Starting phenix.real_space_refine
on Fri Oct 10 16:59:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u62_41941/10_2025/8u62_41941.map"
  }
  resolution = 3.3
  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=   0.001 sd=   0.019
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      46      5.16       5
     C    4977      2.51       5
     N    1374      2.21       5
     O    1487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7884
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 3958
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 507, 3958
          Classifications: {'peptide': 507}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 480}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 3840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3840
          Classifications: {'peptide': 491}
          Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 464}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.94, per 1000 atoms: 0.25
  Number of scatterers: 7884
  At special positions: 0
  Unit cell: (85.41, 117.603, 130.743, 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      46     16.00
     O    1487      8.00
     N    1374      7.00
     C    4977      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 371.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1876

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      48.2% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'B' and resid 2 through 15
      removed outlier: 3.702A  pdb=" N   ALA B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 51
      No H-bonds generated for 'chain 'B' and resid 49 through 51'
    Processing helix  chain 'B' and resid 57 through 62
      removed outlier: 3.832A  pdb=" N   LEU B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ALA B  62 " --> pdb=" O   PRO B  58 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 57 through 62'
    Processing helix  chain 'B' and resid 66 through 71
    Processing helix  chain 'B' and resid 71 through 83
    Processing helix  chain 'B' and resid 130 through 145
    Processing helix  chain 'B' and resid 148 through 165
    Processing helix  chain 'B' and resid 200 through 204
    Processing helix  chain 'B' and resid 205 through 215
    Processing helix  chain 'B' and resid 253 through 264
    Processing helix  chain 'B' and resid 294 through 342
      removed outlier: 3.528A  pdb=" N   GLN B 306 " --> pdb=" O   GLN B 302 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   ASP B 342 " --> pdb=" O   MET B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 352
      removed outlier: 3.883A  pdb=" N   GLN B 352 " --> pdb=" O   GLY B 348 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 361
      removed outlier: 3.628A  pdb=" N   ASP B 358 " --> pdb=" O   GLN B 354 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   VAL B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 396
      removed outlier: 3.605A  pdb=" N   THR B 390 " --> pdb=" O   ARG B 386 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   TRP B 391 " --> pdb=" O   ALA B 387 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   MET B 392 " --> pdb=" O   LEU B 388 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLY B 395 " --> pdb=" O   TRP B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 441 through 446
      removed outlier: 4.147A  pdb=" N   SER B 445 " --> pdb=" O   GLU B 441 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL B 446 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 441 through 446'
    Processing helix  chain 'B' and resid 468 through 480
    Processing helix  chain 'B' and resid 488 through 513
    Processing helix  chain 'B' and resid 513 through 526
      removed outlier: 3.909A  pdb=" N   ALA B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG B 521 " --> pdb=" O   ALA B 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 4 through 15
      removed outlier: 3.502A  pdb=" N   ALA A  14 " --> pdb=" O   GLU A  10 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASN A  15 " --> pdb=" O   VAL A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 3.549A  pdb=" N   GLN A  51 " --> pdb=" O   ALA A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 62
      removed outlier: 3.511A  pdb=" N   ALA A  62 " --> pdb=" O   PRO A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 69
    Processing helix  chain 'A' and resid 71 through 82
    Processing helix  chain 'A' and resid 130 through 146
    Processing helix  chain 'A' and resid 148 through 165
    Processing helix  chain 'A' and resid 200 through 204
    Processing helix  chain 'A' and resid 205 through 214
    Processing helix  chain 'A' and resid 253 through 264
    Processing helix  chain 'A' and resid 294 through 340
      removed outlier: 3.601A  pdb=" N   THR A 340 " --> pdb=" O   GLN A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.545A  pdb=" N   MET A 357 " --> pdb=" O   PRO A 353 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 396
      removed outlier: 3.579A  pdb=" N   ALA A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   TRP A 391 " --> pdb=" O   ALA A 387 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   MET A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   MET A 393 " --> pdb=" O   HIS A 389 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ALA A 394 " --> pdb=" O   THR A 390 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   GLY A 395 " --> pdb=" O   TRP A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.972A  pdb=" N   VAL A 408 " --> pdb=" O   HIS A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 446
      removed outlier: 3.533A  pdb=" N   VAL A 446 " --> pdb=" O   LYS A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 488 through 517
      removed outlier: 3.562A  pdb=" N   ALA A 495 " --> pdb=" O   ASP A 491 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   ALA A 517 " --> pdb=" O   LYS A 513 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 27
