Starting phenix.real_space_refine
on Sat Dec 28 06:19:33 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_41941.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_41941.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_41941.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_41941.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8u62_41941/12_2024/8u62_41941.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 6.78, per 1000 atoms: 0.86
  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: 2.43
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.92
  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: 2.44

  Time building geometry restraints manager: 2.56 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:             7.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.040
  Set scattering table:                    0.070
  Process input model:                     23.860
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.380
-------------------------------------------------------------------------------
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   0.032   8043  Z= 0.211
  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 : 8.41
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (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
 TRP   0.037   0.001   TRP A 391 
 HIS   0.015   0.001   HIS A 295 
 PHE   0.010   0.001   PHE B  34 
 TYR   0.025   0.001   TYR A 409 
 ARG   0.009   0.000   ARG A 322 

*********************** 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  : 0.832 
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: 0.2413
  time to fit residues: 59.8789
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  : 0.858 
-------------------------------------------------------------------------------
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 83 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 41 optimal weight:    0.4980
   chunk 25 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0040
   overall best weight:    0.5592

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

Flipped N/Q/H residues before XYZ refinement:
B 120 GLN
A 275 GLN
A 505 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.1133

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8043  Z= 0.236
  Angle     :  0.560   7.878  10928  Z= 0.281
  Chirality :  0.042   0.153   1225
  Planarity :  0.004   0.041   1423
  Dihedral  :  5.772  55.169   1124
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 26.44 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.28), residues: 984
  helix:  2.12 (0.25), residues: 429
  sheet:  0.17 (0.40), residues: 167
  loop :  0.11 (0.36), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 391 
 HIS   0.009   0.001   HIS A 295 
 PHE   0.012   0.001   PHE A  34 
 TYR   0.016   0.001   TYR A 409 
 ARG   0.007   0.000   ARG A 322 

*********************** 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
  237 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 197
  time to evaluate  : 0.834 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  370 ASP cc_start: 0.6764 (m-30) cc_final: 0.6548 (m-30)
REVERT: B  519 ARG cc_start: 0.5572 (tpt90) cc_final: 0.4757 (tpt90)
REVERT: A  105 LEU cc_start: 0.8260 (mm) cc_final: 0.7973 (mp)
REVERT: A  139 MET cc_start: 0.6495 (tmm) cc_final: 0.6186 (tmm)
REVERT: A  209 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7463 (mtt-85)
REVERT: A  240 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6656 (tm-30)
REVERT: A  275 GLN cc_start: 0.7583 (pp30) cc_final: 0.7323 (pp30)
REVERT: A  299 SER cc_start: 0.8495 (m) cc_final: 0.8247 (m)
REVERT: A  311 GLN cc_start: 0.6874 (mt0) cc_final: 0.6628 (tt0)
REVERT: A  315 MET cc_start: 0.7649 (tpp) cc_final: 0.6973 (mpp)
REVERT: A  352 GLN cc_start: 0.7824 (pp30) cc_final: 0.7228 (pp30)
REVERT: A  369 GLU cc_start: 0.6226 (pp20) cc_final: 0.5907 (pp20)
  outliers start: 40
  outliers final: 21
  residues processed: 220
  average time/residue: 0.2334
  time to fit residues: 66.9473
Evaluate side-chains
  210 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 188
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
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  267 SER
Chi-restraints excluded: chain B residue  334 LEU
Chi-restraints excluded: chain B residue  399 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  115 LEU
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  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 49 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9990
   chunk 74 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 90 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 89 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 72 optimal weight:    0.0070
   overall best weight:    0.5598

-------------------------------------------------------------------------------
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 144 HIS
A 306 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.1366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8043  Z= 0.233
  Angle     :  0.553   7.028  10928  Z= 0.273
  Chirality :  0.042   0.151   1225
  Planarity :  0.004   0.043   1423
  Dihedral  :  5.558  55.904   1120
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 27.14 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.28), residues: 984
  helix:  2.22 (0.25), residues: 430
  sheet:  0.16 (0.39), residues: 167
  loop :  0.01 (0.36), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 391 
 HIS   0.007   0.001   HIS A 295 
 PHE   0.013   0.001   PHE A  34 
 TYR   0.016   0.001   TYR A 409 
 ARG   0.009   0.000   ARG B 466 

