8797 (p0)
REVERT: D  147 ILE cc_start: 0.8423 (pt) cc_final: 0.8124 (mm)
REVERT: D  273 TYR cc_start: 0.8075 (t80) cc_final: 0.7664 (t80)
REVERT: D  321 ARG cc_start: 0.8459 (ptt180) cc_final: 0.8215 (ptt90)
REVERT: D  340 ASN cc_start: 0.8538 (t0) cc_final: 0.8064 (t0)
REVERT: D  394 GLN cc_start: 0.9297 (tt0) cc_final: 0.8863 (tp40)
REVERT: D  538 ILE cc_start: 0.9605 (mt) cc_final: 0.9375 (tp)
REVERT: D  621 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7827 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1011
  time to fit residues: 38.9023
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  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 23 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0270
   chunk 110 optimal weight:    0.8980
   chunk 9 optimal weight:    0.6980
   chunk 55 optimal weight:    0.6980
   chunk 136 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0970
   chunk 90 optimal weight:    0.8980
   chunk 116 optimal weight:    0.8980
   chunk 99 optimal weight:    0.0070
   overall best weight:    0.2854

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

Flipped N/Q/H residues before XYZ refinement:
A 553 HIS
D 151 ASN
D 155 ASN
D 380 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.123145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.099335 restraints weight = 35887.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.100856 restraints weight = 20452.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.101394 restraints weight = 14363.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.101925 restraints weight = 12842.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.102878 restraints weight = 11885.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7988
moved from start:          0.2855

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= 0.122
  Angle     :  0.607   9.070  15224  Z= 0.310
  Chirality :  0.040   0.204   1767
  Planarity :  0.005   0.064   1983
  Dihedral  :  4.420  20.663   1523
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.95 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.24 (0.23), residues: 1381
  helix:  0.96 (0.17), residues: 934
  sheet:  None (None), residues: 0
  loop : -1.53 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  63 
 TYR   0.018   0.001   TYR D 267 
 PHE   0.018   0.002   PHE A 623 
 TRP   0.010   0.001   TRP A 209 
 HIS   0.008   0.001   HIS D 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (11225)
  covalent geometry    : angle       0.60659 (15224)
  hydrogen bonds       : bond        0.03967 (  630)
  hydrogen bonds       : angle       4.55522 ( 1863)

*********************** 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
  280 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 279
  time to evaluate  : 0.446 
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: 0.8700 (mt) cc_final: 0.8289 (mt)
REVERT: A   34 TYR cc_start: 0.8642 (t80) cc_final: 0.7877 (t80)
REVERT: A   41 GLN cc_start: 0.8572 (pp30) cc_final: 0.8349 (pp30)
REVERT: A   58 HIS cc_start: 0.7743 (m90) cc_final: 0.7274 (m-70)
REVERT: A   60 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8441 (mtpp)
REVERT: A  138 LYS cc_start: 0.9377 (tppp) cc_final: 0.9161 (tppt)
REVERT: A  175 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: A  176 GLN cc_start: 0.7814 (mm110) cc_final: 0.7177 (mp10)
REVERT: A  231 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8558 (mmtm)
REVERT: A  268 ASP cc_start: 0.8441 (t0) cc_final: 0.8154 (t0)
REVERT: A  507 CYS cc_start: 0.7892 (m) cc_final: 0.7395 (m)
REVERT: A  541 GLN cc_start: 0.8234 (mt0) cc_final: 0.7328 (tm-30)
REVERT: A  561 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: A  620 LEU cc_start: 0.8586 (mm) cc_final: 0.8246 (mm)
REVERT: B   70 PHE cc_start: 0.8721 (t80) cc_final: 0.8468 (t80)
REVERT: B  118 VAL cc_start: 0.9023 (t) cc_final: 0.8709 (t)
REVERT: C   76 LEU cc_start: 0.8163 (mt) cc_final: 0.7813 (mt)
REVERT: C   92 HIS cc_start: 0.8884 (t70) cc_final: 0.8683 (t70)
REVERT: D   46 ARG cc_start: 0.8553 (ptm-80) cc_final: 0.8282 (ttp80)
REVERT: D  135 ASP cc_start: 0.9067 (p0) cc_final: 0.8850 (p0)
REVERT: D  147 ILE cc_start: 0.8392 (pt) cc_final: 0.8063 (mm)
REVERT: D  196 GLU cc_start: 0.8628 (tt0) cc_final: 0.8305 (pt0)
REVERT: D  273 TYR cc_start: 0.8054 (t80) cc_final: 0.7706 (t80)
REVERT: D  319 GLN cc_start: 0.7730 (pm20) cc_final: 0.7506 (pm20)
REVERT: D  354 TYR cc_start: 0.8451 (m-10) cc_final: 0.8240 (m-10)
REVERT: D  394 GLN cc_start: 0.9308 (tt0) cc_final: 0.8889 (tp40)
REVERT: D  395 MET cc_start: 0.8767 (mtt) cc_final: 0.8354 (ttm)
REVERT: D  495 ASN cc_start: 0.9091 (m-40) cc_final: 0.8819 (p0)
REVERT: D  538 ILE cc_start: 0.9596 (mt) cc_final: 0.9370 (tp)
REVERT: D  568 MET cc_start: 0.8078 (ptt) cc_final: 0.7867 (ptp)
REVERT: D  586 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7412 (pt0)
REVERT: D  621 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7797 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 279
  average time/residue: 0.0998
  time to fit residues: 40.5135
Evaluate side-chains
  224 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9980
   chunk 30 optimal weight:    2.9990
   chunk 41 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 99 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0270
   chunk 110 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 123 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.6838