      removed outlier: 6.575A  pdb=" N   THR B  35 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 4.386A  pdb=" N   VAL B  46 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU B  33 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 4.486A  pdb=" N   LEU B  93 " --> pdb=" O   ALA B 104 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 198 through 199
      removed outlier: 6.629A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLU B 185 " --> pdb=" O   VAL B 169 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   VAL B 169 " --> pdb=" O   GLU B 185 " (cutoff:3.500A)
      removed outlier: 6.323A  pdb=" N   TRP B 280 " --> pdb=" O   PHE B 174 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   LEU B 273 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 4.929A  pdb=" N   LEU B 282 " --> pdb=" O   VAL B 271 " (cutoff:3.500A)
      removed outlier: 6.618A  pdb=" N   VAL B 271 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 4.761A  pdb=" N   SER B 284 " --> pdb=" O   MET B 269 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   MET B 269 " --> pdb=" O   SER B 284 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   GLY B 286 " --> pdb=" O   SER B 267 " (cutoff:3.500A)
      removed outlier: 6.853A  pdb=" N   SER B 267 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 372 through 377
      removed outlier: 3.800A  pdb=" N   GLY B 364 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ILE B 436 " --> pdb=" O   ALA B 366 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA5, first strand: chain 'A' and resid 43 through 46
      removed outlier: 6.366A  pdb=" N   THR A  35 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   VAL A  46 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   LEU A  33 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 198 through 199
      removed outlier: 6.693A  pdb=" N   ILE A 171 " --> pdb=" O   ILE A 183 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   GLU A 185 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL A 169 " --> pdb=" O   GLU A 185 " (cutoff:3.500A)
      removed outlier: 6.464A  pdb=" N   TRP A 280 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      removed outlier: 7.155A  pdb=" N   LEU A 273 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   LEU A 282 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   VAL A 271 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      removed outlier: 4.818A  pdb=" N   SER A 284 " --> pdb=" O   MET A 269 " (cutoff:3.500A)
      removed outlier: 6.588A  pdb=" N   MET A 269 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   GLY A 286 " --> pdb=" O   SER A 267 " (cutoff:3.500A)
      removed outlier: 6.662A  pdb=" N   SER A 267 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 373 through 377
      removed outlier: 3.717A  pdb=" N   GLY A 364 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 421 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)

    424 hydrogen bonds defined for protein.
    1182 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: 1.21

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1472
        1.32 -     1.45: 1938
        1.45 -     1.57: 4555
        1.57 -     1.69: 0
        1.69 -     1.82: 78
  Bond restraints: 8043
  Sorted by residual:
  bond pdb=" C   GLU A  38 "
       pdb=" N   PRO A  39 "
    ideal  model  delta    sigma   weight residual
    1.334  1.364 -0.030 2.34e-02 1.83e+03 1.65e+00
  bond pdb=" CA  GLN A 240 "
       pdb=" CB  GLN A 240 "
    ideal  model  delta    sigma   weight residual
    1.534  1.552 -0.019 1.78e-02 3.16e+03 1.11e+00
  bond pdb=" CB  TRP A 391 "
       pdb=" CG  TRP A 391 "
    ideal  model  delta    sigma   weight residual
    1.498  1.530 -0.032 3.10e-02 1.04e+03 1.06e+00
  bond pdb=" CB  GLU A  40 "
       pdb=" CG  GLU A  40 "
    ideal  model  delta    sigma   weight residual
    1.520  1.549 -0.029 3.00e-02 1.11e+03 9.32e-01
  bond pdb=" CA  GLU A 369 "
       pdb=" CB  GLU A 369 "
    ideal  model  delta    sigma   weight residual
    1.534  1.558 -0.023 2.47e-02 1.64e+03 8.87e-01
  ... (remaining 8038 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 10808
        2.53 -     5.07: 99
        5.07 -     7.60: 12
        7.60 -    10.13: 8
       10.13 -    12.66: 1
  Bond angle restraints: 10928
  Sorted by residual:
  angle pdb=" CA  MET A 139 "
        pdb=" CB  MET A 139 "
        pdb=" CG  MET A 139 "
      ideal   model   delta    sigma   weight residual
     114.10  121.72   -7.62 2.00e+00 2.50e-01 1.45e+01
  angle pdb=" N   GLU A 413 "
        pdb=" CA  GLU A 413 "
        pdb=" C   GLU A 413 "
      ideal   model   delta    sigma   weight residual
     114.56  109.82    4.74 1.27e+00 6.20e-01 1.39e+01
  angle pdb=" CA  LEU A 113 "
        pdb=" CB  LEU A 113 "
        pdb=" CG  LEU A 113 "
      ideal   model   delta    sigma   weight residual
     116.30  128.96  -12.66 3.50e+00 8.16e-02 1.31e+01
  angle pdb=" CB  MET A 139 "
        pdb=" CG  MET A 139 "
        pdb=" SD  MET A 139 "
      ideal   model   delta    sigma   weight residual
     112.70  122.56   -9.86 3.00e+00 1.11e-01 1.08e+01
  angle pdb=" CA  GLU A 369 "
        pdb=" CB  GLU A 369 "
        pdb=" CG  GLU A 369 "
      ideal   model   delta    sigma   weight residual
     114.10  120.46   -6.36 2.00e+00 2.50e-01 1.01e+01
  ... (remaining 10923 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 4145
       17.98 -    35.96: 525
       35.96 -    53.93: 155
       53.93 -    71.91: 43
       71.91 -    89.89: 14
  Dihedral angle restraints: 4882
    sinusoidal: 1991
      harmonic: 2891
  Sorted by residual:
  dihedral pdb=" CA  ILE B 368 "
           pdb=" C   ILE B 368 "
           pdb=" N   GLU B 369 "
           pdb=" CA  GLU B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.27   16.73     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CG  ARG A 322 "
           pdb=" CD  ARG A 322 "
           pdb=" NE  ARG A 322 "
           pdb=" CZ  ARG A 322 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   45.03   44.97     2      1.50e+01 4.44e-03 1.07e+01