*********************** 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
  239 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 198
  time to evaluate  : 0.864 
Fit side-chains
   revert: symmetry clash
REVERT: B  304 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8270 (tt)
REVERT: B  324 ARG cc_start: 0.8028 (ttt180) cc_final: 0.6870 (ttt180)
REVERT: B  354 GLN cc_start: 0.8151 (tp-100) cc_final: 0.7797 (tp40)
REVERT: B  370 ASP cc_start: 0.6795 (m-30) cc_final: 0.6562 (m-30)
REVERT: B  519 ARG cc_start: 0.5257 (tpt90) cc_final: 0.4132 (tpt90)
REVERT: A  105 LEU cc_start: 0.8278 (mm) cc_final: 0.7970 (mt)
REVERT: A  158 ARG cc_start: 0.6975 (ttm-80) cc_final: 0.6704 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7495 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7606 (pp30) cc_final: 0.7315 (pp30)
REVERT: A  324 ARG cc_start: 0.8124 (ptm160) cc_final: 0.7781 (ptm160)
REVERT: A  333 GLN cc_start: 0.7963 (tp-100) cc_final: 0.7714 (tp-100)
REVERT: A  352 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.7360 (pp30)
REVERT: A  369 GLU cc_start: 0.6256 (pp20) cc_final: 0.5862 (pp20)
REVERT: A  500 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7681 (ttm170)
  outliers start: 41
  outliers final: 27
  residues processed: 218
  average time/residue: 0.2472
  time to fit residues: 69.5274
Evaluate side-chains
  225 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 195
  time to evaluate  : 0.898 
-------------------------------------------------------------------------------
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  177 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  304 ILE
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  506 ASP
Chi-restraints excluded: chain A residue   13 LEU
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  115 LEU
Chi-restraints excluded: chain A residue  116 GLU
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  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 88 optimal weight:    0.9980
   chunk 67 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:    0.4980
   chunk 42 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 90 optimal weight:    0.3980
   chunk 95 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 295 HIS
A 302 GLN
A 306 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8043  Z= 0.279
  Angle     :  0.556   6.617  10928  Z= 0.276
  Chirality :  0.042   0.145   1225
  Planarity :  0.004   0.043   1423
  Dihedral  :  5.645  55.135   1120
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 26.79 %
    Favored  : 67.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 984
  helix:  2.23 (0.25), residues: 427
  sheet:  0.20 (0.39), residues: 173
  loop :  0.02 (0.35), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 404 
 PHE   0.013   0.001   PHE A  34 
 TYR   0.012   0.001   TYR A 409 
 ARG   0.006   0.000   ARG B 466 

*********************** 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
  252 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 201
  time to evaluate  : 0.831 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7374 (ttp)
REVERT: B  159 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7025 (tt0)
REVERT: B  337 MET cc_start: 0.7888 (tpp) cc_final: 0.7192 (tpp)
REVERT: B  370 ASP cc_start: 0.6901 (m-30) cc_final: 0.6559 (m-30)
REVERT: B  519 ARG cc_start: 0.5215 (tpt90) cc_final: 0.3833 (tpt170)
REVERT: A   40 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.6331 (pp20)
REVERT: A  105 LEU cc_start: 0.8333 (mm) cc_final: 0.8011 (mt)
REVERT: A  113 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6776 (tt)
REVERT: A  158 ARG cc_start: 0.6982 (ttm-80) cc_final: 0.6712 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7541 (ttm-80)
REVERT: A  275 GLN cc_start: 0.7633 (pp30) cc_final: 0.7331 (pp30)
REVERT: A  316 GLU cc_start: 0.7940 (tt0) cc_final: 0.7730 (tp30)
REVERT: A  333 GLN cc_start: 0.8002 (tp-100) cc_final: 0.7728 (tp-100)
REVERT: A  369 GLU cc_start: 0.6301 (pp20) cc_final: 0.5807 (pp20)
  outliers start: 51
  outliers final: 35
  residues processed: 233
  average time/residue: 0.2303
  time to fit residues: 69.6747
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  : 0.880 
-------------------------------------------------------------------------------
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  139 MET
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  272 SER
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  485 THR
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   13 LEU
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  115 LEU
Chi-restraints excluded: chain A residue  142 GLN
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  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 79 optimal weight:    1.9990
   chunk 54 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0570
   chunk 71 optimal weight:    0.5980
   chunk 39 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** B  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN
A 352 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8043  Z= 0.239
  Angle     :  0.548   7.534  10928  Z= 0.272
  Chirality :  0.042   0.156   1225
  Planarity :  0.004   0.044   1423
  Dihedral  :  5.647  56.228   1120
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 26.79 %
    Favored  : 67.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.28), residues: 984
  helix:  2.39 (0.25), residues: 427
  sheet:  0.25 (0.39), residues: 166
  loop : -0.21 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 391 
 HIS   0.007   0.001   HIS B 404 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.012   0.001   TYR A 409 
 ARG   0.006   0.000   ARG B 466 

