Starting phenix.real_space_refine
on Wed Feb  4 06:07:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9hui_52414/02_2026/9hui_52414.cif"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
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      60      5.16       5
     C    5651      2.51       5
     N    1468      2.21       5
     O    1644      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8823
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4444
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 568, 4444
          Classifications: {'peptide': 568}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 41, 'TRANS': 526}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 4
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 4379
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 559, 4379
          Classifications: {'peptide': 559}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 40, 'TRANS': 518}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 2.14, per 1000 atoms: 0.24
  Number of scatterers: 8823
  At special positions: 0
  Unit cell: (76.104, 97.244, 141.215, 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      60     16.00
     O    1644      8.00
     N    1468      7.00
     C    5651      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.74
  Conformation dependent library (CDL) restraints added in 385.6 milliseconds
  

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 23 sheets defined
      20.5% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 190 through 196
      removed outlier: 3.923A  pdb=" N   PHE A 194 " --> pdb=" O   LYS A 191 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   THR A 195 " --> pdb=" O   ASP A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 211
    Processing helix  chain 'A' and resid 316 through 331
    Processing helix  chain 'A' and resid 402 through 406
      removed outlier: 3.617A  pdb=" N   ASP A 405 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 454
      removed outlier: 3.705A  pdb=" N   GLN A 448 " --> pdb=" O   HIS A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 474
    Processing helix  chain 'A' and resid 493 through 508
      removed outlier: 4.133A  pdb=" N   CYS A 497 " --> pdb=" O   SER A 493 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY A 508 " --> pdb=" O   GLN A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 531
    Processing helix  chain 'A' and resid 533 through 557
    Processing helix  chain 'A' and resid 560 through 562
      No H-bonds generated for 'chain 'A' and resid 560 through 562'
    Processing helix  chain 'A' and resid 575 through 577
      No H-bonds generated for 'chain 'A' and resid 575 through 577'
    Processing helix  chain 'A' and resid 611 through 621
      removed outlier: 3.513A  pdb=" N   GLU A 621 " --> pdb=" O   CYS A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 657 through 661
      removed outlier: 3.556A  pdb=" N   MET A 661 " --> pdb=" O   TRP A 658 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 173 through 180
    Processing helix  chain 'B' and resid 192 through 195
    Processing helix  chain 'B' and resid 315 through 331
      removed outlier: 4.091A  pdb=" N   LYS B 321 " --> pdb=" O   GLU B 317 " (cutoff:3.500A)
      removed outlier: 4.224A  pdb=" N   SER B 322 " --> pdb=" O   ASP B 318 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL B 323 " --> pdb=" O   PHE B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 408
      No H-bonds generated for 'chain 'B' and resid 406 through 408'
    Processing helix  chain 'B' and resid 444 through 454
      removed outlier: 3.590A  pdb=" N   GLN B 454 " --> pdb=" O   PHE B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 493 through 506
      removed outlier: 4.035A  pdb=" N   CYS B 497 " --> pdb=" O   SER B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 525 through 531
    Processing helix  chain 'B' and resid 532 through 557
      removed outlier: 3.520A  pdb=" N   TRP B 548 " --> pdb=" O   ARG B 544 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASN B 549 " --> pdb=" O   CYS B 545 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 562
      No H-bonds generated for 'chain 'B' and resid 560 through 562'
    Processing helix  chain 'B' and resid 610 through 621
    Processing helix  chain 'B' and resid 622 through 624
      No H-bonds generated for 'chain 'B' and resid 622 through 624'
    Processing helix  chain 'B' and resid 657 through 661
      removed outlier: 3.676A  pdb=" N   MET B 661 " --> pdb=" O   TRP B 658 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26
      removed outlier: 3.750A  pdb=" N   THR A  79 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   VAL A  49 " --> pdb=" O   THR A  79 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 40
      removed outlier: 4.201A  pdb=" N   SER A  39 " --> pdb=" O   TYR A  97 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   GLN A  90 " --> pdb=" O   LEU A 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 118