  dihedral pdb=" CG  ARG B 162 "
           pdb=" CD  ARG B 162 "
           pdb=" NE  ARG B 162 "
           pdb=" CZ  ARG B 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.01   43.99     2      1.50e+01 4.44e-03 1.03e+01
  ... (remaining 4879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 796
       0.033 -    0.065: 295
       0.065 -    0.098: 82
       0.098 -    0.130: 43
       0.130 -    0.163: 9
  Chirality restraints: 1225
  Sorted by residual:
  chirality pdb=" CG  LEU A 113 "
            pdb=" CB  LEU A 113 "
            pdb=" CD1 LEU A 113 "
            pdb=" CD2 LEU A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.61e-01
  chirality pdb=" CG  LEU A 117 "
            pdb=" CB  LEU A 117 "
            pdb=" CD1 LEU A 117 "
            pdb=" CD2 LEU A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ILE A 220 "
            pdb=" N   ILE A 220 "
            pdb=" C   ILE A 220 "
            pdb=" CB  ILE A 220 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.23e-01
  ... (remaining 1222 not shown)

  Planarity restraints: 1423
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 391 "   -0.016 2.00e-02 2.50e+03   1.36e-02 4.64e+00
        pdb=" CG  TRP A 391 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 391 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 391 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 391 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 391 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 391 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 391 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 391 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 391 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A  40 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.71e+00
        pdb=" C   GLU A  40 "    0.028 2.00e-02 2.50e+03
        pdb=" O   GLU A  40 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   LEU A  41 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 410 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO A 411 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 411 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 411 "    0.023 5.00e-02 4.00e+02
  ... (remaining 1420 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 307
        2.72 -     3.26: 7758
        3.26 -     3.81: 12860
        3.81 -     4.35: 14986
        4.35 -     4.90: 25833
  Nonbonded interactions: 61744
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 225 "
            pdb=" OG  SER B 251 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" O   GLN A 416 "
            pdb=" OG  SER A 420 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   ALA A 387 "
            pdb=" OG1 THR A 390 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OG  SER A  47 "
            pdb=" OD1 ASN A  49 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OE1 GLU A 381 "
            pdb=" OG  SER A 383 "
     model   vdw
     2.274 3.040
  ... (remaining 61739 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 'B' and (resid 3 through 123 or resid 129 through 340 or resid 345 throug \ 
h 517 or resid 900))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.010
  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:0.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
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   0.067   8045  Z= 0.177
  Angle     :  0.614  12.663  10928  Z= 0.296
  Chirality :  0.042   0.163   1225
  Planarity :  0.004   0.041   1423
  Dihedral  : 18.211  89.888   3006
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  0.59 %
    Allowed  : 31.02 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    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:  0.96 (0.28), residues: 984
  helix:  1.50 (0.26), residues: 414
  sheet: -0.07 (0.39), residues: 169
  loop :  0.19 (0.35), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 322 
 TYR   0.025   0.001   TYR A 409 
 PHE   0.010   0.001   PHE B  34 
 TRP   0.037   0.001   TRP A 391 
 HIS   0.015   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8043)
  covalent geometry    : angle       0.61393 (10928)
  hydrogen bonds       : bond        0.22741 (  424)
  hydrogen bonds       : angle       6.90400 ( 1182)
  Misc. bond           : bond        0.06558 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 190
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.8378 (ttm110) cc_final: 0.8020 (ptp-110)
REVERT: B  337 MET cc_start: 0.7501 (tpp) cc_final: 0.7193 (tpp)
REVERT: B  370 ASP cc_start: 0.6754 (m-30) cc_final: 0.6549 (m-30)
  outliers start: 5
  outliers final: 3
  residues processed: 192
  average time/residue: 0.1038
  time to fit residues: 26.0035
Evaluate side-chains
  193 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 190
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  248 THR
Chi-restraints excluded: chain A residue  275 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 275 GLN
A 354 GLN
A 505 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.148990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.127688 restraints weight = 11961.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3621 rms_B_bonded: 2.78
r_work: 0.3471 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.1207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   8045  Z= 0.205
  Angle     :  0.585   8.069  10928  Z= 0.294
  Chirality :  0.043   0.150   1225
  Planarity :  0.005   0.042   1423
  Dihedral  :  5.888  54.354   1124
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 27.14 %
    Favored  : 68.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.28), residues: 984
  helix:  2.04 (0.25), residues: 428
  sheet:  0.10 (0.39), residues: 173
  loop :  0.08 (0.36), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 322 
 TYR   0.016   0.001   TYR A 409 
 PHE   0.012   0.001   PHE A  34 
 TRP   0.020   0.002   TRP A 391 
 HIS   0.008   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8043)