*********************** 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
  251 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 200
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7411 (ttp)
REVERT: B  159 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.6994 (tt0)
REVERT: B  203 ASP cc_start: 0.7217 (m-30) cc_final: 0.6878 (t0)
REVERT: B  337 MET cc_start: 0.7858 (tpp) cc_final: 0.7151 (tpp)
REVERT: B  354 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7907 (tp40)
REVERT: B  519 ARG cc_start: 0.5132 (tpt90) cc_final: 0.3641 (tpt170)
REVERT: A   40 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.6295 (pp20)
REVERT: A   79 ARG cc_start: 0.8233 (ttp-110) cc_final: 0.7880 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8291 (mm) cc_final: 0.7973 (mt)
REVERT: A  113 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6760 (tt)
REVERT: A  158 ARG cc_start: 0.6981 (ttm-80) cc_final: 0.6709 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7473 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7632 (pp30) cc_final: 0.7300 (pp30)
REVERT: A  316 GLU cc_start: 0.7932 (tt0) cc_final: 0.7723 (tp30)
REVERT: A  333 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7692 (tp-100)
REVERT: A  351 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.7214 (mp10)
REVERT: A  369 GLU cc_start: 0.6304 (pp20) cc_final: 0.5801 (pp20)
  outliers start: 51
  outliers final: 33
  residues processed: 232
  average time/residue: 0.2153
  time to fit residues: 65.7447
Evaluate side-chains
  234 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 195
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  139 MET
Chi-restraints excluded: chain B residue  159 GLU
Chi-restraints excluded: chain B residue  193 LEU
Chi-restraints excluded: chain B residue  272 SER
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  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   13 LEU
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  142 GLN
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  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 32 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 18 optimal weight:    0.3980
   chunk 56 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 95 optimal weight:    0.3980
   chunk 79 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 50 optimal weight:    0.0980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
** B  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 302 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7383
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8043  Z= 0.203
  Angle     :  0.537   7.876  10928  Z= 0.266
  Chirality :  0.041   0.173   1225
  Planarity :  0.004   0.044   1423
  Dihedral  :  5.593  57.221   1120
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  5.64 %
    Allowed  : 26.56 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.28), residues: 984
  helix:  2.47 (0.25), residues: 426
  sheet:  0.20 (0.39), residues: 166
  loop : -0.20 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 
 PHE   0.010   0.001   PHE A  34 
 TYR   0.011   0.001   TYR A 409 
 ARG   0.006   0.000   ARG B 466 

