Starting phenix.real_space_refine
on Wed Sep 17 13:24:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuz_50783/09_2025/9fuz_50783.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 2.49, per 1000 atoms: 0.28
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (113.56, 115.6, 135.32, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 371.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 5 sheets defined
      68.8% alpha, 4.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'B' and resid 16 through 21
      removed outlier: 3.752A  pdb=" N   ILE B  20 " --> pdb=" O   LEU B  16 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 23 through 54
      removed outlier: 3.542A  pdb=" N   LEU B  27 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LYS B  49 " --> pdb=" O   LEU B  45 " (cutoff:3.500A)
      Proline residue:  B  50  - end of helix
    Processing helix  chain 'B' and resid 61 through 111
      removed outlier: 3.598A  pdb=" N   TRP B  66 " --> pdb=" O   SER B  62 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   MET B  67 " --> pdb=" O   VAL B  63 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.660A  pdb=" N   GLY B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 112 through 117
      removed outlier: 3.722A  pdb=" N   PHE B 116 " --> pdb=" O   PRO B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 122 through 164
      removed outlier: 3.819A  pdb=" N   ASP B 131 " --> pdb=" O   ARG B 127 " (cutoff:3.500A)
      removed outlier: 5.004A  pdb=" N   SER B 132 " --> pdb=" O   ILE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 213
      removed outlier: 3.773A  pdb=" N   SER B 168 " --> pdb=" O   SER B 164 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ILE B 169 " --> pdb=" O   TRP B 165 " (cutoff:3.500A)
      Proline residue:  B 176  - end of helix
      removed outlier: 4.557A  pdb=" N   GLY B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 221
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.569A  pdb=" N   SER B 251 " --> pdb=" O   ALA B 247 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
    Processing helix  chain 'B' and resid 282 through 303
      removed outlier: 4.000A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 3.592A  pdb=" N   THR B 302 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ASN B 303 " --> pdb=" O   LYS B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 303 through 323
      removed outlier: 3.667A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 3.748A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 458
    Processing helix  chain 'B' and resid 459 through 464
    Processing helix  chain 'B' and resid 482 through 498
    Processing helix  chain 'B' and resid 515 through 528
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
      removed outlier: 3.656A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 16 through 21
    Processing helix  chain 'A' and resid 23 through 47
      removed outlier: 3.682A  pdb=" N   ALA A  33 " --> pdb=" O   VAL A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 54
    Processing helix  chain 'A' and resid 62 through 109
      Proline residue:  A  68  - end of helix
      removed outlier: 4.039A  pdb=" N   ILE A  72 " --> pdb=" O   PRO A  68 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   GLY A  73 " --> pdb=" O   LEU A  69 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LYS A  95 " --> pdb=" O   TRP A  91 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   MET A 100 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   HIS A 107 " --> pdb=" O   ARG A 103 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   MET A 108 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 4.371A  pdb=" N   MET A 109 " --> pdb=" O   PHE A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 4.402A  pdb=" N   PHE A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 163
      removed outlier: 3.627A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   TYR A 130 " --> pdb=" O   SER A 126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 213
      removed outlier: 3.655A  pdb=" N   ALA A 175 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
      removed outlier: 3.661A  pdb=" N   GLN A 209 " --> pdb=" O   THR A 205 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   MET A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   LEU A 211 " --> pdb=" O   ALA A 207 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 221
    Processing helix  chain 'A' and resid 222 through 270
      removed outlier: 3.958A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 4.053A  pdb=" N   ALA A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 276
      removed outlier: 6.642A  pdb=" N   SER A 274 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   VAL A 275 " --> pdb=" O   PHE A 272 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   MET A 276 " --> pdb=" O   PRO A 273 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 271 through 276'
    Processing helix  chain 'A' and resid 283 through 302
      removed outlier: 3.514A  pdb=" N   MET A 291 " --> pdb=" O   VAL A 287 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 3.621A  pdb=" N   SER A 300 " --> pdb=" O   ARG A 296 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   THR A 302 " --> pdb=" O   LEU A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 324
      removed outlier: 3.687A  pdb=" N   ARG A 310 " --> pdb=" O   ALA A 306 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ILE A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 391
      removed outlier: 4.471A  pdb=" N   ALA A 386 " --> pdb=" O   LYS A 382 " (cutoff:3.500A)
      removed outlier: 5.458A  pdb=" N   SER A 387 " --> pdb=" O   SER A 383 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 432 through 438
      removed outlier: 3.762A  pdb=" N   ALA A 438 " --> pdb=" O   ALA A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 515 through 529
      removed outlier: 4.165A  pdb=" N   ASN A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 544
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 579
    Processing sheet with id=AA1, first strand: chain 'B' and resid 359 through 362
      removed outlier: 3.511A  pdb=" N   ASN B 361 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
      removed outlier: 5.313A  pdb=" N   VAL B 347 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   VAL B 347 " --> pdb=" O   GLU B 397 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLU B 397 " --> pdb=" O   VAL B 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.733A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.948A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.121A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 342 through 343
    Processing sheet with id=AA4, first strand: chain 'A' and resid 419 through 421
      removed outlier: 6.428A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.959A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 401 through 402

    557 hydrogen bonds defined for protein.