  covalent geometry    : angle       0.58475 (10928)
  hydrogen bonds       : bond        0.04569 (  424)
  hydrogen bonds       : angle       4.62935 ( 1182)
  Misc. bond           : bond        0.00084 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 197
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  324 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7839 (ttt180)
REVERT: B  402 SER cc_start: 0.8681 (p) cc_final: 0.8437 (p)
REVERT: B  519 ARG cc_start: 0.5535 (tpt90) cc_final: 0.4864 (tpt170)
REVERT: A  105 LEU cc_start: 0.8278 (mm) cc_final: 0.7978 (mt)
REVERT: A  158 ARG cc_start: 0.7267 (ttm-80) cc_final: 0.6978 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7444 (mtt-85)
REVERT: A  240 GLN cc_start: 0.6970 (tm-30) cc_final: 0.6653 (tm-30)
REVERT: A  275 GLN cc_start: 0.7611 (pp30) cc_final: 0.7346 (pp30)
REVERT: A  299 SER cc_start: 0.8444 (m) cc_final: 0.8215 (m)
REVERT: A  352 GLN cc_start: 0.7936 (pp30) cc_final: 0.7296 (pp30)
  outliers start: 39
  outliers final: 21
  residues processed: 221
  average time/residue: 0.1032
  time to fit residues: 29.7664
Evaluate side-chains
  217 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 195
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  431 VAL
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  142 GLN
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  390 THR
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 52 optimal weight:    0.7980
   chunk 82 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9990
   chunk 78 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 75 optimal weight:    0.5980
   chunk 90 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9990
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.149300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.128069 restraints weight = 11866.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.3632 rms_B_bonded: 2.78
r_work: 0.3481 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8045  Z= 0.178
  Angle     :  0.563   7.030  10928  Z= 0.280
  Chirality :  0.042   0.149   1225
  Planarity :  0.004   0.043   1423
  Dihedral  :  5.660  55.455   1120
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 25.97 %
    Favored  : 68.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.28), residues: 984
  helix:  2.17 (0.25), residues: 429
  sheet:  0.16 (0.39), residues: 173
  loop : -0.01 (0.35), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 322 
 TYR   0.013   0.001   TYR A 409 
 PHE   0.012   0.001   PHE A  34 
 TRP   0.018   0.001   TRP A 391 
 HIS   0.007   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 ( 8043)
  covalent geometry    : angle       0.56321 (10928)
  hydrogen bonds       : bond        0.04125 (  424)
  hydrogen bonds       : angle       4.42480 ( 1182)
  Misc. bond           : bond        0.00058 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8034 (tpp) cc_final: 0.7551 (ttp)
REVERT: B  159 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7067 (tt0)
REVERT: B  304 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8220 (mt)
REVERT: B  324 ARG cc_start: 0.8133 (ttt180) cc_final: 0.7850 (ttt180)
REVERT: B  519 ARG cc_start: 0.5369 (tpt90) cc_final: 0.4126 (tpt170)
REVERT: A  105 LEU cc_start: 0.8278 (mm) cc_final: 0.7974 (mt)
REVERT: A  158 ARG cc_start: 0.7255 (ttm-80) cc_final: 0.6963 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7415 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7622 (pp30) cc_final: 0.7332 (pp30)
REVERT: A  333 GLN cc_start: 0.7962 (tp-100) cc_final: 0.7702 (tp-100)
REVERT: A  337 MET cc_start: 0.7571 (tpt) cc_final: 0.7348 (tpt)
REVERT: A  352 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7412 (pp30)
  outliers start: 48
  outliers final: 30
  residues processed: 226
  average time/residue: 0.1026
  time to fit residues: 30.0258
Evaluate side-chains
  226 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 192
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 GLN
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 21 optimal weight:    0.0040
   chunk 75 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0970
   chunk 14 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.2990

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 258 GLN
A 302 GLN
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.151474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.130306 restraints weight = 12020.835|
|-----------------------------------------------------------------------------|
r_work (start): 0.3654 rms_B_bonded: 2.80
r_work: 0.3508 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3508
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7392
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8045  Z= 0.111
  Angle     :  0.517   6.975  10928  Z= 0.255
  Chirality :  0.041   0.148   1225
  Planarity :  0.004   0.044   1423
  Dihedral  :  5.510  58.235   1120
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 27.38 %
    Favored  : 67.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.62 (0.28), residues: 984
  helix:  2.48 (0.25), residues: 428
  sheet:  0.18 (0.39), residues: 165
  loop : -0.08 (0.35), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.012   0.001   TYR A 409 
 PHE   0.013   0.001   PHE B 199 
 TRP   0.012   0.001   TRP A 391 
 HIS   0.006   0.001   HIS A 295 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8043)
  covalent geometry    : angle       0.51732 (10928)
  hydrogen bonds       : bond        0.03366 (  424)
  hydrogen bonds       : angle       4.16591 ( 1182)
  Misc. bond           : bond        0.00037 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 194
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8037 (tpp) cc_final: 0.7421 (ttp)
REVERT: B  142 GLN cc_start: 0.7971 (mm-40) cc_final: 0.7527 (mm-40)
REVERT: B  159 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.7012 (tt0)
REVERT: B  304 ILE cc_start: 0.8468 (OUTLIER) cc_final: 0.8101 (tt)