      removed outlier: 3.842A  pdb=" N   SER A 181 " --> pdb=" O   VAL A 251 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 149 through 150
      removed outlier: 4.571A  pdb=" N   LEU A 199 " --> pdb=" O   LEU A 238 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 333 through 335
      removed outlier: 7.116A  pdb=" N   GLN A 306 " --> pdb=" O   LYS A 333 " (cutoff:3.500A)
      removed outlier: 7.404A  pdb=" N   THR A 335 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
      removed outlier: 6.362A  pdb=" N   VAL A 308 " --> pdb=" O   THR A 335 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   ARG A 650 " --> pdb=" O   GLN A 306 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 356
    Processing sheet with id=AA7, first strand: chain 'A' and resid 411 through 413
      removed outlier: 3.519A  pdb=" N   ARG A 427 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
      removed outlier: 6.431A  pdb=" N   ILE A 428 " --> pdb=" O   VAL A 460 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   LEU A 462 " --> pdb=" O   ILE A 428 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   PHE A 430 " --> pdb=" O   LEU A 462 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 416 through 418
    Processing sheet with id=AA9, first strand: chain 'A' and resid 476 through 480
    Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 573
    Processing sheet with id=AB2, first strand: chain 'A' and resid 590 through 591
      removed outlier: 3.649A  pdb=" N   LEU A 590 " --> pdb=" O   GLY A 597 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   LEU A 596 " --> pdb=" O   THR A 628 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   ILE A 630 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 6.122A  pdb=" N   ILE A 598 " --> pdb=" O   ILE A 630 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 605 through 606
    Processing sheet with id=AB4, first strand: chain 'B' and resid 6 through 7
      removed outlier: 3.898A  pdb=" N   ILE B   7 " --> pdb=" O   GLN B  26 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 16
      removed outlier: 6.919A  pdb=" N   THR B  15 " --> pdb=" O   TYR B 109 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA B 106 " --> pdb=" O   ILE B  94 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   ILE B  94 " --> pdb=" O   ALA B 106 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   SER B  95 " --> pdb=" O   SER B  41 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 19 through 20
      removed outlier: 6.874A  pdb=" N   CYS B  19 " --> pdb=" O   VAL B 113 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ILE B 115 " --> pdb=" O   CYS B  19 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU B 185 " --> pdb=" O   MET B 247 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   MET B 247 " --> pdb=" O   LEU B 185 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   THR B 187 " --> pdb=" O   HIS B 245 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   HIS B 245 " --> pdb=" O   THR B 187 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   VAL B 213 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER B 226 " --> pdb=" O   GLN B 215 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 148 through 150
      removed outlier: 5.724A  pdb=" N   ALA B 148 " --> pdb=" O   ARG B 292 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   LEU B 271 " --> pdb=" O   VAL B 284 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   GLN B 286 " --> pdb=" O   ILE B 269 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ILE B 269 " --> pdb=" O   GLN B 286 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   SER B 288 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LEU B 267 " --> pdb=" O   SER B 288 " (cutoff:3.500A)
      removed outlier: 5.872A  pdb=" N   VAL B 290 " --> pdb=" O   ILE B 265 " (cutoff:3.500A)
      removed outlier: 7.852A  pdb=" N   ILE B 265 " --> pdb=" O   VAL B 290 " (cutoff:3.500A)
      removed outlier: 4.655A  pdb=" N   LEU B 199 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 333 through 334
      removed outlier: 4.340A  pdb=" N   LYS B 333 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   VAL B 308 " --> pdb=" O   LYS B 333 " (cutoff:3.500A)
      removed outlier: 7.568A  pdb=" N   ARG B 650 " --> pdb=" O   GLN B 306 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 353 through 356
    Processing sheet with id=AC1, first strand: chain 'B' and resid 410 through 412
    Processing sheet with id=AC2, first strand: chain 'B' and resid 416 through 418
    Processing sheet with id=AC3, first strand: chain 'B' and resid 476 through 480
      removed outlier: 7.919A  pdb=" N   ILE B 565 " --> pdb=" O   PHE B 487 " (cutoff:3.500A)
      removed outlier: 6.057A  pdb=" N   LEU B 489 " --> pdb=" O   ILE B 565 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   ILE B 567 " --> pdb=" O   LEU B 489 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   LEU B 491 " --> pdb=" O   ILE B 567 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 573
    Processing sheet with id=AC5, first strand: chain 'B' and resid 595 through 599

    265 hydrogen bonds defined for protein.