    1656 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.40

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2306
        1.33 -     1.46: 1566
        1.46 -     1.58: 4974
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   ASP A 252 "
       pdb=" CA  ASP A 252 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 9.20e-03 1.18e+04 1.22e+01
  bond pdb=" N   VAL B 245 "
       pdb=" CA  VAL B 245 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.23e-02 6.61e+03 7.78e+00
  bond pdb=" N   MET A 111 "
       pdb=" CA  MET A 111 "
    ideal  model  delta    sigma   weight residual
    1.453  1.493 -0.040 1.44e-02 4.82e+03 7.61e+00
  bond pdb=" N   SER A 251 "
       pdb=" CA  SER A 251 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.17e-02 7.31e+03 6.63e+00
  bond pdb=" N   MET B 244 "
       pdb=" CA  MET B 244 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.031 1.21e-02 6.83e+03 6.54e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 11642
        2.32 -     4.65: 378
        4.65 -     6.97: 56
        6.97 -     9.29: 12
        9.29 -    11.61: 4
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" CA  GLU B 208 "
        pdb=" CB  GLU B 208 "
        pdb=" CG  GLU B 208 "
      ideal   model   delta    sigma   weight residual
     114.10  123.55   -9.45 2.00e+00 2.50e-01 2.23e+01
  angle pdb=" N   GLU B 208 "
        pdb=" CA  GLU B 208 "
        pdb=" CB  GLU B 208 "
      ideal   model   delta    sigma   weight residual
     110.12  116.30   -6.18 1.47e+00 4.63e-01 1.77e+01
  angle pdb=" CB  MET A 244 "
        pdb=" CG  MET A 244 "
        pdb=" SD  MET A 244 "
      ideal   model   delta    sigma   weight residual
     112.70  124.31  -11.61 3.00e+00 1.11e-01 1.50e+01
  angle pdb=" CB  MET A 200 "
        pdb=" CG  MET A 200 "
        pdb=" SD  MET A 200 "
      ideal   model   delta    sigma   weight residual
     112.70  124.03  -11.33 3.00e+00 1.11e-01 1.43e+01
  angle pdb=" CB  MET B 200 "
        pdb=" CG  MET B 200 "
        pdb=" SD  MET B 200 "
      ideal   model   delta    sigma   weight residual
     112.70  123.59  -10.89 3.00e+00 1.11e-01 1.32e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.19: 4660
       17.19 -    34.38: 594
       34.38 -    51.58: 160
       51.58 -    68.77: 30
       68.77 -    85.96: 10
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" CA  ARG A  14 "
           pdb=" C   ARG A  14 "
           pdb=" N   ARG A  15 "
           pdb=" CA  ARG A  15 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.05   21.95     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  ARG A 391 "
           pdb=" C   ARG A 391 "
           pdb=" N   PHE A 392 "
           pdb=" CA  PHE A 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.56   21.44     0      5.00e+00 4.00e-02 1.84e+01
  dihedral pdb=" CA  ALA B 536 "
           pdb=" C   ALA B 536 "
           pdb=" N   HIS B 537 "
           pdb=" CA  HIS B 537 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.63   20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1188
       0.059 -    0.117: 217
       0.117 -    0.176: 29
       0.176 -    0.235: 5
       0.235 -    0.293: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CB  VAL B  96 "
            pdb=" CA  VAL B  96 "
            pdb=" CG1 VAL B  96 "
            pdb=" CG2 VAL B  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.34   -0.29 2.00e-01 2.50e+01 2.15e+00
  chirality pdb=" CG  LEU B  34 "
            pdb=" CB  LEU B  34 "
            pdb=" CD1 LEU B  34 "
            pdb=" CD2 LEU B  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.37   -0.21 2.00e-01 2.50e+01 1.15e+00
  chirality pdb=" CA  GLU B 226 "
            pdb=" N   GLU B 226 "
            pdb=" C   GLU B 226 "
            pdb=" CB  GLU B 226 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 272 "    0.051 5.00e-02 4.00e+02   7.67e-02 9.40e+00
        pdb=" N   PRO A 273 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 273 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 273 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 250 "    0.011 2.00e-02 2.50e+03   2.24e-02 5.03e+00
        pdb=" C   ILE A 250 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   ILE A 250 "    0.015 2.00e-02 2.50e+03
        pdb=" N   SER A 251 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 311 "   -0.011 2.00e-02 2.50e+03   2.20e-02 4.83e+00
        pdb=" C   GLY A 311 "    0.038 2.00e-02 2.50e+03
        pdb=" O   GLY A 311 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   MET A 312 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 898
        2.74 -     3.28: 10125
        3.28 -     3.82: 15103
        3.82 -     4.36: 17336
        4.36 -     4.90: 27646
  Nonbonded interactions: 71108
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  16 "
            pdb=" OG1 THR A  19 "
     model   vdw
     2.201 3.040
  nonbonded pdb=" O   ILE A 128 "
            pdb=" OG  SER A 132 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" O   PRO B 176 "
            pdb=" OG  SER B 179 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   TRP A 165 "
            pdb=" OG  SER A 168 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   SER B  86 "
            pdb=" OG  SER B  90 "
     model   vdw
     2.253 3.040
  ... (remaining 71103 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.370
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
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      :  0.005   0.069   8950  Z= 0.246
  Angle     :  0.982  11.614  12092  Z= 0.528
  Chirality :  0.047   0.293   1440
  Planarity :  0.006   0.077   1532
  Dihedral  : 16.668  85.961   3326
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  4.59 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 28.51 %
    Favored  : 70.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.25 (0.24), residues: 1134
  helix:  0.48 (0.18), residues: 724
  sheet: -0.33 (0.87), residues: 36
  loop : -1.31 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 488 
 TYR   0.013   0.001   TYR B 163 