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

Flipped N/Q/H residues before XYZ refinement:
A 100 HIS
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3850 r_free = 0.3850 target = 0.121952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.098307 restraints weight = 36065.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.098960 restraints weight = 21553.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.099984 restraints weight = 16058.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100370 restraints weight = 13241.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.100668 restraints weight = 12256.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.3069

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= 0.148
  Angle     :  0.615   9.109  15224  Z= 0.316
  Chirality :  0.040   0.304   1767
  Planarity :  0.005   0.063   1983
  Dihedral  :  4.437  21.471   1523
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 13.70
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.23), residues: 1381
  helix:  0.98 (0.17), residues: 938
  sheet:  None (None), residues: 0
  loop : -1.45 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 126 
 TYR   0.018   0.001   TYR D 267 
 PHE   0.034   0.002   PHE C 119 
 TRP   0.015   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (11225)
  covalent geometry    : angle       0.61475 (15224)
  hydrogen bonds       : bond        0.03806 (  630)
  hydrogen bonds       : angle       4.56183 ( 1863)

*********************** 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
  271 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 271
  time to evaluate  : 0.463 
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: 0.8675 (t80) cc_final: 0.7955 (t80)
REVERT: A   58 HIS cc_start: 0.7800 (m90) cc_final: 0.7278 (m-70)
REVERT: A   60 LYS cc_start: 0.9035 (mmmm) cc_final: 0.8453 (mtpp)
REVERT: A   86 ILE cc_start: 0.8117 (mm) cc_final: 0.7894 (mm)
REVERT: A  175 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8318 (mt-10)
REVERT: A  231 LYS cc_start: 0.8903 (mmtp) cc_final: 0.8614 (mmtt)
REVERT: A  268 ASP cc_start: 0.8458 (t0) cc_final: 0.8237 (t0)
REVERT: A  507 CYS cc_start: 0.7848 (m) cc_final: 0.7353 (m)
REVERT: A  541 GLN cc_start: 0.8227 (mt0) cc_final: 0.7217 (tm-30)
REVERT: A  561 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8198 (tm-30)
REVERT: A  620 LEU cc_start: 0.8576 (mm) cc_final: 0.8221 (mm)
REVERT: B   70 PHE cc_start: 0.8694 (t80) cc_final: 0.8449 (t80)
REVERT: B  118 VAL cc_start: 0.9046 (t) cc_final: 0.8770 (t)
REVERT: C   76 LEU cc_start: 0.8142 (mt) cc_final: 0.7854 (mt)
REVERT: D    1 MET cc_start: 0.1670 (mpp) cc_final: 0.1321 (mpp)
REVERT: D   46 ARG cc_start: 0.8522 (ptm-80) cc_final: 0.8281 (ttp80)
REVERT: D  135 ASP cc_start: 0.9078 (p0) cc_final: 0.8832 (p0)
REVERT: D  147 ILE cc_start: 0.8428 (pt) cc_final: 0.8140 (mm)
REVERT: D  260 PHE cc_start: 0.8916 (m-80) cc_final: 0.8608 (m-80)
REVERT: D  273 TYR cc_start: 0.8126 (t80) cc_final: 0.7783 (t80)
REVERT: D  319 GLN cc_start: 0.7719 (pm20) cc_final: 0.7496 (pm20)
REVERT: D  394 GLN cc_start: 0.9299 (tt0) cc_final: 0.8867 (tp40)
REVERT: D  417 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7779 (tm-30)
REVERT: D  443 ASN cc_start: 0.8446 (t0) cc_final: 0.7620 (t0)
REVERT: D  538 ILE cc_start: 0.9588 (mt) cc_final: 0.9366 (tp)
REVERT: D  586 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7469 (pt0)
REVERT: D  621 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7823 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 271
  average time/residue: 0.1007
  time to fit residues: 40.0043
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  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 83 optimal weight:    5.9990
   chunk 48 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 125 optimal weight:    0.0370
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 25 optimal weight:    0.1980
   chunk 115 optimal weight:    0.6980
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.123026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098739 restraints weight = 36149.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100293 restraints weight = 20528.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.100896 restraints weight = 14461.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.102033 restraints weight = 12847.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.101901 restraints weight = 11543.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.3222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11225  Z= 0.130