REVERT: B  324 ARG cc_start: 0.8114 (ttt180) cc_final: 0.7902 (ttt180)
REVERT: B  337 MET cc_start: 0.7897 (tpp) cc_final: 0.7228 (tpp)
REVERT: B  519 ARG cc_start: 0.5230 (tpt90) cc_final: 0.3079 (mmt180)
REVERT: A   40 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6467 (pp20)
REVERT: A  105 LEU cc_start: 0.8262 (mm) cc_final: 0.7956 (mt)
REVERT: A  113 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6685 (tt)
REVERT: A  275 GLN cc_start: 0.7602 (pp30) cc_final: 0.7280 (pp30)
REVERT: A  315 MET cc_start: 0.7706 (tpp) cc_final: 0.6948 (mpp)
REVERT: A  316 GLU cc_start: 0.7918 (tt0) cc_final: 0.7668 (tp30)
REVERT: A  337 MET cc_start: 0.7513 (tpt) cc_final: 0.7308 (tpp)
REVERT: A  369 GLU cc_start: 0.6319 (pp20) cc_final: 0.5821 (pp20)
REVERT: A  500 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7504 (ttp-170)
  outliers start: 41
  outliers final: 25
  residues processed: 217
  average time/residue: 0.0910
  time to fit residues: 26.2413
Evaluate side-chains
  221 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 192
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 1 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 45 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 41 optimal weight:    0.1980
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.149994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128570 restraints weight = 11991.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3630 rms_B_bonded: 2.82
r_work: 0.3479 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.1626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8045  Z= 0.157
  Angle     :  0.544   7.478  10928  Z= 0.268
  Chirality :  0.042   0.167   1225
  Planarity :  0.004   0.042   1423
  Dihedral  :  5.560  56.240   1120
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 26.44 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.28), residues: 984
  helix:  2.40 (0.25), residues: 428
  sheet:  0.18 (0.39), residues: 166
  loop : -0.09 (0.35), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  79 
 TYR   0.010   0.001   TYR A 409 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.014   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8043)
  covalent geometry    : angle       0.54391 (10928)
  hydrogen bonds       : bond        0.03637 (  424)
  hydrogen bonds       : angle       4.15371 ( 1182)
  Misc. bond           : bond        0.00036 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 199
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8018 (tpp) cc_final: 0.7371 (ttp)
REVERT: B  159 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7016 (tt0)
REVERT: B  304 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8116 (tt)
REVERT: B  324 ARG cc_start: 0.8127 (ttt180) cc_final: 0.7831 (ttt180)
REVERT: B  337 MET cc_start: 0.7931 (tpp) cc_final: 0.7234 (tpp)
REVERT: B  354 GLN cc_start: 0.8238 (tp40) cc_final: 0.7935 (tp40)
REVERT: B  519 ARG cc_start: 0.5229 (tpt90) cc_final: 0.3655 (tpt170)
REVERT: A   40 GLU cc_start: 0.6729 (OUTLIER) cc_final: 0.6340 (pp20)
REVERT: A  105 LEU cc_start: 0.8292 (mm) cc_final: 0.7984 (mt)
REVERT: A  113 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6725 (tt)
REVERT: A  209 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7236 (ttm-80)
REVERT: A  275 GLN cc_start: 0.7637 (pp30) cc_final: 0.7302 (pp30)
REVERT: A  315 MET cc_start: 0.7741 (tpp) cc_final: 0.6951 (mpp)
REVERT: A  316 GLU cc_start: 0.7947 (tt0) cc_final: 0.7693 (tp30)
REVERT: A  333 GLN cc_start: 0.7975 (tp-100) cc_final: 0.7722 (tp-100)
REVERT: A  351 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.7268 (mp10)
REVERT: A  369 GLU cc_start: 0.6366 (pp20) cc_final: 0.5835 (pp20)
REVERT: A  500 ARG cc_start: 0.8055 (ttp-170) cc_final: 0.7548 (ttp-170)
  outliers start: 48
  outliers final: 34
  residues processed: 227
  average time/residue: 0.0963
  time to fit residues: 28.7445
Evaluate side-chains
  236 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 196
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 92 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 89 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** 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 = 0.3933 r_free = 0.3933 target = 0.149663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.128282 restraints weight = 11870.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.3634 rms_B_bonded: 2.79
r_work: 0.3481 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7430
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   8045  Z= 0.176
  Angle     :  0.554   6.773  10928  Z= 0.274
  Chirality :  0.042   0.179   1225
  Planarity :  0.004   0.041   1423
  Dihedral  :  5.665  55.837   1120
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  6.23 %
    Allowed  : 26.09 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.28), residues: 984
  helix:  2.29 (0.25), residues: 428
  sheet:  0.08 (0.39), residues: 167
  loop : -0.04 (0.35), residues: 389

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  79 
 TYR   0.008   0.001   TYR A 409 
 PHE   0.011   0.001   PHE A  34 
 TRP   0.017   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00395 ( 8043)
  covalent geometry    : angle       0.55354 (10928)
  hydrogen bonds       : bond        0.03698 (  424)
  hydrogen bonds       : angle       4.19384 ( 1182)
  Misc. bond           : bond        0.00035 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 198
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8013 (tpp) cc_final: 0.7370 (ttp)
REVERT: B  159 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7025 (tt0)
REVERT: B  304 ILE cc_start: 0.8473 (OUTLIER) cc_final: 0.8225 (mt)
REVERT: B  337 MET cc_start: 0.7949 (tpp) cc_final: 0.7230 (tpp)
REVERT: B  354 GLN cc_start: 0.8205 (tp40) cc_final: 0.7890 (tp40)
REVERT: B  519 ARG cc_start: 0.5192 (tpt90) cc_final: 0.3328 (tpt170)
REVERT: A   40 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6358 (pp20)
REVERT: A   79 ARG cc_start: 0.8288 (ttp-110) cc_final: 0.7910 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8293 (mm) cc_final: 0.7981 (mt)