 PHE   0.032   0.002   PHE A 115 
 TRP   0.020   0.002   TRP A  66 
 HIS   0.012   0.002   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 ( 8950)
  covalent geometry    : angle       0.98206 (12092)
  hydrogen bonds       : bond        0.14856 (  557)
  hydrogen bonds       : angle       7.12758 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 227
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9331 (ttt) cc_final: 0.8850 (tpp)
REVERT: B  115 PHE cc_start: 0.9394 (t80) cc_final: 0.9105 (t80)
REVERT: B  210 MET cc_start: 0.8211 (tpp) cc_final: 0.7999 (tpp)
REVERT: B  242 MET cc_start: 0.9122 (mmm) cc_final: 0.8896 (mmm)
REVERT: B  244 MET cc_start: 0.9371 (ppp) cc_final: 0.9009 (ppp)
REVERT: B  255 ILE cc_start: 0.9590 (mp) cc_final: 0.9335 (tp)
REVERT: B  360 ARG cc_start: 0.9495 (ttt180) cc_final: 0.9281 (mmm160)
REVERT: A  109 MET cc_start: 0.8577 (mmp) cc_final: 0.7501 (tmm)
REVERT: A  226 GLU cc_start: 0.9280 (tp30) cc_final: 0.8985 (tp30)
REVERT: A  276 MET cc_start: 0.8065 (mmt) cc_final: 0.7818 (mmm)
REVERT: A  402 MET cc_start: 0.9444 (tmm) cc_final: 0.9160 (tmm)
REVERT: A  410 TYR cc_start: 0.8721 (m-80) cc_final: 0.8436 (t80)
REVERT: A  538 ARG cc_start: 0.8180 (tpp-160) cc_final: 0.7929 (tpp-160)
  outliers start: 6
  outliers final: 2
  residues processed: 228
  average time/residue: 0.0837
  time to fit residues: 27.9858
Evaluate side-chains
  211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 209
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   overall best weight:    1.4988

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

Flipped N/Q/H residues before XYZ refinement:
B 256 GLN
A 134 GLN
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.076233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.056082 restraints weight = 33780.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.058282 restraints weight = 20696.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059956 restraints weight = 14625.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.061175 restraints weight = 11141.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.062171 restraints weight = 9043.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   8950  Z= 0.171
  Angle     :  0.631   7.170  12092  Z= 0.342
  Chirality :  0.043   0.213   1440
  Planarity :  0.005   0.062   1532
  Dihedral  :  4.916  20.181   1238
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.47 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1134
  helix:  1.17 (0.19), residues: 730
  sheet: -0.14 (0.85), residues: 36
  loop : -1.31 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 360 
 TYR   0.022   0.002   TYR B 410 
 PHE   0.020   0.002   PHE B 157 
 TRP   0.017   0.001   TRP A 165 
 HIS   0.005   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00350 ( 8950)
  covalent geometry    : angle       0.63124 (12092)
  hydrogen bonds       : bond        0.05190 (  557)
  hydrogen bonds       : angle       5.09068 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 MET cc_start: 0.9516 (mmm) cc_final: 0.9168 (tpt)
REVERT: B   98 MET cc_start: 0.9340 (ttt) cc_final: 0.8997 (ttt)
REVERT: B  100 MET cc_start: 0.9581 (ttp) cc_final: 0.9333 (tmm)
REVERT: B  115 PHE cc_start: 0.9395 (t80) cc_final: 0.8788 (t80)
REVERT: B  200 MET cc_start: 0.9291 (tmm) cc_final: 0.8930 (tmm)
REVERT: B  242 MET cc_start: 0.9101 (mmm) cc_final: 0.8843 (mmm)
REVERT: B  244 MET cc_start: 0.9259 (ppp) cc_final: 0.8964 (ppp)
REVERT: B  332 LYS cc_start: 0.9653 (mttt) cc_final: 0.9374 (mmtt)
REVERT: B  359 LEU cc_start: 0.9586 (tp) cc_final: 0.9327 (tp)
REVERT: B  527 GLN cc_start: 0.9301 (pt0) cc_final: 0.9074 (pp30)
REVERT: A   98 MET cc_start: 0.9199 (ttm) cc_final: 0.8911 (ttt)
REVERT: A  109 MET cc_start: 0.8705 (mmp) cc_final: 0.8252 (tmm)
REVERT: A  160 MET cc_start: 0.9339 (mmm) cc_final: 0.9032 (mmm)
REVERT: A  200 MET cc_start: 0.9426 (tmm) cc_final: 0.9167 (tmm)
REVERT: A  210 MET cc_start: 0.8807 (mmt) cc_final: 0.8449 (mmm)
REVERT: A  226 GLU cc_start: 0.9326 (tp30) cc_final: 0.9112 (tp30)
REVERT: A  244 MET cc_start: 0.9349 (ppp) cc_final: 0.9071 (ppp)
REVERT: A  312 MET cc_start: 0.9134 (tpp) cc_final: 0.8101 (mmm)
REVERT: A  390 THR cc_start: 0.9143 (p) cc_final: 0.8585 (p)
REVERT: A  392 PHE cc_start: 0.9324 (m-10) cc_final: 0.9067 (m-10)
REVERT: A  439 TYR cc_start: 0.8962 (t80) cc_final: 0.8723 (t80)
REVERT: A  456 MET cc_start: 0.9145 (mmp) cc_final: 0.8927 (mmm)
  outliers start: 1
  outliers final: 0
  residues processed: 247
  average time/residue: 0.0730
  time to fit residues: 26.7239
Evaluate side-chains
  203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   chunk 38 optimal weight:    0.7980
   chunk 96 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
B 209 GLN
B 214 HIS
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.076554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.055987 restraints weight = 34008.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.058265 restraints weight = 21178.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.059990 restraints weight = 15021.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.061181 restraints weight = 11448.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.062229 restraints weight = 9343.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.154
  Angle     :  0.589   6.279  12092  Z= 0.318
  Chirality :  0.042   0.169   1440
  Planarity :  0.004   0.052   1532
  Dihedral  :  4.773  20.979   1238
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 11.62
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  4.94 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.51 %
    Favored  : 96.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.25), residues: 1134
  helix:  1.36 (0.19), residues: 724
  sheet:  0.14 (0.86), residues: 32
  loop : -1.23 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 360 
 TYR   0.014   0.002   TYR B 410 
 PHE   0.013   0.002   PHE B 105 
 TRP   0.015   0.001   TRP A  66 
 HIS   0.005   0.001   HIS B 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 8950)