  Angle     :  0.609   9.093  15224  Z= 0.313
  Chirality :  0.040   0.217   1767
  Planarity :  0.005   0.060   1983
  Dihedral  :  4.422  21.528   1523
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.23), residues: 1381
  helix:  1.04 (0.17), residues: 934
  sheet:  None (None), residues: 0
  loop : -1.50 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  63 
 TYR   0.021   0.001   TYR A  38 
 PHE   0.040   0.002   PHE A 549 
 TRP   0.024   0.002   TRP A  93 
 HIS   0.009   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (11225)
  covalent geometry    : angle       0.60949 (15224)
  hydrogen bonds       : bond        0.03722 (  630)
  hydrogen bonds       : angle       4.47358 ( 1863)

*********************** 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
  264 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 264
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8662 (t80) cc_final: 0.7946 (t80)
REVERT: A   58 HIS cc_start: 0.7740 (m90) cc_final: 0.7234 (m-70)
REVERT: A   60 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8419 (mtpp)
REVERT: A   63 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8897 (ttm110)
REVERT: A  472 TYR cc_start: 0.8260 (t80) cc_final: 0.8052 (t80)
REVERT: A  507 CYS cc_start: 0.7878 (m) cc_final: 0.7406 (m)
REVERT: A  541 GLN cc_start: 0.8179 (mt0) cc_final: 0.7246 (tm-30)
REVERT: A  561 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8158 (tm-30)
REVERT: A  592 GLN cc_start: 0.6764 (mm-40) cc_final: 0.6369 (mm-40)
REVERT: A  620 LEU cc_start: 0.8554 (mm) cc_final: 0.8203 (mm)
REVERT: B   70 PHE cc_start: 0.8633 (t80) cc_final: 0.8384 (t80)
REVERT: B  118 VAL cc_start: 0.9020 (t) cc_final: 0.8644 (t)
REVERT: C   76 LEU cc_start: 0.8217 (mt) cc_final: 0.7925 (mt)
REVERT: D    1 MET cc_start: 0.1882 (mpp) cc_final: 0.1452 (mpp)
REVERT: D   46 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8279 (ttp80)
REVERT: D  135 ASP cc_start: 0.9097 (p0) cc_final: 0.8821 (p0)
REVERT: D  147 ILE cc_start: 0.8382 (pt) cc_final: 0.8100 (mm)
REVERT: D  236 GLU cc_start: 0.8850 (mp0) cc_final: 0.8592 (mp0)
REVERT: D  260 PHE cc_start: 0.8890 (m-80) cc_final: 0.8569 (m-80)
REVERT: D  273 TYR cc_start: 0.8064 (t80) cc_final: 0.7736 (t80)
REVERT: D  319 GLN cc_start: 0.7758 (pm20) cc_final: 0.7558 (pm20)
REVERT: D  394 GLN cc_start: 0.9297 (tt0) cc_final: 0.8851 (tp40)
REVERT: D  395 MET cc_start: 0.8705 (mtt) cc_final: 0.8274 (ttm)
REVERT: D  538 ILE cc_start: 0.9642 (mt) cc_final: 0.9358 (tp)
REVERT: D  586 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7472 (pt0)
REVERT: D  621 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7830 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 264
  average time/residue: 0.0947
  time to fit residues: 37.0182
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  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 112 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 134 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 119 optimal weight:    4.9990
   chunk 63 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 99 optimal weight:    0.5980
   chunk 31 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 262 ASN ** 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 = 0.3852 r_free = 0.3852 target = 0.122165 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.097624 restraints weight = 36111.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.099004 restraints weight = 20859.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.099550 restraints weight = 15063.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.100182 restraints weight = 13542.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.100685 restraints weight = 12546.638|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  11225  Z= 0.151
  Angle     :  0.631   9.779  15224  Z= 0.322
  Chirality :  0.040   0.224   1767
  Planarity :  0.005   0.056   1983
  Dihedral  :  4.486  21.712   1523
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.31 (0.23), residues: 1381
  helix:  1.00 (0.17), residues: 938
  sheet:  None (None), residues: 0
  loop : -1.49 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 350 
 TYR   0.032   0.002   TYR A 354 
 PHE   0.035   0.002   PHE A 549 
 TRP   0.027   0.003   TRP A 209 
 HIS   0.008   0.001   HIS A 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 (11225)
  covalent geometry    : angle       0.63077 (15224)
  hydrogen bonds       : bond        0.03729 (  630)
  hydrogen bonds       : angle       4.53630 ( 1863)