REVERT: A  113 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6750 (tt)
REVERT: A  158 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.6990 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7506 (ttm-80)
REVERT: A  275 GLN cc_start: 0.7655 (pp30) cc_final: 0.7309 (pp30)
REVERT: A  315 MET cc_start: 0.7754 (tpp) cc_final: 0.6937 (mpp)
REVERT: A  316 GLU cc_start: 0.7975 (tt0) cc_final: 0.7704 (tp30)
REVERT: A  326 THR cc_start: 0.7877 (m) cc_final: 0.7000 (p)
REVERT: A  333 GLN cc_start: 0.7974 (tp-100) cc_final: 0.7704 (tp-100)
REVERT: A  351 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7168 (mp10)
REVERT: A  369 GLU cc_start: 0.6399 (pp20) cc_final: 0.5909 (pp20)
  outliers start: 53
  outliers final: 39
  residues processed: 228
  average time/residue: 0.0984
  time to fit residues: 29.5218
Evaluate side-chains
  239 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  351 GLN
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 52 optimal weight:    0.4980
   chunk 49 optimal weight:    0.0010
   chunk 0 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.4786

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

Flipped N/Q/H residues before XYZ refinement:
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.150775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.129528 restraints weight = 11940.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 2.80
r_work: 0.3490 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7416
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8045  Z= 0.141
  Angle     :  0.544   7.012  10928  Z= 0.268
  Chirality :  0.042   0.161   1225
  Planarity :  0.004   0.042   1423
  Dihedral  :  5.594  57.037   1120
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  5.88 %
    Allowed  : 26.44 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.28), residues: 984
  helix:  2.41 (0.25), residues: 426
  sheet:  0.06 (0.39), residues: 165
  loop : -0.11 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  79 
 TYR   0.009   0.001   TYR A 409 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.022   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 8043)
  covalent geometry    : angle       0.54395 (10928)
  hydrogen bonds       : bond        0.03465 (  424)
  hydrogen bonds       : angle       4.14998 ( 1182)
  Misc. bond           : bond        0.00032 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 200
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   13 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7714 (tp)
REVERT: B  139 MET cc_start: 0.8021 (tpp) cc_final: 0.7342 (ttp)
REVERT: B  159 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7012 (tt0)
REVERT: B  203 ASP cc_start: 0.7161 (m-30) cc_final: 0.6873 (t0)
REVERT: B  304 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8150 (tt)
REVERT: B  324 ARG cc_start: 0.8245 (ttt90) cc_final: 0.7945 (ttt180)
REVERT: B  337 MET cc_start: 0.7914 (tpp) cc_final: 0.7192 (tpp)
REVERT: B  354 GLN cc_start: 0.8206 (tp40) cc_final: 0.7914 (tp40)
REVERT: B  519 ARG cc_start: 0.5124 (tpt90) cc_final: 0.3245 (tpt170)
REVERT: A   40 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6259 (pp20)
REVERT: A   79 ARG cc_start: 0.8260 (ttp-110) cc_final: 0.7899 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8276 (mm) cc_final: 0.7966 (mt)
REVERT: A  113 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6743 (tt)
REVERT: A  158 ARG cc_start: 0.7258 (ttm-80) cc_final: 0.6972 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7371 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7639 (pp30) cc_final: 0.7279 (pp30)
REVERT: A  316 GLU cc_start: 0.8001 (tt0) cc_final: 0.7735 (tp30)
REVERT: A  326 THR cc_start: 0.7901 (m) cc_final: 0.6992 (p)
REVERT: A  333 GLN cc_start: 0.7980 (tp-100) cc_final: 0.7701 (tp-100)
REVERT: A  369 GLU cc_start: 0.6392 (pp20) cc_final: 0.5924 (pp20)
  outliers start: 50
  outliers final: 41
  residues processed: 229
  average time/residue: 0.1006
  time to fit residues: 30.3200
Evaluate side-chains
  244 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 197
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0000
   chunk 64 optimal weight:    0.2980
   chunk 15 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.5184

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
A 352 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.150654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129239 restraints weight = 12046.184|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 2.81
r_work: 0.3490 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7419
moved from start:          0.1794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8045  Z= 0.148
  Angle     :  0.548   7.264  10928  Z= 0.270
  Chirality :  0.042   0.152   1225
  Planarity :  0.004   0.042   1423
  Dihedral  :  5.628  56.743   1120
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  6.35 %
    Allowed  : 26.32 %
    Favored  : 67.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.28), residues: 984
  helix:  2.36 (0.25), residues: 427
  sheet:  0.09 (0.39), residues: 166
  loop : -0.09 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  79 
 TYR   0.011   0.001   TYR A 409 
 PHE   0.010   0.001   PHE B 199 
 TRP   0.021   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8043)
  covalent geometry    : angle       0.54809 (10928)
  hydrogen bonds       : bond        0.03477 (  424)
  hydrogen bonds       : angle       4.13785 ( 1182)
  Misc. bond           : bond        0.00031 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 199
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8016 (tpp) cc_final: 0.7370 (ttp)
REVERT: B  159 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7002 (tt0)
REVERT: B  203 ASP cc_start: 0.7167 (m-30) cc_final: 0.6883 (t0)
REVERT: B  337 MET cc_start: 0.7895 (tpp) cc_final: 0.7165 (tpp)
REVERT: B  354 GLN cc_start: 0.8181 (tp40) cc_final: 0.7892 (tp40)