  covalent geometry    : angle       0.58929 (12092)
  hydrogen bonds       : bond        0.04754 (  557)
  hydrogen bonds       : angle       4.93832 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 248
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9357 (ttt) cc_final: 0.9013 (ttt)
REVERT: B  100 MET cc_start: 0.9569 (ttp) cc_final: 0.9304 (tmm)
REVERT: B  108 MET cc_start: 0.9467 (mtp) cc_final: 0.9203 (mtp)
REVERT: B  115 PHE cc_start: 0.9091 (t80) cc_final: 0.8673 (t80)
REVERT: B  200 MET cc_start: 0.9352 (tmm) cc_final: 0.8989 (tmm)
REVERT: B  242 MET cc_start: 0.9101 (mmm) cc_final: 0.8865 (mmm)
REVERT: B  244 MET cc_start: 0.9268 (ppp) cc_final: 0.8919 (ppp)
REVERT: B  527 GLN cc_start: 0.9336 (pt0) cc_final: 0.9086 (pp30)
REVERT: B  538 ARG cc_start: 0.8355 (tpm170) cc_final: 0.8127 (tpp-160)
REVERT: A   98 MET cc_start: 0.9190 (ttm) cc_final: 0.8954 (ttt)
REVERT: A  109 MET cc_start: 0.8843 (mmp) cc_final: 0.8321 (tmm)
REVERT: A  116 PHE cc_start: 0.8972 (m-80) cc_final: 0.8602 (m-80)
REVERT: A  149 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8699 (mm-30)
REVERT: A  160 MET cc_start: 0.9336 (mmm) cc_final: 0.8984 (mmm)
REVERT: A  200 MET cc_start: 0.9420 (tmm) cc_final: 0.9133 (tmm)
REVERT: A  210 MET cc_start: 0.8708 (mmt) cc_final: 0.8278 (mmm)
REVERT: A  226 GLU cc_start: 0.9316 (tp30) cc_final: 0.9105 (tp30)
REVERT: A  295 MET cc_start: 0.8352 (ttt) cc_final: 0.8140 (ttt)
REVERT: A  312 MET cc_start: 0.9242 (tpp) cc_final: 0.8555 (mmm)
REVERT: A  315 CYS cc_start: 0.8910 (t) cc_final: 0.8696 (t)
REVERT: A  392 PHE cc_start: 0.9307 (m-10) cc_final: 0.8944 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0837
  time to fit residues: 30.2777
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 89 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 71 optimal weight:    0.9990
   chunk 66 optimal weight:    0.6980
   chunk 36 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0270
   chunk 53 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.6240

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

Flipped N/Q/H residues before XYZ refinement:
A 527 GLN
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.077848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057318 restraints weight = 33579.283|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059661 restraints weight = 20649.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.061400 restraints weight = 14530.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.062726 restraints weight = 11060.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.063742 restraints weight = 8898.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.128
  Angle     :  0.564   6.406  12092  Z= 0.302
  Chirality :  0.041   0.211   1440
  Planarity :  0.004   0.050   1532
  Dihedral  :  4.625  19.982   1238
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.56
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.20 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.13 %
    Favored  : 95.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.82 (0.25), residues: 1134
  helix:  1.45 (0.19), residues: 728
  sheet:  0.32 (0.88), residues: 32
  loop : -1.25 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 236 
 TYR   0.014   0.001   TYR B 410 
 PHE   0.012   0.001   PHE B 288 
 TRP   0.015   0.001   TRP A  66 
 HIS   0.003   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8950)
  covalent geometry    : angle       0.56389 (12092)
  hydrogen bonds       : bond        0.04374 (  557)
  hydrogen bonds       : angle       4.71459 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9325 (ttt) cc_final: 0.8976 (ttt)
REVERT: B  100 MET cc_start: 0.9530 (ttp) cc_final: 0.9282 (tmm)
REVERT: B  108 MET cc_start: 0.9495 (mtp) cc_final: 0.9195 (mtp)
REVERT: B  111 MET cc_start: 0.9189 (ttp) cc_final: 0.8934 (tmm)
REVERT: B  149 GLU cc_start: 0.8980 (mp0) cc_final: 0.8606 (mp0)
REVERT: B  200 MET cc_start: 0.9369 (tmm) cc_final: 0.9003 (tmm)
REVERT: B  209 GLN cc_start: 0.8612 (tt0) cc_final: 0.8376 (tt0)
REVERT: B  237 MET cc_start: 0.9116 (ttp) cc_final: 0.8538 (ptm)
REVERT: B  242 MET cc_start: 0.9050 (mmm) cc_final: 0.8799 (mmm)
REVERT: B  244 MET cc_start: 0.9262 (ppp) cc_final: 0.8887 (ppp)
REVERT: B  312 MET cc_start: 0.8442 (mmm) cc_final: 0.7872 (mmm)
REVERT: B  315 CYS cc_start: 0.8170 (m) cc_final: 0.7828 (m)
REVERT: B  538 ARG cc_start: 0.8372 (tpm170) cc_final: 0.8117 (tpp-160)
REVERT: A  109 MET cc_start: 0.8797 (mmp) cc_final: 0.8179 (tmm)
REVERT: A  116 PHE cc_start: 0.9072 (m-80) cc_final: 0.8771 (m-80)
REVERT: A  149 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8672 (mm-30)
REVERT: A  160 MET cc_start: 0.9367 (mmm) cc_final: 0.9074 (mmm)
REVERT: A  200 MET cc_start: 0.9416 (tmm) cc_final: 0.9108 (tmm)
REVERT: A  210 MET cc_start: 0.8699 (mmt) cc_final: 0.8245 (mmm)
REVERT: A  217 VAL cc_start: 0.9582 (t) cc_final: 0.9305 (t)
REVERT: A  226 GLU cc_start: 0.9256 (tp30) cc_final: 0.9029 (tp30)
REVERT: A  244 MET cc_start: 0.9356 (ppp) cc_final: 0.9078 (ppp)
REVERT: A  312 MET cc_start: 0.9200 (tpp) cc_final: 0.8585 (mmm)
REVERT: A  390 THR cc_start: 0.9075 (p) cc_final: 0.8683 (p)
REVERT: A  392 PHE cc_start: 0.9236 (m-10) cc_final: 0.8880 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.0726
  time to fit residues: 27.1338
Evaluate side-chains
  214 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 214
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:   10.0000
   chunk 111 optimal weight:   20.0000
   chunk 44 optimal weight:    5.9990
   chunk 83 optimal weight:    0.0980
   chunk 16 optimal weight:    0.0570
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 47 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.5100

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

Flipped N/Q/H residues before XYZ refinement:
** B 427 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 537 HIS
A 574 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.078323 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.057511 restraints weight = 33200.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.059953 restraints weight = 20434.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.061744 restraints weight = 14334.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.062991 restraints weight = 10896.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.064034 restraints weight = 8848.127|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.3673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.055   8950  Z= 0.121
  Angle     :  0.568   6.732  12092  Z= 0.300
  Chirality :  0.041   0.183   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.516  18.922   1238
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.03 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.17 %
    Favored  : 97.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1134
  helix:  1.45 (0.19), residues: 730
  sheet:  0.35 (0.89), residues: 32
  loop : -1.25 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 236 
 TYR   0.014   0.001   TYR B 351 
 PHE   0.016   0.001   PHE B 157 
 TRP   0.014   0.001   TRP A  66 
 HIS   0.003   0.001   HIS B 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 8950)
  covalent geometry    : angle       0.56841 (12092)
  hydrogen bonds       : bond        0.04177 (  557)
  hydrogen bonds       : angle       4.59343 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 250
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   98 MET cc_start: 0.9317 (ttt) cc_final: 0.8948 (ttt)
REVERT: B  100 MET cc_start: 0.9526 (ttp) cc_final: 0.9159 (tmm)
REVERT: B  108 MET cc_start: 0.9513 (mtp) cc_final: 0.9269 (mtp)
REVERT: B  115 PHE cc_start: 0.9003 (t80) cc_final: 0.8748 (t80)
REVERT: B  116 PHE cc_start: 0.9023 (m-10) cc_final: 0.8743 (m-10)
REVERT: B  149 GLU cc_start: 0.9003 (mp0) cc_final: 0.8670 (mp0)
REVERT: B  200 MET cc_start: 0.9367 (tmm) cc_final: 0.8941 (tmm)
REVERT: B  203 VAL cc_start: 0.9295 (t) cc_final: 0.9085 (p)
REVERT: B  229 ARG cc_start: 0.9212 (ttm-80) cc_final: 0.8994 (ttm170)
REVERT: B  237 MET cc_start: 0.9073 (ttp) cc_final: 0.8855 (ppp)
REVERT: B  244 MET cc_start: 0.9287 (ppp) cc_final: 0.8946 (ppp)
REVERT: B  312 MET cc_start: 0.8353 (mmm) cc_final: 0.7850 (mmm)
REVERT: B  315 CYS cc_start: 0.8250 (m) cc_final: 0.7908 (m)
REVERT: B  538 ARG cc_start: 0.8377 (tpm170) cc_final: 0.8106 (tpp-160)
REVERT: A   98 MET cc_start: 0.9139 (tpp) cc_final: 0.8565 (tpp)
REVERT: A  109 MET cc_start: 0.8764 (mmp) cc_final: 0.8127 (tmm)
REVERT: A  111 MET cc_start: 0.9165 (tmm) cc_final: 0.8588 (tmm)
REVERT: A  115 PHE cc_start: 0.9057 (t80) cc_final: 0.8146 (t80)
REVERT: A  116 PHE cc_start: 0.9087 (m-80) cc_final: 0.8277 (m-80)
REVERT: A  149 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8685 (mm-30)
REVERT: A  160 MET cc_start: 0.9406 (mmm) cc_final: 0.9104 (mmm)
REVERT: A  174 LEU cc_start: 0.9254 (mt) cc_final: 0.9035 (mt)
REVERT: A  200 MET cc_start: 0.9412 (tmm) cc_final: 0.9087 (tmm)
REVERT: A  210 MET cc_start: 0.8700 (mmt) cc_final: 0.8237 (mmm)
REVERT: A  217 VAL cc_start: 0.9581 (t) cc_final: 0.9211 (t)
REVERT: A  226 GLU cc_start: 0.9249 (tp30) cc_final: 0.9017 (tp30)
REVERT: A  244 MET cc_start: 0.9363 (ppp) cc_final: 0.9065 (ppp)
REVERT: A  312 MET cc_start: 0.9364 (mmp) cc_final: 0.8947 (mmm)
REVERT: A  390 THR cc_start: 0.9072 (p) cc_final: 0.8675 (p)
REVERT: A  392 PHE cc_start: 0.9238 (m-10) cc_final: 0.8881 (m-10)
REVERT: A  410 TYR cc_start: 0.8212 (m-10) cc_final: 0.7766 (m-80)
REVERT: A  437 ILE cc_start: 0.9464 (tt) cc_final: 0.9226 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 250
  average time/residue: 0.0752
  time to fit residues: 27.8456
Evaluate side-chains
  216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:   10.0000
   chunk 95 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 108 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    5.9990
   chunk 58 optimal weight:    0.9990
   chunk 45 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
B 363 ASN
** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 307 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.075368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.055207 restraints weight = 34256.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.057455 restraints weight = 21265.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.059128 restraints weight = 15040.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.060296 restraints weight = 11458.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.061287 restraints weight = 9350.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.173
  Angle     :  0.594   6.894  12092  Z= 0.320
  Chirality :  0.042   0.314   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.540  19.117   1238
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.47 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.27 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.25), residues: 1134
  helix:  1.44 (0.19), residues: 728
  sheet:  0.26 (0.90), residues: 32
  loop : -1.17 (0.33), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 236 
 TYR   0.014   0.002   TYR B 410 
 PHE   0.014   0.002   PHE B 105 
 TRP   0.019   0.002   TRP A  66 
 HIS   0.006   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 8950)
  covalent geometry    : angle       0.59396 (12092)
  hydrogen bonds       : bond        0.04412 (  557)
  hydrogen bonds       : angle       4.71456 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 242
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9112 (mt) cc_final: 0.8896 (mt)
REVERT: B   98 MET cc_start: 0.9335 (ttt) cc_final: 0.8997 (ttt)
REVERT: B  100 MET cc_start: 0.9566 (ttp) cc_final: 0.9205 (tmm)
REVERT: B  115 PHE cc_start: 0.8960 (t80) cc_final: 0.8727 (t80)
REVERT: B  116 PHE cc_start: 0.8995 (m-10) cc_final: 0.8724 (m-10)
REVERT: B  149 GLU cc_start: 0.9002 (mp0) cc_final: 0.8676 (mp0)
REVERT: B  200 MET cc_start: 0.9389 (tmm) cc_final: 0.9008 (tmm)
REVERT: B  203 VAL cc_start: 0.9366 (t) cc_final: 0.9153 (p)
REVERT: B  210 MET cc_start: 0.8610 (tpt) cc_final: 0.8389 (tpp)