*********************** 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
  260 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8656 (t80) cc_final: 0.7896 (t80)
REVERT: A   58 HIS cc_start: 0.7693 (m90) cc_final: 0.7195 (m-70)
REVERT: A   60 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8379 (mtpp)
REVERT: A   63 ARG cc_start: 0.9121 (ttm110) cc_final: 0.8868 (ttm110)
REVERT: A  507 CYS cc_start: 0.7848 (m) cc_final: 0.7362 (m)
REVERT: A  541 GLN cc_start: 0.8253 (mt0) cc_final: 0.7278 (tm-30)
REVERT: A  561 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8142 (tm-30)
REVERT: A  592 GLN cc_start: 0.6647 (mm-40) cc_final: 0.6284 (mm-40)
REVERT: A  620 LEU cc_start: 0.8574 (mm) cc_final: 0.8227 (mm)
REVERT: B   70 PHE cc_start: 0.8711 (t80) cc_final: 0.8481 (t80)
REVERT: B   91 ASP cc_start: 0.8771 (t70) cc_final: 0.8571 (t70)
REVERT: B  118 VAL cc_start: 0.9023 (t) cc_final: 0.8643 (t)
REVERT: C   76 LEU cc_start: 0.8296 (mt) cc_final: 0.8002 (mt)
REVERT: D    1 MET cc_start: 0.1652 (mpp) cc_final: 0.1287 (mpp)
REVERT: D   46 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.8228 (ttp80)
REVERT: D  135 ASP cc_start: 0.9111 (p0) cc_final: 0.8836 (p0)
REVERT: D  147 ILE cc_start: 0.8426 (pt) cc_final: 0.8136 (mm)
REVERT: D  260 PHE cc_start: 0.8924 (m-80) cc_final: 0.8554 (m-80)
REVERT: D  273 TYR cc_start: 0.8080 (t80) cc_final: 0.7737 (t80)
REVERT: D  319 GLN cc_start: 0.7755 (pm20) cc_final: 0.7543 (pm20)
REVERT: D  394 GLN cc_start: 0.9301 (tt0) cc_final: 0.8870 (tp40)
REVERT: D  538 ILE cc_start: 0.9631 (mt) cc_final: 0.9370 (tp)
REVERT: D  586 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7480 (pt0)
REVERT: D  621 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7835 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.0957
  time to fit residues: 36.7612
Evaluate side-chains
  209 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 136 optimal weight:    0.9980
   chunk 87 optimal weight:    1.9990
   chunk 70 optimal weight:    8.9990
   chunk 58 optimal weight:    1.9990
   chunk 131 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0670
   chunk 108 optimal weight:    0.6980
   chunk 124 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 130 optimal weight:    0.7980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 112 GLN
** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN
** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.122528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.098341 restraints weight = 35964.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.099804 restraints weight = 20331.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.100375 restraints weight = 14632.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.101374 restraints weight = 13068.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.101312 restraints weight = 11835.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3499