*********************** 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
  246 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 198
  time to evaluate  : 0.904 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7390 (ttp)
REVERT: B  159 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.6963 (tt0)
REVERT: B  203 ASP cc_start: 0.7210 (m-30) cc_final: 0.6841 (t0)
REVERT: B  337 MET cc_start: 0.7845 (tpp) cc_final: 0.7122 (tpp)
REVERT: B  354 GLN cc_start: 0.8170 (tp-100) cc_final: 0.7908 (tp40)
REVERT: B  519 ARG cc_start: 0.5095 (tpt90) cc_final: 0.3546 (tpt170)
REVERT: A   40 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6234 (pp20)
REVERT: A  105 LEU cc_start: 0.8261 (mm) cc_final: 0.7950 (mt)
REVERT: A  113 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6751 (tt)
REVERT: A  158 ARG cc_start: 0.6972 (ttm-80) cc_final: 0.6703 (ttm-80)
REVERT: A  275 GLN cc_start: 0.7636 (pp30) cc_final: 0.7285 (pp30)
REVERT: A  316 GLU cc_start: 0.7914 (tt0) cc_final: 0.7708 (tp30)
REVERT: A  333 GLN cc_start: 0.8000 (tp-100) cc_final: 0.7694 (tp-100)
REVERT: A  351 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7087 (mp10)
REVERT: A  355 LEU cc_start: 0.7977 (mt) cc_final: 0.7710 (mt)
REVERT: A  369 GLU cc_start: 0.6320 (pp20) cc_final: 0.5865 (pp20)
  outliers start: 48
  outliers final: 34
  residues processed: 226
  average time/residue: 0.2165
  time to fit residues: 64.7002
Evaluate side-chains
  232 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 193
  time to evaluate  : 0.906 
-------------------------------------------------------------------------------
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  139 MET
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  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  425 MET
Chi-restraints excluded: chain B residue  431 VAL
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   36 LEU
Chi-restraints excluded: chain A residue   40 GLU
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   94 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  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  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 92 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 58 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   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  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 372 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8043  Z= 0.299
  Angle     :  0.578   7.210  10928  Z= 0.286
  Chirality :  0.043   0.175   1225
  Planarity :  0.005   0.043   1423
  Dihedral  :  5.747  54.603   1120
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  6.58 %
    Allowed  : 25.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.28), residues: 984
  helix:  2.30 (0.25), residues: 425
  sheet:  0.10 (0.39), residues: 168
  loop : -0.18 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 391 
 HIS   0.008   0.001   HIS B 404 
 PHE   0.013   0.001   PHE A  34 
 TYR   0.010   0.001   TYR A 409 
 ARG   0.007   0.000   ARG A 218 

*********************** 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
  249 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 193
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7417 (ttp)
REVERT: B  159 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7036 (tt0)
REVERT: B  203 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.6833 (t0)
REVERT: B  337 MET cc_start: 0.7833 (tpp) cc_final: 0.7106 (tpp)
REVERT: B  354 GLN cc_start: 0.8187 (tp-100) cc_final: 0.7804 (tp40)
REVERT: B  358 ASP cc_start: 0.7967 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  370 ASP cc_start: 0.6798 (m-30) cc_final: 0.6585 (m-30)
REVERT: B  519 ARG cc_start: 0.5093 (tpt90) cc_final: 0.3356 (tpt170)
REVERT: A   40 GLU cc_start: 0.6629 (OUTLIER) cc_final: 0.6264 (pp20)
REVERT: A   79 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.7876 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8299 (mm) cc_final: 0.7991 (mt)
REVERT: A  113 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6809 (tt)
REVERT: A  158 ARG cc_start: 0.6988 (ttm-80) cc_final: 0.6719 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7487 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7663 (pp30) cc_final: 0.7308 (pp30)
REVERT: A  316 GLU cc_start: 0.7927 (tt0) cc_final: 0.7725 (tp30)
REVERT: A  326 THR cc_start: 0.7922 (m) cc_final: 0.7014 (p)
REVERT: A  333 GLN cc_start: 0.8009 (tp-100) cc_final: 0.7699 (tp-100)
REVERT: A  351 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.7093 (mp10)
REVERT: A  355 LEU cc_start: 0.8043 (mt) cc_final: 0.7755 (mt)
REVERT: A  369 GLU cc_start: 0.6370 (pp20) cc_final: 0.5926 (pp20)
  outliers start: 56
  outliers final: 38
  residues processed: 230
  average time/residue: 0.2290
  time to fit residues: 68.9952
Evaluate side-chains
  238 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 193
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
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  139 MET
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  203 ASP
Chi-restraints excluded: chain B residue  272 SER
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  352 GLN
Chi-restraints excluded: chain B residue  372 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  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain B residue  507 LEU
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   13 LEU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9990
   chunk 8 optimal weight:    0.2980
   chunk 75 optimal weight:    0.5980
   chunk 86 optimal weight:    3.9990
   chunk 91 optimal weight:    0.6980
   chunk 83 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 372 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7396
moved from start:          0.1806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8043  Z= 0.237
  Angle     :  0.560   7.332  10928  Z= 0.277
  Chirality :  0.042   0.148   1225
  Planarity :  0.005   0.043   1423
  Dihedral  :  5.692  56.363   1120
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 26.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.28), residues: 984
  helix:  2.34 (0.25), residues: 427
  sheet:  0.10 (0.39), residues: 166
  loop : -0.19 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 
 PHE   0.010   0.001   PHE A  34 
 TYR   0.011   0.001   TYR A 409 
 ARG   0.007   0.000   ARG B  79 