    705 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: 1.46

  Time building geometry restraints manager: 0.98 seconds

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

  Histogram of bond lengths:
        1.20 -     1.44: 3754
        1.44 -     1.68: 5179
        1.68 -     1.92: 91
        1.92 -     2.15: 2
        2.15 -     2.39: 1
  Bond restraints: 9027
  Sorted by residual:
  bond pdb=" CE3 TRP A 139 "
       pdb=" CZ3 TRP A 139 "
    ideal  model  delta    sigma   weight residual
    1.382  2.393 -1.011 3.00e-02 1.11e+03 1.13e+03
  bond pdb=" CZ3 TRP A 139 "
       pdb=" CH2 TRP A 139 "
    ideal  model  delta    sigma   weight residual
    1.400  2.033 -0.633 2.50e-02 1.60e+03 6.40e+02
  bond pdb=" CE2 TRP A 139 "
       pdb=" CZ2 TRP A 139 "
    ideal  model  delta    sigma   weight residual
    1.394  1.923 -0.529 2.10e-02 2.27e+03 6.33e+02
  bond pdb=" CD  ARG A 123 "
       pdb=" NE  ARG A 123 "
    ideal  model  delta    sigma   weight residual
    1.458  1.755 -0.297 1.40e-02 5.10e+03 4.49e+02
  bond pdb=" CZ2 TRP A 139 "
       pdb=" CH2 TRP A 139 "
    ideal  model  delta    sigma   weight residual
    1.368  1.743 -0.375 1.90e-02 2.77e+03 3.89e+02
  ... (remaining 9022 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.77: 12247
       14.77 -    29.55: 3
       29.55 -    44.32: 3
       44.32 -    59.10: 0
       59.10 -    73.87: 1
  Bond angle restraints: 12254
  Sorted by residual:
  angle pdb=" CB  PRO B 414 "
        pdb=" CG  PRO B 414 "
        pdb=" CD  PRO B 414 "
      ideal   model   delta    sigma   weight residual
     106.10  179.97  -73.87 3.20e+00 9.77e-02 5.33e+02
  angle pdb=" CD  ARG A 123 "
        pdb=" NE  ARG A 123 "
        pdb=" CZ  ARG A 123 "
      ideal   model   delta    sigma   weight residual
     124.40  155.70  -31.30 1.40e+00 5.10e-01 5.00e+02
  angle pdb=" N   PRO B 414 "
        pdb=" CD  PRO B 414 "
        pdb=" CG  PRO B 414 "
      ideal   model   delta    sigma   weight residual
     103.20   70.84   32.36 1.50e+00 4.44e-01 4.65e+02
  angle pdb=" CA  PRO B 414 "
        pdb=" CB  PRO B 414 "
        pdb=" CG  PRO B 414 "
      ideal   model   delta    sigma   weight residual
     104.50   73.21   31.29 1.90e+00 2.77e-01 2.71e+02
  angle pdb=" CA  PRO B 604 "
        pdb=" N   PRO B 604 "
        pdb=" CD  PRO B 604 "
      ideal   model   delta    sigma   weight residual
     112.00   93.53   18.47 1.40e+00 5.10e-01 1.74e+02
  ... (remaining 12249 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.19: 5088
       28.19 -    56.39: 337
       56.39 -    84.58: 17
       84.58 -   112.78: 2
      112.78 -   140.97: 2
  Dihedral angle restraints: 5446
    sinusoidal: 2197
      harmonic: 3249
  Sorted by residual:
  dihedral pdb=" CA  VAL B 289 "
           pdb=" C   VAL B 289 "
           pdb=" N   VAL B 290 "
           pdb=" CA  VAL B 290 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -137.37  -42.63     0      5.00e+00 4.00e-02 7.27e+01
  dihedral pdb=" N   PRO B 414 "
           pdb=" CG  PRO B 414 "
           pdb=" CD  PRO B 414 "
           pdb=" CB  PRO B 414 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00  154.18 -124.18     1      1.50e+01 4.44e-03 6.66e+01
  dihedral pdb=" CA  LEU B 264 "
           pdb=" C   LEU B 264 "
           pdb=" N   ILE B 265 "
           pdb=" CA  ILE B 265 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  145.82   34.18     0      5.00e+00 4.00e-02 4.67e+01
  ... (remaining 5443 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.093: 1284
       0.093 -    0.186: 105
       0.186 -    0.279: 2
       0.279 -    0.373: 2
       0.373 -    0.466: 2