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= 0.142
  Angle     :  0.639  10.906  15224  Z= 0.324
  Chirality :  0.040   0.189   1767
  Planarity :  0.004   0.055   1983
  Dihedral  :  4.488  22.537   1523
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.29 (0.23), residues: 1381
  helix:  0.99 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -1.51 (0.31), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 126 
 TYR   0.021   0.001   TYR D 267 
 PHE   0.020   0.002   PHE D 388 
 TRP   0.025   0.002   TRP A 209 
 HIS   0.008   0.001   HIS D 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (11225)
  covalent geometry    : angle       0.63861 (15224)
  hydrogen bonds       : bond        0.03709 (  630)
  hydrogen bonds       : angle       4.50629 ( 1863)

*********************** 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
  261 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 TYR cc_start: 0.8636 (t80) cc_final: 0.7880 (t80)
REVERT: A   58 HIS cc_start: 0.7673 (m90) cc_final: 0.7157 (m-70)
REVERT: A   60 LYS cc_start: 0.8997 (mmmm) cc_final: 0.8379 (mtpp)
REVERT: A   63 ARG cc_start: 0.9125 (ttm110) cc_final: 0.8831 (ttm110)
REVERT: A  439 ASN cc_start: 0.8116 (t0) cc_final: 0.7853 (t0)
REVERT: A  507 CYS cc_start: 0.7741 (m) cc_final: 0.7237 (m)
REVERT: A  541 GLN cc_start: 0.8258 (mt0) cc_final: 0.7269 (tm-30)
REVERT: A  561 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8127 (tm-30)
REVERT: A  592 GLN cc_start: 0.6632 (mm-40) cc_final: 0.6227 (mm-40)
REVERT: A  620 LEU cc_start: 0.8558 (mm) cc_final: 0.8205 (mm)
REVERT: B   70 PHE cc_start: 0.8687 (t80) cc_final: 0.8459 (t80)
REVERT: B   91 ASP cc_start: 0.8779 (t70) cc_final: 0.8574 (t70)
REVERT: B  118 VAL cc_start: 0.9013 (t) cc_final: 0.8702 (t)
REVERT: C  112 GLN cc_start: 0.8690 (mm110) cc_final: 0.8147 (mp10)
REVERT: D    1 MET cc_start: 0.1680 (mpp) cc_final: 0.1291 (mpp)
REVERT: D   46 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8258 (ttp80)
REVERT: D  135 ASP cc_start: 0.9100 (p0) cc_final: 0.8846 (p0)
REVERT: D  147 ILE cc_start: 0.8464 (pt) cc_final: 0.8173 (mm)
REVERT: D  273 TYR cc_start: 0.8055 (t80) cc_final: 0.7702 (t80)
REVERT: D  319 GLN cc_start: 0.7754 (pm20) cc_final: 0.7401 (pm20)
REVERT: D  394 GLN cc_start: 0.9294 (tt0) cc_final: 0.8840 (tp40)
REVERT: D  395 MET cc_start: 0.8659 (mtt) cc_final: 0.8164 (ttm)
REVERT: D  538 ILE cc_start: 0.9612 (mt) cc_final: 0.9346 (mm)
REVERT: D  586 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7514 (pt0)
REVERT: D  621 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7836 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.0961
  time to fit residues: 37.3403
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  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 86 optimal weight:    3.9990
   chunk 4 optimal weight:    6.9990
   chunk 76 optimal weight:   10.0000
   chunk 56 optimal weight:    0.2980
   chunk 93 optimal weight:    0.1980
   chunk 71 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 45 optimal weight:    0.1980
   chunk 120 optimal weight:    0.9980
   chunk 135 optimal weight:    5.9990
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN
** D 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.123230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099623 restraints weight = 35716.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.100083 restraints weight = 20479.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.101012 restraints weight = 16214.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.101343 restraints weight = 13485.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.101520 restraints weight = 12390.105|
|-----------------------------------------------------------------------------|
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.3624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  11225  Z= 0.126
  Angle     :  0.632   9.380  15224  Z= 0.320
  Chirality :  0.040   0.187   1767
  Planarity :  0.004   0.057   1983
  Dihedral  :  4.468  22.794   1523
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 14.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.95 %
    Favored  : 93.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.23), residues: 1381
  helix:  1.02 (0.17), residues: 936
  sheet:  None (None), residues: 0
  loop : -1.54 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  63 
 TYR   0.032   0.001   TYR A  38 
 PHE   0.024   0.001   PHE A 549 
 TRP   0.023   0.002   TRP A 209 
 HIS   0.009   0.001   HIS D 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (11225)
  covalent geometry    : angle       0.63250 (15224)
  hydrogen bonds       : bond        0.03668 (  630)
  hydrogen bonds       : angle       4.45260 ( 1863)