*********************** 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
  241 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 192
  time to evaluate  : 0.783 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7400 (ttp)
REVERT: B  159 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.7003 (tt0)
REVERT: B  203 ASP cc_start: 0.7204 (OUTLIER) cc_final: 0.6812 (t0)
REVERT: B  337 MET cc_start: 0.7832 (tpp) cc_final: 0.7094 (tpp)
REVERT: B  354 GLN cc_start: 0.8176 (tp-100) cc_final: 0.7913 (tp40)
REVERT: B  370 ASP cc_start: 0.6695 (m-30) cc_final: 0.6492 (m-30)
REVERT: B  372 GLN cc_start: 0.7345 (OUTLIER) cc_final: 0.7058 (mt0)
REVERT: B  480 MET cc_start: 0.8152 (mmp) cc_final: 0.7919 (mmp)
REVERT: B  519 ARG cc_start: 0.5027 (tpt90) cc_final: 0.3327 (tpt170)
REVERT: A   40 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6209 (pp20)
REVERT: A   79 ARG cc_start: 0.8240 (ttp-110) cc_final: 0.7881 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8276 (mm) cc_final: 0.7967 (mt)
REVERT: A  113 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6789 (tt)
REVERT: A  158 ARG cc_start: 0.6989 (ttm-80) cc_final: 0.6718 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7472 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7653 (pp30) cc_final: 0.7288 (pp30)
REVERT: A  316 GLU cc_start: 0.7923 (tt0) cc_final: 0.7718 (tp30)
REVERT: A  326 THR cc_start: 0.7905 (m) cc_final: 0.6993 (p)
REVERT: A  333 GLN cc_start: 0.8010 (tp-100) cc_final: 0.7698 (tp-100)
REVERT: A  351 GLN cc_start: 0.7296 (OUTLIER) cc_final: 0.7070 (mp10)
REVERT: A  355 LEU cc_start: 0.8029 (mt) cc_final: 0.7738 (mt)
REVERT: A  369 GLU cc_start: 0.6346 (pp20) cc_final: 0.5899 (pp20)
REVERT: A  406 SER cc_start: 0.7666 (OUTLIER) cc_final: 0.6687 (p)
  outliers start: 49
  outliers final: 33
  residues processed: 224
  average time/residue: 0.2272
  time to fit residues: 66.6647
Evaluate side-chains
  231 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 189
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  139 MET
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  203 ASP
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  372 GLN
Chi-restraints excluded: chain B residue  399 VAL
Chi-restraints excluded: chain B residue  404 HIS
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   13 LEU
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  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  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  406 SER
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 88 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 69 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9980
   chunk 58 optimal weight:    0.0980
   chunk 94 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   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  64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 372 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.1834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8043  Z= 0.234
  Angle     :  0.563   7.829  10928  Z= 0.278
  Chirality :  0.042   0.150   1225
  Planarity :  0.004   0.043   1423
  Dihedral  :  5.733  56.306   1120
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 26.67 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.28), residues: 984
  helix:  2.34 (0.25), residues: 427
  sheet:  0.12 (0.40), residues: 166
  loop : -0.17 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 
 PHE   0.010   0.001   PHE A  34 
 TYR   0.012   0.001   TYR A 409 
 ARG   0.007   0.000   ARG B  79 