REVERT: B  519 ARG cc_start: 0.5137 (tpt90) cc_final: 0.3208 (tpt170)
REVERT: A   40 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.6248 (pp20)
REVERT: A   79 ARG cc_start: 0.8270 (ttp-110) cc_final: 0.7916 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8278 (mm) cc_final: 0.7971 (mt)
REVERT: A  113 LEU cc_start: 0.7057 (OUTLIER) cc_final: 0.6738 (tt)
REVERT: A  158 ARG cc_start: 0.7251 (ttm-80) cc_final: 0.6965 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7369 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7641 (pp30) cc_final: 0.7275 (pp30)
REVERT: A  316 GLU cc_start: 0.7985 (tt0) cc_final: 0.7718 (tp30)
REVERT: A  326 THR cc_start: 0.7887 (m) cc_final: 0.6975 (p)
REVERT: A  333 GLN cc_start: 0.7988 (tp-100) cc_final: 0.7702 (tp-100)
REVERT: A  369 GLU cc_start: 0.6395 (pp20) cc_final: 0.5937 (pp20)
  outliers start: 54
  outliers final: 41
  residues processed: 230
  average time/residue: 0.0976
  time to fit residues: 29.5988
Evaluate side-chains
  240 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 195
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  211 LEU
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  242 LEU
Chi-restraints excluded: chain A residue  245 SER
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 GLN
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 46 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9980
   chunk 75 optimal weight:    0.2980
   chunk 49 optimal weight:    0.0040
   chunk 86 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 17 optimal weight:    0.2980
   chunk 90 optimal weight:    0.6980
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.3392

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
A 352 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.149559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.128067 restraints weight = 11944.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.79
r_work: 0.3505 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1850

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8045  Z= 0.118
  Angle     :  0.539   7.528  10928  Z= 0.266
  Chirality :  0.041   0.156   1225
  Planarity :  0.004   0.043   1423
  Dihedral  :  5.604  58.071   1120
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.41 %
    Allowed  : 26.67 %
    Favored  : 67.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.28), residues: 984
  helix:  2.45 (0.25), residues: 426
  sheet:  0.01 (0.39), residues: 165
  loop : -0.07 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  79 
 TYR   0.012   0.001   TYR A 409 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.018   0.001   TRP A 391 
 HIS   0.005   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8043)
  covalent geometry    : angle       0.53910 (10928)
  hydrogen bonds       : bond        0.03267 (  424)
  hydrogen bonds       : angle       4.08013 ( 1182)
  Misc. bond           : bond        0.00032 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 199
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.7984 (tpp) cc_final: 0.7341 (ttp)
REVERT: B  159 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7031 (tt0)
REVERT: B  203 ASP cc_start: 0.7158 (m-30) cc_final: 0.6885 (t0)
REVERT: B  337 MET cc_start: 0.7874 (tpp) cc_final: 0.7139 (tpp)
REVERT: B  354 GLN cc_start: 0.8199 (tp40) cc_final: 0.7941 (tp40)
REVERT: B  519 ARG cc_start: 0.4943 (tpt90) cc_final: 0.2556 (tpt90)
REVERT: A   40 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6195 (pp20)
REVERT: A  105 LEU cc_start: 0.8229 (mm) cc_final: 0.7941 (mp)
REVERT: A  113 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6708 (tt)
REVERT: A  209 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7388 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7639 (pp30) cc_final: 0.7266 (pp30)
REVERT: A  316 GLU cc_start: 0.7961 (tt0) cc_final: 0.7690 (tp30)
REVERT: A  326 THR cc_start: 0.7853 (m) cc_final: 0.6949 (p)
REVERT: A  333 GLN cc_start: 0.7994 (tp-100) cc_final: 0.7706 (tp-100)
REVERT: A  354 GLN cc_start: 0.6810 (tp40) cc_final: 0.6464 (tp-100)
REVERT: A  369 GLU cc_start: 0.6403 (pp20) cc_final: 0.5942 (pp20)
  outliers start: 46
  outliers final: 36
  residues processed: 227
  average time/residue: 0.0999
  time to fit residues: 29.6792
Evaluate side-chains
  234 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 194
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain B residue  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  304 ILE
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 36 optimal weight:    0.0670
   chunk 80 optimal weight:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 22 optimal weight:    0.1980
   chunk 24 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.149609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.128189 restraints weight = 11884.237|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 2.77
r_work: 0.3504 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8045  Z= 0.130
  Angle     :  0.555   7.741  10928  Z= 0.274
  Chirality :  0.042   0.155   1225
  Planarity :  0.005   0.043   1423
  Dihedral  :  5.693  57.749   1120
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 27.26 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.50 (0.28), residues: 984
  helix:  2.38 (0.25), residues: 427
  sheet:  0.03 (0.39), residues: 165
  loop : -0.08 (0.35), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 324 
 TYR   0.023   0.001   TYR A 409 
 PHE   0.011   0.001   PHE B 199 
 TRP   0.019   0.001   TRP A 391 
 HIS   0.005   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8043)
  covalent geometry    : angle       0.55530 (10928)
  hydrogen bonds       : bond        0.03341 (  424)
  hydrogen bonds       : angle       4.10273 ( 1182)
  Misc. bond           : bond        0.00029 (    2)

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

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

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1968 Ramachandran restraints generated.