*********************** 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
  257 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.432 
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: 0.8664 (t80) cc_final: 0.7936 (t80)
REVERT: A   58 HIS cc_start: 0.7707 (m90) cc_final: 0.7156 (m-70)
REVERT: A   60 LYS cc_start: 0.8965 (mmmm) cc_final: 0.8332 (mtpp)
REVERT: A   63 ARG cc_start: 0.9129 (ttm110) cc_final: 0.8822 (ttm110)
REVERT: A  264 ARG cc_start: 0.7673 (ptt-90) cc_final: 0.7148 (ptt-90)
REVERT: A  507 CYS cc_start: 0.7726 (m) cc_final: 0.7241 (m)
REVERT: A  541 GLN cc_start: 0.8265 (mt0) cc_final: 0.7290 (tm-30)
REVERT: A  542 TYR cc_start: 0.7835 (t80) cc_final: 0.7430 (t80)
REVERT: A  561 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8157 (tm-30)
REVERT: A  592 GLN cc_start: 0.6608 (mm-40) cc_final: 0.6191 (mm-40)
REVERT: A  620 LEU cc_start: 0.8551 (mm) cc_final: 0.8202 (mm)
REVERT: B   70 PHE cc_start: 0.8708 (t80) cc_final: 0.8494 (t80)
REVERT: B  118 VAL cc_start: 0.9014 (t) cc_final: 0.8742 (t)
REVERT: C  112 GLN cc_start: 0.8719 (mm110) cc_final: 0.8167 (mp10)
REVERT: D    1 MET cc_start: 0.1473 (mpp) cc_final: 0.1116 (mpp)
REVERT: D   46 ARG cc_start: 0.8544 (ptm-80) cc_final: 0.8266 (ttp80)
REVERT: D  125 LEU cc_start: 0.9617 (tt) cc_final: 0.9416 (tt)
REVERT: D  135 ASP cc_start: 0.9135 (p0) cc_final: 0.8880 (p0)
REVERT: D  147 ILE cc_start: 0.8450 (pt) cc_final: 0.8186 (mm)
REVERT: D  264 ARG cc_start: 0.8592 (ttm110) cc_final: 0.8277 (ttm-80)
REVERT: D  273 TYR cc_start: 0.8068 (t80) cc_final: 0.7707 (t80)
REVERT: D  319 GLN cc_start: 0.7689 (pm20) cc_final: 0.7343 (pm20)
REVERT: D  394 GLN cc_start: 0.9265 (tt0) cc_final: 0.8821 (tp40)
REVERT: D  538 ILE cc_start: 0.9607 (mt) cc_final: 0.9320 (mm)
REVERT: D  586 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7447 (pt0)
REVERT: D  621 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7814 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0898
  time to fit residues: 34.2706
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  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 46 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 71 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   chunk 11 optimal weight:   20.0000
   chunk 54 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.122132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.097839 restraints weight = 36025.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.099405 restraints weight = 20522.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.100097 restraints weight = 14594.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.100432 restraints weight = 12960.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.100693 restraints weight = 12127.655|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11225  Z= 0.165
  Angle     :  0.664  10.846  15224  Z= 0.337
  Chirality :  0.041   0.182   1767
  Planarity :  0.004   0.055   1983
  Dihedral  :  4.504  22.607   1523
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.23 (0.23), residues: 1381
  helix:  0.96 (0.17), residues: 933
  sheet:  None (None), residues: 0
  loop : -1.55 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 126 
 TYR   0.031   0.001   TYR A  38 
 PHE   0.013   0.002   PHE C 119 
 TRP   0.026   0.002   TRP A 209 
 HIS   0.009   0.001   HIS D 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (11225)
  covalent geometry    : angle       0.66434 (15224)
  hydrogen bonds       : bond        0.03739 (  630)
  hydrogen bonds       : angle       4.57911 ( 1863)