*********************** 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
  239 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 194
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
REVERT: B  139 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7400 (ttp)
REVERT: B  159 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7009 (tt0)
REVERT: B  203 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6801 (t0)
REVERT: B  337 MET cc_start: 0.7817 (tpp) cc_final: 0.7078 (tpp)
REVERT: B  354 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7926 (tp40)
REVERT: B  370 ASP cc_start: 0.6677 (m-30) cc_final: 0.6468 (m-30)
REVERT: B  372 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.7010 (mt0)
REVERT: B  480 MET cc_start: 0.8100 (mmp) cc_final: 0.7646 (mmp)
REVERT: B  519 ARG cc_start: 0.4959 (tpt90) cc_final: 0.3292 (tpt170)
REVERT: A   40 GLU cc_start: 0.6584 (OUTLIER) cc_final: 0.6207 (pp20)
REVERT: A   79 ARG cc_start: 0.8229 (ttp-110) cc_final: 0.7867 (ttp-110)
REVERT: A  105 LEU cc_start: 0.8263 (mm) cc_final: 0.7972 (mp)
REVERT: A  113 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6798 (tt)
REVERT: A  158 ARG cc_start: 0.6987 (ttm-80) cc_final: 0.6715 (ttm-80)
REVERT: A  209 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7475 (mtt-85)
REVERT: A  275 GLN cc_start: 0.7651 (pp30) cc_final: 0.7284 (pp30)
REVERT: A  316 GLU cc_start: 0.7916 (tt0) cc_final: 0.7708 (tp30)
REVERT: A  326 THR cc_start: 0.7892 (m) cc_final: 0.6984 (p)
REVERT: A  333 GLN cc_start: 0.8021 (tp-100) cc_final: 0.7707 (tp-100)
REVERT: A  351 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.7064 (mp10)
REVERT: A  355 LEU cc_start: 0.8035 (mt) cc_final: 0.7748 (mt)
REVERT: A  369 GLU cc_start: 0.6344 (pp20) cc_final: 0.5908 (pp20)
REVERT: A  406 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.6682 (p)
  outliers start: 45
  outliers final: 35
  residues processed: 223
  average time/residue: 0.2267
  time to fit residues: 66.3452
Evaluate side-chains
  235 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 191
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  139 MET
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  203 ASP
Chi-restraints excluded: chain B residue  272 SER
Chi-restraints excluded: chain B residue  328 ILE
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  372 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  497 ASP
Chi-restraints excluded: chain B residue  506 ASP
Chi-restraints excluded: chain A residue   10 GLU
Chi-restraints excluded: chain A residue   13 LEU
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  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  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  406 SER
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 44 optimal weight:    0.1980
   chunk 65 optimal weight:    0.5980
   chunk 98 optimal weight:    0.8980
   chunk 90 optimal weight:    0.0010
   chunk 78 optimal weight:    0.0970
   chunk 8 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.6980
   chunk 62 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0870
   overall best weight:    0.1562

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

Flipped N/Q/H residues before XYZ refinement:
B  30 HIS
B  64 GLN
B 120 GLN
** B 179 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 372 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.1987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8043  Z= 0.140
  Angle     :  0.544   8.182  10928  Z= 0.267
  Chirality :  0.041   0.161   1225
  Planarity :  0.004   0.046   1423
  Dihedral  :  5.537  59.845   1120
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  3.76 %
    Allowed  : 28.67 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.28), residues: 984
  helix:  2.51 (0.25), residues: 427
  sheet:  0.08 (0.39), residues: 165
  loop : -0.10 (0.34), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 391 
 HIS   0.004   0.001   HIS A 389 
 PHE   0.007   0.001   PHE A 199 
 TYR   0.014   0.001   TYR A 409 
 ARG   0.008   0.000   ARG B  79 