REVERT: B  237 MET cc_start: 0.9174 (ttp) cc_final: 0.8945 (ppp)
REVERT: B  242 MET cc_start: 0.9075 (mmm) cc_final: 0.8853 (mmm)
REVERT: B  244 MET cc_start: 0.9284 (ppp) cc_final: 0.8940 (ppp)
REVERT: B  295 MET cc_start: 0.8159 (ttt) cc_final: 0.7881 (ttp)
REVERT: B  312 MET cc_start: 0.8792 (mmm) cc_final: 0.8094 (mmm)
REVERT: B  315 CYS cc_start: 0.8296 (m) cc_final: 0.7920 (m)
REVERT: B  538 ARG cc_start: 0.8464 (tpm170) cc_final: 0.8123 (tpm170)
REVERT: A   98 MET cc_start: 0.9241 (ttm) cc_final: 0.8812 (ttm)
REVERT: A  111 MET cc_start: 0.9212 (tmm) cc_final: 0.8972 (tmm)
REVERT: A  115 PHE cc_start: 0.9198 (t80) cc_final: 0.8688 (t80)
REVERT: A  156 LEU cc_start: 0.9678 (mt) cc_final: 0.9406 (mt)
REVERT: A  160 MET cc_start: 0.9383 (mmm) cc_final: 0.9091 (mmm)
REVERT: A  200 MET cc_start: 0.9435 (tmm) cc_final: 0.9116 (tmm)
REVERT: A  210 MET cc_start: 0.8803 (mmt) cc_final: 0.8362 (mmm)
REVERT: A  244 MET cc_start: 0.9363 (ppp) cc_final: 0.9042 (ppp)
REVERT: A  312 MET cc_start: 0.9390 (mmp) cc_final: 0.8903 (mmm)
REVERT: A  315 CYS cc_start: 0.9021 (t) cc_final: 0.8804 (t)
REVERT: A  390 THR cc_start: 0.8997 (p) cc_final: 0.8629 (p)
REVERT: A  392 PHE cc_start: 0.9314 (m-10) cc_final: 0.8957 (m-10)
REVERT: A  437 ILE cc_start: 0.9506 (tt) cc_final: 0.9264 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0718
  time to fit residues: 26.2483
Evaluate side-chains
  210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 57 optimal weight:    0.4980
   chunk 104 optimal weight:    8.9990
   chunk 37 optimal weight:    2.9990
   chunk 88 optimal weight:   30.0000
   chunk 65 optimal weight:    0.7980
   chunk 109 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 93 optimal weight:    0.8980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.075909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.055403 restraints weight = 34155.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.057654 restraints weight = 21227.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.059349 restraints weight = 15083.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.060632 restraints weight = 11489.398|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.061649 restraints weight = 9283.760|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.3959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.149
  Angle     :  0.584   7.658  12092  Z= 0.310
  Chirality :  0.042   0.298   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.491  19.184   1238
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.20 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.25), residues: 1134
  helix:  1.54 (0.19), residues: 730
  sheet:  0.26 (0.90), residues: 32
  loop : -1.16 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 102 
 TYR   0.010   0.001   TYR B 410 
 PHE   0.021   0.001   PHE B 157 
 TRP   0.020   0.002   TRP A  66 
 HIS   0.003   0.000   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 8950)
  covalent geometry    : angle       0.58403 (12092)
  hydrogen bonds       : bond        0.04299 (  557)
  hydrogen bonds       : angle       4.67687 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9152 (mt) cc_final: 0.8939 (mt)
REVERT: B   98 MET cc_start: 0.9354 (ttt) cc_final: 0.8982 (ttt)
REVERT: B  100 MET cc_start: 0.9549 (ttp) cc_final: 0.9200 (tmm)
REVERT: B  108 MET cc_start: 0.9476 (mtp) cc_final: 0.9128 (mtp)
REVERT: B  111 MET cc_start: 0.9093 (ttp) cc_final: 0.8826 (tmm)
REVERT: B  149 GLU cc_start: 0.8980 (mp0) cc_final: 0.8675 (mp0)
REVERT: B  200 MET cc_start: 0.9402 (tmm) cc_final: 0.9058 (tmm)
REVERT: B  244 MET cc_start: 0.9286 (ppp) cc_final: 0.8927 (ppp)
REVERT: B  295 MET cc_start: 0.8194 (ttt) cc_final: 0.7931 (ttp)
REVERT: B  315 CYS cc_start: 0.8283 (m) cc_final: 0.7976 (m)
REVERT: B  332 LYS cc_start: 0.9675 (mttt) cc_final: 0.9409 (mmtt)
REVERT: B  402 MET cc_start: 0.8799 (tmm) cc_final: 0.8493 (tmm)
REVERT: B  456 MET cc_start: 0.9230 (mpp) cc_final: 0.9002 (mmp)
REVERT: B  538 ARG cc_start: 0.8471 (tpm170) cc_final: 0.8112 (tpm170)
REVERT: A   67 MET cc_start: 0.8405 (mmp) cc_final: 0.8178 (mmp)
REVERT: A  109 MET cc_start: 0.8877 (mmp) cc_final: 0.8161 (tmm)
REVERT: A  111 MET cc_start: 0.9192 (tmm) cc_final: 0.8941 (tmm)
REVERT: A  115 PHE cc_start: 0.9158 (t80) cc_final: 0.8671 (t80)
REVERT: A  156 LEU cc_start: 0.9664 (mt) cc_final: 0.9416 (mt)
REVERT: A  160 MET cc_start: 0.9396 (mmm) cc_final: 0.9095 (mmm)
REVERT: A  200 MET cc_start: 0.9444 (tmm) cc_final: 0.9125 (tmm)
REVERT: A  210 MET cc_start: 0.8820 (mmt) cc_final: 0.8348 (mmm)
REVERT: A  244 MET cc_start: 0.9357 (ppp) cc_final: 0.9023 (ppp)
REVERT: A  291 MET cc_start: 0.9591 (tpp) cc_final: 0.9364 (tpt)
REVERT: A  312 MET cc_start: 0.9360 (mmp) cc_final: 0.8896 (mmm)
REVERT: A  315 CYS cc_start: 0.9037 (t) cc_final: 0.8823 (t)
REVERT: A  392 PHE cc_start: 0.9339 (m-10) cc_final: 0.8985 (m-10)
REVERT: A  437 ILE cc_start: 0.9471 (tt) cc_final: 0.9216 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0752
  time to fit residues: 27.1534
Evaluate side-chains
  202 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 53 optimal weight:   10.0000
   chunk 88 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0170
   chunk 99 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7420

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.077195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.056618 restraints weight = 33282.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.058944 restraints weight = 20741.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.060653 restraints weight = 14659.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.061846 restraints weight = 11205.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.062870 restraints weight = 9168.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3145
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.4090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.126
  Angle     :  0.582   6.812  12092  Z= 0.307
  Chirality :  0.042   0.293   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.500  18.587   1238