  Chirality restraints: 1395
  Sorted by residual:
  chirality pdb=" CA  PRO B 414 "
            pdb=" N   PRO B 414 "
            pdb=" C   PRO B 414 "
            pdb=" CB  PRO B 414 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    3.18   -0.47 2.00e-01 2.50e+01 5.42e+00
  chirality pdb=" CA  ARG B 137 "
            pdb=" N   ARG B 137 "
            pdb=" C   ARG B 137 "
            pdb=" CB  ARG B 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.58e+00
  chirality pdb=" CB  VAL B 289 "
            pdb=" CA  VAL B 289 "
            pdb=" CG1 VAL B 289 "
            pdb=" CG2 VAL B 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.45e+00
  ... (remaining 1392 not shown)

  Planarity restraints: 1569
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 603 "   -0.122 5.00e-02 4.00e+02   1.65e-01 4.35e+01
        pdb=" N   PRO B 604 "    0.284 5.00e-02 4.00e+02
        pdb=" CA  PRO B 604 "   -0.081 5.00e-02 4.00e+02
        pdb=" CD  PRO B 604 "   -0.081 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 142 "   -0.082 5.00e-02 4.00e+02   1.20e-01 2.29e+01
        pdb=" N   PRO B 143 "    0.207 5.00e-02 4.00e+02
        pdb=" CA  PRO B 143 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO B 143 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  96 "   -0.019 2.00e-02 2.50e+03   2.94e-02 1.73e+01
        pdb=" CG  TYR B  96 "    0.067 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  96 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  96 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  96 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  96 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  96 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  96 "    0.004 2.00e-02 2.50e+03
  ... (remaining 1566 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 98
        2.54 -     3.13: 6614
        3.13 -     3.72: 13573
        3.72 -     4.31: 18289
        4.31 -     4.90: 29687
  Nonbonded interactions: 68261
  Sorted by model distance:
  nonbonded pdb=" NE  ARG A 123 "
            pdb=" CZ2 TRP A 139 "
     model   vdw
     1.955 2.736
  nonbonded pdb=" NE  ARG A 123 "
            pdb=" CE2 TRP A 139 "
     model   vdw
     2.016 3.340
  nonbonded pdb=" NE  ARG A 123 "
            pdb=" CD2 TRP A 139 "
     model   vdw
     2.114 2.672
  nonbonded pdb=" OE2 GLU A 281 "
            pdb=" OH  TYR B 435 "
     model   vdw
     2.136 3.040
  nonbonded pdb=" O   ARG B 137 "
            pdb=" O   ILE B 265 "
     model   vdw
     2.150 3.040
  ... (remaining 68256 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 5 through 370 or resid 400 through 663))
  selection = (chain 'B' and (resid 5 through 314 or (resid 315 and (name N or name CA or name \ 
 C or name O or name CB )) or resid 316 through 663))
}

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:             6.160
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.690
  Find NCS groups from input model:        0.150
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.2767
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      :  0.018   1.011   9028  Z= 0.836
  Angle     :  1.370  73.872  12254  Z= 0.729
  Chirality :  0.053   0.466   1395
  Planarity :  0.010   0.165   1569
  Dihedral  : 17.058 140.969   3328
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 25.96
  Ramachandran Plot:
    Outliers :  0.28 %
    Allowed  :  5.33 %
    Favored  : 94.40 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 27.15 %
    Favored  : 72.06 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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 are not related in a simple way.