********************** 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
  249 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.545 
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: 0.8655 (t80) cc_final: 0.7928 (t80)
REVERT: A   58 HIS cc_start: 0.7705 (m90) cc_final: 0.7159 (m-70)
REVERT: A   60 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8661 (mmmm)
REVERT: A  395 MET cc_start: 0.8813 (mmm) cc_final: 0.8527 (mmm)
REVERT: A  507 CYS cc_start: 0.7715 (m) cc_final: 0.7234 (m)
REVERT: A  541 GLN cc_start: 0.8297 (mt0) cc_final: 0.7281 (tm-30)
REVERT: A  542 TYR cc_start: 0.7788 (t80) cc_final: 0.7439 (t80)
REVERT: A  561 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: A  592 GLN cc_start: 0.6551 (mm-40) cc_final: 0.6121 (mm-40)
REVERT: A  620 LEU cc_start: 0.8578 (mm) cc_final: 0.8318 (mm)
REVERT: B   70 PHE cc_start: 0.8717 (t80) cc_final: 0.8501 (t80)
REVERT: B  118 VAL cc_start: 0.9018 (t) cc_final: 0.8756 (t)
REVERT: D    1 MET cc_start: 0.1509 (mpp) cc_final: 0.1168 (mpp)
REVERT: D   46 ARG cc_start: 0.8562 (ptm-80) cc_final: 0.8269 (ttp80)
REVERT: D  125 LEU cc_start: 0.9609 (tt) cc_final: 0.9395 (tt)
REVERT: D  135 ASP cc_start: 0.9145 (p0) cc_final: 0.8915 (p0)
REVERT: D  147 ILE cc_start: 0.8498 (pt) cc_final: 0.8220 (mm)
REVERT: D  260 PHE cc_start: 0.8944 (m-80) cc_final: 0.8450 (m-80)
REVERT: D  273 TYR cc_start: 0.8081 (t80) cc_final: 0.7767 (t80)
REVERT: D  319 GLN cc_start: 0.7714 (pm20) cc_final: 0.7381 (pm20)
REVERT: D  394 GLN cc_start: 0.9246 (tt0) cc_final: 0.8781 (tp40)
REVERT: D  538 ILE cc_start: 0.9590 (mt) cc_final: 0.9302 (mm)
REVERT: D  586 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7519 (pt0)
REVERT: D  621 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7793 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0901
  time to fit residues: 33.1982
Evaluate side-chains
  204 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 79 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 86 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    9.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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**
** D 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 380 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.121785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.097458 restraints weight = 36012.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.098613 restraints weight = 20986.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.099156 restraints weight = 15309.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.099535 restraints weight = 13660.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.099862 restraints weight = 12828.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.080  11225  Z= 0.164
  Angle     :  0.664  10.456  15224  Z= 0.337
  Chirality :  0.041   0.309   1767
  Planarity :  0.004   0.054   1983
  Dihedral  :  4.509  21.787   1523
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.88 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.21 (0.23), residues: 1381
  helix:  0.95 (0.17), residues: 931
  sheet:  None (None), residues: 0
  loop : -1.56 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  63 
 TYR   0.022   0.001   TYR D 267 
 PHE   0.028   0.002   PHE A 549 
 TRP   0.027   0.003   TRP A 209 
 HIS   0.009   0.001   HIS D 274 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (11225)
  covalent geometry    : angle       0.66411 (15224)
  hydrogen bonds       : bond        0.03693 (  630)
  hydrogen bonds       : angle       4.60395 ( 1863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2499.87 seconds
wall clock time: 44 minutes 5.46 seconds (2645.46 seconds total)