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.56 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1134
  helix:  1.50 (0.19), residues: 734
  sheet:  1.44 (1.09), residues: 22
  loop : -1.09 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 236 
 TYR   0.017   0.001   TYR A 130 
 PHE   0.029   0.001   PHE B 115 
 TRP   0.017   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8950)
  covalent geometry    : angle       0.58224 (12092)
  hydrogen bonds       : bond        0.04121 (  557)
  hydrogen bonds       : angle       4.60658 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9114 (mt) cc_final: 0.8898 (mt)
REVERT: B   98 MET cc_start: 0.9331 (ttt) cc_final: 0.8969 (ttt)
REVERT: B  100 MET cc_start: 0.9544 (ttp) cc_final: 0.9201 (tmm)
REVERT: B  111 MET cc_start: 0.9142 (ttp) cc_final: 0.8549 (ppp)
REVERT: B  116 PHE cc_start: 0.9026 (m-80) cc_final: 0.8637 (m-80)
REVERT: B  200 MET cc_start: 0.9418 (tmm) cc_final: 0.9050 (tmm)
REVERT: B  244 MET cc_start: 0.9283 (ppp) cc_final: 0.8902 (ppp)
REVERT: B  295 MET cc_start: 0.8119 (ttt) cc_final: 0.7845 (ttp)
REVERT: B  312 MET cc_start: 0.8689 (mmm) cc_final: 0.8348 (mmm)
REVERT: B  315 CYS cc_start: 0.8317 (m) cc_final: 0.8036 (m)
REVERT: B  402 MET cc_start: 0.8825 (tmm) cc_final: 0.8510 (tmm)
REVERT: B  456 MET cc_start: 0.9224 (mpp) cc_final: 0.8997 (mmp)
REVERT: B  538 ARG cc_start: 0.8457 (tpm170) cc_final: 0.8092 (tpp-160)
REVERT: A   98 MET cc_start: 0.9196 (tpp) cc_final: 0.8496 (tpp)
REVERT: A  109 MET cc_start: 0.8836 (mmp) cc_final: 0.7968 (tmm)
REVERT: A  111 MET cc_start: 0.9181 (tmm) cc_final: 0.8820 (tmm)
REVERT: A  115 PHE cc_start: 0.9149 (t80) cc_final: 0.8717 (t80)
REVERT: A  116 PHE cc_start: 0.9142 (m-80) cc_final: 0.8598 (m-80)
REVERT: A  149 GLU cc_start: 0.8962 (mm-30) cc_final: 0.8745 (mm-30)
REVERT: A  156 LEU cc_start: 0.9653 (mt) cc_final: 0.9426 (mt)
REVERT: A  160 MET cc_start: 0.9375 (mmm) cc_final: 0.9090 (mmm)
REVERT: A  200 MET cc_start: 0.9439 (tmm) cc_final: 0.9123 (tmm)
REVERT: A  210 MET cc_start: 0.8837 (mmt) cc_final: 0.8346 (mmm)
REVERT: A  244 MET cc_start: 0.9351 (ppp) cc_final: 0.9013 (ppp)
REVERT: A  312 MET cc_start: 0.9304 (mmp) cc_final: 0.8855 (mmm)
REVERT: A  390 THR cc_start: 0.9059 (p) cc_final: 0.8741 (p)
REVERT: A  392 PHE cc_start: 0.9324 (m-10) cc_final: 0.8963 (m-10)
REVERT: A  410 TYR cc_start: 0.8258 (m-10) cc_final: 0.7804 (m-80)
REVERT: A  437 ILE cc_start: 0.9468 (tt) cc_final: 0.9196 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 238
  average time/residue: 0.0725
  time to fit residues: 26.1024
Evaluate side-chains
  199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 26 optimal weight:    8.9990
   chunk 1 optimal weight:    0.8980
   chunk 105 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 68 optimal weight:    3.9990
   chunk 83 optimal weight:    0.8980
   chunk 89 optimal weight:    8.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.077788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.056747 restraints weight = 33720.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.059079 restraints weight = 21307.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.060809 restraints weight = 15174.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.062012 restraints weight = 11655.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.063071 restraints weight = 9567.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.4245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.131
  Angle     :  0.605   7.764  12092  Z= 0.315
  Chirality :  0.042   0.274   1440
  Planarity :  0.004   0.046   1532
  Dihedral  :  4.501  26.664   1238
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.03 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.26), residues: 1134
  helix:  1.51 (0.19), residues: 734
  sheet: -0.23 (0.74), residues: 48
  loop : -1.04 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 101 
 TYR   0.016   0.001   TYR B 351 
 PHE   0.015   0.001   PHE B 344 
 TRP   0.018   0.001   TRP A  66 
 HIS   0.004   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 8950)
  covalent geometry    : angle       0.60506 (12092)
  hydrogen bonds       : bond        0.04067 (  557)
  hydrogen bonds       : angle       4.59128 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9151 (mt) cc_final: 0.8927 (mt)
REVERT: B   98 MET cc_start: 0.9346 (ttt) cc_final: 0.8970 (ttt)
REVERT: B  100 MET cc_start: 0.9540 (ttp) cc_final: 0.9170 (tmm)
REVERT: B  200 MET cc_start: 0.9424 (tmm) cc_final: 0.9041 (tmm)
REVERT: B  203 VAL cc_start: 0.9380 (t) cc_final: 0.9141 (p)
REVERT: B  244 MET cc_start: 0.9292 (ppp) cc_final: 0.8918 (ppp)
REVERT: B  312 MET cc_start: 0.8663 (mmm) cc_final: 0.8291 (mmm)
REVERT: B  315 CYS cc_start: 0.8368 (m) cc_final: 0.8079 (m)
REVERT: B  402 MET cc_start: 0.8829 (tmm) cc_final: 0.8536 (tmm)
REVERT: B  538 ARG cc_start: 0.8482 (tpm170) cc_final: 0.8093 (tpm170)
REVERT: A  109 MET cc_start: 0.8551 (mmp) cc_final: 0.7930 (tmm)
REVERT: A  111 MET cc_start: 0.9179 (tmm) cc_final: 0.8966 (tmm)
REVERT: A  115 PHE cc_start: 0.9143 (t80) cc_final: 0.8811 (t80)
REVERT: A  116 PHE cc_start: 0.9191 (m-80) cc_final: 0.8790 (m-80)
REVERT: A  156 LEU cc_start: 0.9661 (mt) cc_final: 0.9440 (mt)
REVERT: A  160 MET cc_start: 0.9361 (mmm) cc_final: 0.9073 (mmm)
REVERT: A  180 ILE cc_start: 0.9003 (tt) cc_final: 0.8798 (pt)
REVERT: A  200 MET cc_start: 0.9434 (tmm) cc_final: 0.9119 (tmm)
REVERT: A  210 MET cc_start: 0.8846 (mmt) cc_final: 0.8377 (mmm)
REVERT: A  226 GLU cc_start: 0.9280 (tp30) cc_final: 0.9036 (tp30)
REVERT: A  244 MET cc_start: 0.9346 (ppp) cc_final: 0.9002 (ppp)
REVERT: A  312 MET cc_start: 0.9282 (mmp) cc_final: 0.8818 (mmm)
REVERT: A  315 CYS cc_start: 0.9014 (t) cc_final: 0.8794 (t)
REVERT: A  390 THR cc_start: 0.9043 (p) cc_final: 0.8704 (p)
REVERT: A  392 PHE cc_start: 0.9312 (m-10) cc_final: 0.8946 (m-10)
REVERT: A  410 TYR cc_start: 0.8248 (m-10) cc_final: 0.7781 (m-80)
REVERT: A  437 ILE cc_start: 0.9464 (tt) cc_final: 0.9199 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0767