  whole: -2.30 (0.23), residues: 1089
  helix: -0.74 (0.37), residues: 180
  sheet: -1.21 (0.28), residues: 342
  loop : -1.99 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 123 
 TYR   0.067   0.003   TYR B  96 
 PHE   0.065   0.003   PHE B 291 
 TRP   0.023   0.003   TRP A 658 
 HIS   0.016   0.001   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.01757 ( 9027)
  covalent geometry    : angle       1.37049 (12254)
  hydrogen bonds       : bond        0.18809 (  265)
  hydrogen bonds       : angle       8.52847 (  705)
  Misc. bond           : bond        0.33226 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 192
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: -0.0232 (mtt) cc_final: -0.0882 (ptp)
REVERT: A  267 LEU cc_start: 0.2521 (mt) cc_final: 0.2301 (mt)
REVERT: A  405 ASP cc_start: 0.6093 (p0) cc_final: 0.5329 (t70)
REVERT: A  484 ARG cc_start: 0.3153 (mmp-170) cc_final: 0.2333 (mpt180)
REVERT: A  658 TRP cc_start: 0.4856 (p-90) cc_final: 0.3610 (p-90)
REVERT: A  661 MET cc_start: 0.3089 (ppp) cc_final: 0.2840 (ptt)
REVERT: B  199 LEU cc_start: 0.3184 (mt) cc_final: 0.2878 (tp)
REVERT: B  239 MET cc_start: 0.2088 (tmm) cc_final: 0.1433 (mmm)
REVERT: B  454 GLN cc_start: 0.7287 (mp10) cc_final: 0.6583 (mp10)
  outliers start: 8
  outliers final: 3
  residues processed: 198
  average time/residue: 0.1028
  time to fit residues: 27.2644
Evaluate side-chains
  111 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 108
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 TRP
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain B residue  237 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.0030
   chunk 100 optimal weight:    0.7980
   chunk 106 optimal weight:    0.6980
   overall best weight:    0.7170

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

Flipped N/Q/H residues before XYZ refinement:
** A 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 444 HIS
A 523 GLN
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5098 r_free = 0.5098 target = 0.212719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.189638 restraints weight = 17839.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.193411 restraints weight = 11139.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4911 r_free = 0.4911 target = 0.196200 restraints weight = 7840.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4933 r_free = 0.4933 target = 0.198021 restraints weight = 5972.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.199543 restraints weight = 4865.623|
|-----------------------------------------------------------------------------|
r_work (final): 0.4922
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3286
moved from start:          0.2871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076   9028  Z= 0.193
  Angle     :  0.837  15.785  12254  Z= 0.426
  Chirality :  0.049   0.339   1395
  Planarity :  0.007   0.067   1569
  Dihedral  :  5.857  59.090   1178
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.05 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 24.25 %
    Favored  : 71.36 %
  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 are not related in a simple way.
  whole: -2.00 (0.24), residues: 1089
  helix: -0.58 (0.38), residues: 186
  sheet: -0.80 (0.29), residues: 315
  loop : -1.90 (0.23), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG A 123 
 TYR   0.017   0.002   TYR A 423 
 PHE   0.043   0.002   PHE B 291 
 TRP   0.018   0.002   TRP A 466 
 HIS   0.011   0.002   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 9027)
  covalent geometry    : angle       0.83690 (12254)
  hydrogen bonds       : bond        0.04704 (  265)
  hydrogen bonds       : angle       6.68563 (  705)
  Misc. bond           : bond        0.00613 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 121
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLU cc_start: 0.3691 (mp0) cc_final: 0.3385 (mp0)
REVERT: A   80 MET cc_start: -0.0432 (mtt) cc_final: -0.1280 (ttm)
REVERT: A  139 TRP cc_start: 0.3254 (OUTLIER) cc_final: 0.1300 (t60)
REVERT: A  189 THR cc_start: 0.5646 (OUTLIER) cc_final: 0.5400 (p)
REVERT: A  247 MET cc_start: 0.1513 (tpt) cc_final: 0.0866 (tpt)
REVERT: A  276 ASN cc_start: 0.7441 (m110) cc_final: 0.6782 (t0)
REVERT: A  405 ASP cc_start: 0.6168 (p0) cc_final: 0.5579 (t70)
REVERT: A  658 TRP cc_start: 0.4977 (p-90) cc_final: 0.3953 (p-90)
REVERT: B  239 MET cc_start: 0.2414 (tmm) cc_final: 0.1802 (mmm)
REVERT: B  252 GLU cc_start: 0.4046 (pt0) cc_final: 0.2730 (pt0)
REVERT: B  336 ILE cc_start: 0.5741 (mp) cc_final: 0.5525 (tt)
  outliers start: 44
  outliers final: 15
  residues processed: 159
  average time/residue: 0.0676
  time to fit residues: 15.8815
Evaluate side-chains
  122 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 TRP
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  317 GLU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  629 PHE