    984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 196
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8009 (tpp) cc_final: 0.7358 (ttp)
REVERT: B  159 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7006 (tt0)
REVERT: B  203 ASP cc_start: 0.7164 (m-30) cc_final: 0.6899 (t0)
REVERT: B  324 ARG cc_start: 0.7849 (ttt90) cc_final: 0.7628 (ttt180)
REVERT: B  337 MET cc_start: 0.7896 (tpp) cc_final: 0.7153 (tpp)
REVERT: B  354 GLN cc_start: 0.8181 (tp40) cc_final: 0.7943 (tp40)
REVERT: B  386 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8252 (mmm160)
REVERT: B  519 ARG cc_start: 0.4993 (tpt90) cc_final: 0.3070 (tpt170)
REVERT: A   40 GLU cc_start: 0.6578 (OUTLIER) cc_final: 0.6193 (pp20)
REVERT: A  105 LEU cc_start: 0.8228 (mm) cc_final: 0.7944 (mp)
REVERT: A  113 LEU cc_start: 0.7020 (OUTLIER) cc_final: 0.6720 (tt)
REVERT: A  209 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7406 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7625 (pp30) cc_final: 0.7258 (pp30)
REVERT: A  315 MET cc_start: 0.7740 (tpp) cc_final: 0.7030 (mpp)
REVERT: A  316 GLU cc_start: 0.7968 (tt0) cc_final: 0.7692 (tp30)
REVERT: A  324 ARG cc_start: 0.7834 (ptm160) cc_final: 0.7338 (ptm160)
REVERT: A  326 THR cc_start: 0.7843 (m) cc_final: 0.7076 (p)
REVERT: A  333 GLN cc_start: 0.8014 (tp-100) cc_final: 0.7732 (tp-100)
REVERT: A  369 GLU cc_start: 0.6400 (pp20) cc_final: 0.5959 (pp20)
  outliers start: 43
  outliers final: 35
  residues processed: 222
  average time/residue: 0.1066
  time to fit residues: 31.0043
Evaluate side-chains
  235 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 196
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   53 VAL
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  140 LEU
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  202 SER
Chi-restraints excluded: chain B residue  267 SER
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  284 SER
Chi-restraints excluded: chain B residue  304 ILE
Chi-restraints excluded: chain B residue  308 LEU
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  485 THR
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue  113 LEU
Chi-restraints excluded: chain A residue  114 VAL
Chi-restraints excluded: chain A residue  116 GLU
Chi-restraints excluded: chain A residue  170 LEU
Chi-restraints excluded: chain A residue  202 SER
Chi-restraints excluded: chain A residue  209 ARG
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  352 GLN
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  393 MET
Chi-restraints excluded: chain A residue  485 THR
Chi-restraints excluded: chain A residue  514 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 61 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 29 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 69 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 287 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 352 GLN ** 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 = 0.3925 r_free = 0.3925 target = 0.148186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.126671 restraints weight = 11946.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3637 rms_B_bonded: 2.78
r_work: 0.3486 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7429
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   8045  Z= 0.170
  Angle     :  0.581   7.955  10928  Z= 0.287
  Chirality :  0.042   0.152   1225
  Planarity :  0.005   0.054   1423
  Dihedral  :  5.696  56.436   1120
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 27.26 %
    Favored  : 67.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.28), residues: 984
  helix:  2.32 (0.25), residues: 425
  sheet:  0.03 (0.39), residues: 167
  loop : -0.09 (0.35), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 324 
 TYR   0.022   0.001   TYR A 409 
 PHE   0.012   0.001   PHE A  34 
 TRP   0.021   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8043)
  covalent geometry    : angle       0.58128 (10928)
  hydrogen bonds       : bond        0.03538 (  424)
  hydrogen bonds       : angle       4.15788 ( 1182)
  Misc. bond           : bond        0.00030 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2290.02 seconds
wall clock time: 39 minutes 53.28 seconds (2393.28 seconds total)