********************** 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
  228 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 196
  time to evaluate  : 0.927 
Fit side-chains
   revert: symmetry clash
REVERT: B   79 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7914 (ptp-110)
REVERT: B  139 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.7387 (ttp)
REVERT: B  159 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6913 (tt0)
REVERT: B  337 MET cc_start: 0.7796 (tpp) cc_final: 0.7060 (tpp)
REVERT: B  354 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7915 (tp40)
REVERT: B  372 GLN cc_start: 0.7300 (OUTLIER) cc_final: 0.6926 (mt0)
REVERT: B  480 MET cc_start: 0.8021 (mmp) cc_final: 0.7670 (mmp)
REVERT: B  519 ARG cc_start: 0.4765 (tpt90) cc_final: 0.3306 (tpt170)
REVERT: A   40 GLU cc_start: 0.6428 (OUTLIER) cc_final: 0.6048 (pp20)
REVERT: A  105 LEU cc_start: 0.8183 (mm) cc_final: 0.7882 (mp)
REVERT: A  113 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6731 (tt)
REVERT: A  139 MET cc_start: 0.6548 (tmm) cc_final: 0.5880 (tmm)
REVERT: A  258 GLN cc_start: 0.7912 (tp40) cc_final: 0.7361 (tp-100)
REVERT: A  275 GLN cc_start: 0.7610 (pp30) cc_final: 0.7242 (pp30)
REVERT: A  307 VAL cc_start: 0.7664 (t) cc_final: 0.7464 (m)
REVERT: A  316 GLU cc_start: 0.7874 (tt0) cc_final: 0.7642 (tp30)
REVERT: A  326 THR cc_start: 0.7844 (m) cc_final: 0.7090 (p)
REVERT: A  333 GLN cc_start: 0.8042 (tp-100) cc_final: 0.7829 (tp-100)
REVERT: A  351 GLN cc_start: 0.7249 (OUTLIER) cc_final: 0.7026 (mp10)
REVERT: A  355 LEU cc_start: 0.7963 (mt) cc_final: 0.7706 (mt)
REVERT: A  369 GLU cc_start: 0.6254 (pp20) cc_final: 0.5863 (pp20)
REVERT: A  500 ARG cc_start: 0.8012 (ttp-170) cc_final: 0.7569 (ttp-170)
  outliers start: 32
  outliers final: 19
  residues processed: 216
  average time/residue: 0.2442
  time to fit residues: 68.1060
Evaluate side-chains
  215 residues out of total 851 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue   57 VAL
Chi-restraints excluded: chain B residue   69 VAL
Chi-restraints excluded: chain B residue  120 GLN
Chi-restraints excluded: chain B residue  139 MET
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  272 SER
Chi-restraints excluded: chain B residue  331 LEU
Chi-restraints excluded: chain B residue  352 GLN
Chi-restraints excluded: chain B residue  372 GLN
Chi-restraints excluded: chain B residue  425 MET
Chi-restraints excluded: chain B residue  446 VAL
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  170 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  514 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 78 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 4 optimal weight:    1.9990
   chunk 56 optimal weight:    0.1980
   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**
B 372 GLN
A 144 HIS
A 306 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.149123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.127505 restraints weight = 11850.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3640 rms_B_bonded: 2.77
r_work: 0.3495 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3495
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7413
moved from start:          0.1930

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8043  Z= 0.235
  Angle     :  0.579   8.631  10928  Z= 0.284
  Chirality :  0.042   0.158   1225
  Planarity :  0.005   0.044   1423
  Dihedral  :  5.659  56.911   1120
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 28.55 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.51 (0.28), residues: 984
  helix:  2.41 (0.25), residues: 425
  sheet:  0.08 (0.39), residues: 166
  loop : -0.12 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 391 
 HIS   0.006   0.001   HIS B 404 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.022   0.001   TYR A 409 
 ARG   0.010   0.001   ARG B 466 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2824.03 seconds
wall clock time: 51 minutes 39.28 seconds (3099.28 seconds total)