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  425 LEU
Chi-restraints excluded: chain B residue  580 GLU
Chi-restraints excluded: chain B residue  605 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 73 optimal weight:    6.9990
   chunk 10 optimal weight:    8.9990
   chunk 39 optimal weight:    0.0050
   chunk 55 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 96 optimal weight:    4.9990
   chunk 79 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
A 444 HIS
A 538 HIS
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5108 r_free = 0.5108 target = 0.212357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4842 r_free = 0.4842 target = 0.189396 restraints weight = 18262.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4887 r_free = 0.4887 target = 0.193208 restraints weight = 11438.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4920 r_free = 0.4920 target = 0.195991 restraints weight = 8080.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4943 r_free = 0.4943 target = 0.197909 restraints weight = 6174.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4956 r_free = 0.4956 target = 0.199065 restraints weight = 5011.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.4962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3904
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081   9028  Z= 0.197
  Angle     :  0.788  11.492  12254  Z= 0.402
  Chirality :  0.049   0.299   1395
  Planarity :  0.007   0.057   1569
  Dihedral  :  5.682  59.397   1175
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 15.39
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.79 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 24.35 %
    Favored  : 70.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.29 %

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 are not related in a simple way.
  whole: -1.82 (0.24), residues: 1089
  helix: -0.43 (0.37), residues: 182
  sheet: -0.64 (0.29), residues: 310
  loop : -1.79 (0.23), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 544 
 TYR   0.025   0.002   TYR A 237 
 PHE   0.044   0.002   PHE B 291 
 TRP   0.025   0.002   TRP B 141 
 HIS   0.009   0.002   HIS A 444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 ( 9027)
  covalent geometry    : angle       0.78839 (12254)
  hydrogen bonds       : bond        0.04181 (  265)
  hydrogen bonds       : angle       6.38480 (  705)
  Misc. bond           : bond        0.00247 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 118
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: -0.0272 (mtt) cc_final: -0.0788 (ttm)
REVERT: A  139 TRP cc_start: 0.2918 (OUTLIER) cc_final: 0.1336 (t60)
REVERT: A  208 MET cc_start: 0.3090 (mpp) cc_final: 0.2778 (mpp)
REVERT: A  276 ASN cc_start: 0.7815 (m110) cc_final: 0.7142 (t0)
REVERT: A  388 ASP cc_start: 0.3491 (OUTLIER) cc_final: 0.3124 (p0)
REVERT: A  405 ASP cc_start: 0.6164 (p0) cc_final: 0.5434 (t70)
REVERT: A  500 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4460 (pp)
REVERT: A  589 MET cc_start: 0.4105 (OUTLIER) cc_final: 0.3854 (tmm)
REVERT: B  239 MET cc_start: 0.2984 (tmm) cc_final: 0.2166 (mmm)
REVERT: B  252 GLU cc_start: 0.4731 (pt0) cc_final: 0.4457 (pt0)
REVERT: B  265 ILE cc_start: 0.0290 (OUTLIER) cc_final: 0.0063 (mt)
REVERT: B  297 ILE cc_start: 0.4663 (mm) cc_final: 0.4165 (mm)
REVERT: B  450 PHE cc_start: 0.4990 (OUTLIER) cc_final: 0.4577 (t80)
  outliers start: 53
  outliers final: 25
  residues processed: 158
  average time/residue: 0.0749
  time to fit residues: 17.2863
Evaluate side-chains
  123 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 92
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 TRP
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  289 VAL
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  526 ILE
Chi-restraints excluded: chain A residue  589 MET
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain A residue  627 CYS
Chi-restraints excluded: chain A residue  629 PHE
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  141 TRP
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  265 ILE
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  283 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  475 PHE
Chi-restraints excluded: chain B residue  589 MET
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  647 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 45 optimal weight:    0.6980
   chunk 71 optimal weight:    0.4980
   chunk 66 optimal weight:    0.8980
   chunk 36 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 85 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 33 optimal weight:    5.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 444 HIS