  time to fit residues: 27.3422
Evaluate side-chains
  201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 33 optimal weight:    6.9990
   chunk 81 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0270
   chunk 76 optimal weight:    0.8980
   chunk 61 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0670
   chunk 108 optimal weight:    3.9990
   chunk 44 optimal weight:   10.0000
   chunk 109 optimal weight:    8.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.078314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.057014 restraints weight = 33904.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.059377 restraints weight = 21559.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.061135 restraints weight = 15370.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.062463 restraints weight = 11807.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.063507 restraints weight = 9540.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.4372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8950  Z= 0.130
  Angle     :  0.617   8.293  12092  Z= 0.324
  Chirality :  0.043   0.260   1440
  Planarity :  0.004   0.045   1532
  Dihedral  :  4.505  24.588   1238
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.29 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.26), residues: 1134
  helix:  1.52 (0.19), residues: 734
  sheet: -0.13 (0.75), residues: 48
  loop : -1.06 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 517 
 TYR   0.021   0.001   TYR A 130 
 PHE   0.035   0.001   PHE B 115 
 TRP   0.019   0.001   TRP A  66 
 HIS   0.006   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 8950)
  covalent geometry    : angle       0.61744 (12092)
  hydrogen bonds       : bond        0.04071 (  557)
  hydrogen bonds       : angle       4.65137 ( 1656)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 236
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 LEU cc_start: 0.9127 (mt) cc_final: 0.8912 (mt)
REVERT: B   98 MET cc_start: 0.9321 (ttt) cc_final: 0.8989 (ttt)
REVERT: B  100 MET cc_start: 0.9538 (ttp) cc_final: 0.9180 (tmm)
REVERT: B  108 MET cc_start: 0.9452 (mtp) cc_final: 0.9161 (mtp)
REVERT: B  200 MET cc_start: 0.9442 (tmm) cc_final: 0.9066 (tmm)
REVERT: B  203 VAL cc_start: 0.9392 (t) cc_final: 0.9161 (p)
REVERT: B  208 GLU cc_start: 0.9079 (mp0) cc_final: 0.8836 (mp0)
REVERT: B  244 MET cc_start: 0.9289 (ppp) cc_final: 0.8922 (ppp)
REVERT: B  312 MET cc_start: 0.8592 (mmm) cc_final: 0.8191 (mmm)
REVERT: B  315 CYS cc_start: 0.8406 (m) cc_final: 0.8120 (m)
REVERT: B  456 MET cc_start: 0.9215 (mpp) cc_final: 0.8993 (mmp)
REVERT: B  503 ILE cc_start: 0.9727 (mm) cc_final: 0.9460 (tp)
REVERT: B  538 ARG cc_start: 0.8477 (tpm170) cc_final: 0.8065 (tpm170)
REVERT: A   67 MET cc_start: 0.8490 (mmp) cc_final: 0.8243 (mmp)
REVERT: A   98 MET cc_start: 0.9137 (tpp) cc_final: 0.8334 (tpt)
REVERT: A  109 MET cc_start: 0.8649 (mmp) cc_final: 0.7656 (tmm)
REVERT: A  111 MET cc_start: 0.9170 (tmm) cc_final: 0.8963 (tmm)
REVERT: A  115 PHE cc_start: 0.9142 (t80) cc_final: 0.8837 (t80)
REVERT: A  116 PHE cc_start: 0.9194 (m-80) cc_final: 0.8802 (m-80)
REVERT: A  156 LEU cc_start: 0.9664 (mt) cc_final: 0.9375 (mt)
REVERT: A  160 MET cc_start: 0.9362 (mmm) cc_final: 0.9017 (mmm)
REVERT: A  200 MET cc_start: 0.9432 (tmm) cc_final: 0.9111 (tmm)
REVERT: A  210 MET cc_start: 0.8856 (mmt) cc_final: 0.8381 (mmm)
REVERT: A  244 MET cc_start: 0.9336 (ppp) cc_final: 0.8983 (ppp)
REVERT: A  291 MET cc_start: 0.9374 (tpt) cc_final: 0.9159 (tpp)
REVERT: A  312 MET cc_start: 0.9271 (mmp) cc_final: 0.8812 (mmm)
REVERT: A  315 CYS cc_start: 0.9047 (t) cc_final: 0.8844 (t)
REVERT: A  390 THR cc_start: 0.9050 (p) cc_final: 0.8724 (p)
REVERT: A  392 PHE cc_start: 0.9325 (m-10) cc_final: 0.8959 (m-10)
REVERT: A  410 TYR cc_start: 0.8226 (m-10) cc_final: 0.7774 (m-80)
REVERT: A  437 ILE cc_start: 0.9458 (tt) cc_final: 0.9192 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 236
  average time/residue: 0.0714
  time to fit residues: 25.5567
Evaluate side-chains
  207 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.9980
   chunk 104 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 59 optimal weight:    0.9990
   chunk 5 optimal weight:    0.8980
   chunk 65 optimal weight:    0.6980
   chunk 94 optimal weight:    0.6980
   chunk 30 optimal weight:    0.0470
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 520 GLN
** A 537 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 574 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.078815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.057856 restraints weight = 32770.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.060134 restraints weight = 20978.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.061887 restraints weight = 15105.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.063217 restraints weight = 11634.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.064262 restraints weight = 9428.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8125
moved from start:          0.4518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   8950  Z= 0.125
  Angle     :  0.606   8.135  12092  Z= 0.316
  Chirality :  0.042   0.264   1440
  Planarity :  0.003   0.044   1532
  Dihedral  :  4.429  24.726   1238
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  5.03 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.00 (0.26), residues: 1134
  helix:  1.53 (0.19), residues: 734
  sheet: -0.06 (0.75), residues: 48
  loop : -1.08 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 517 
 TYR   0.028   0.001   TYR A 130 
 PHE   0.013   0.001   PHE B 344 
 TRP   0.018   0.001   TRP A  66 
 HIS   0.007   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8950)
  covalent geometry    : angle       0.60629 (12092)
  hydrogen bonds       : bond        0.03965 (  557)
  hydrogen bonds       : angle       4.57347 ( 1656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1967.92 seconds
wall clock time: 34 minutes 41.68 seconds (2081.68 seconds total)