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5108 r_free = 0.5108 target = 0.211746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.188510 restraints weight = 18525.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.4884 r_free = 0.4884 target = 0.192379 restraints weight = 11546.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4916 r_free = 0.4916 target = 0.195091 restraints weight = 8203.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4938 r_free = 0.4938 target = 0.197011 restraints weight = 6319.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4950 r_free = 0.4950 target = 0.198124 restraints weight = 5161.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.4956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4265
moved from start:          0.6122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   9028  Z= 0.193
  Angle     :  0.742  11.072  12254  Z= 0.375
  Chirality :  0.048   0.265   1395
  Planarity :  0.007   0.062   1569
  Dihedral  :  5.422  54.830   1175
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 15.91
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.42 %
    Favored  : 94.49 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.05 %
    Favored  : 69.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.72 (0.24), residues: 1089
  helix: -0.28 (0.37), residues: 187
  sheet: -0.56 (0.29), residues: 306
  loop : -1.78 (0.24), residues: 596

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 441 
 TYR   0.014   0.002   TYR B  96 
 PHE   0.059   0.002   PHE B 291 
 TRP   0.039   0.004   TRP A 658 
 HIS   0.005   0.001   HIS A 444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 ( 9027)
  covalent geometry    : angle       0.74176 (12254)
  hydrogen bonds       : bond        0.03795 (  265)
  hydrogen bonds       : angle       6.15175 (  705)
  Misc. bond           : bond        0.00180 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 100
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 MET cc_start: -0.0135 (mtt) cc_final: -0.0808 (ttm)
REVERT: A  208 MET cc_start: 0.3430 (mpp) cc_final: 0.3007 (mpp)
REVERT: A  281 GLU cc_start: 0.4491 (OUTLIER) cc_final: 0.4218 (pm20)
REVERT: A  441 ARG cc_start: 0.4155 (tmm160) cc_final: 0.3197 (ptt90)
REVERT: A  500 LEU cc_start: 0.5038 (OUTLIER) cc_final: 0.4539 (pp)
REVERT: A  661 MET cc_start: -0.1400 (ptt) cc_final: -0.1845 (ptt)
REVERT: B  239 MET cc_start: 0.3550 (tmm) cc_final: 0.2091 (mtp)
REVERT: B  328 MET cc_start: 0.7306 (tmm) cc_final: 0.7012 (tmm)
REVERT: B  443 MET cc_start: 0.2633 (OUTLIER) cc_final: 0.2103 (mtm)
REVERT: B  450 PHE cc_start: 0.5267 (OUTLIER) cc_final: 0.4804 (t80)
REVERT: B  475 PHE cc_start: 0.5507 (OUTLIER) cc_final: 0.4628 (p90)
REVERT: B  569 GLN cc_start: 0.5202 (mm-40) cc_final: 0.4812 (tm-30)
REVERT: B  580 GLU cc_start: 0.4915 (OUTLIER) cc_final: 0.4558 (mm-30)
  outliers start: 40
  outliers final: 24
  residues processed: 128
  average time/residue: 0.0774
  time to fit residues: 14.2246
Evaluate side-chains
  115 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 85
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  149 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  357 ILE
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  596 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  629 PHE
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  443 MET
Chi-restraints excluded: chain B residue  450 PHE
Chi-restraints excluded: chain B residue  460 VAL
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  475 PHE
Chi-restraints excluded: chain B residue  580 GLU
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  605 VAL
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 47 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 99 optimal weight:    0.6980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   chunk 14 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9980
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
A 444 HIS
A 448 GLN
** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 409 ASN
** B 538 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5055 r_free = 0.5055 target = 0.206254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4765 r_free = 0.4765 target = 0.182307 restraints weight = 18771.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4813 r_free = 0.4813 target = 0.186132 restraints weight = 11992.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4846 r_free = 0.4846 target = 0.188776 restraints weight = 8649.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.4869 r_free = 0.4869 target = 0.190621 restraints weight = 6745.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4881 r_free = 0.4881 target = 0.191608 restraints weight = 5615.353|
|-----------------------------------------------------------------------------|
r_work (final): 0.4884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4914
moved from start:          0.8640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.092   9028  Z= 0.213
  Angle     :  0.835  11.006  12254  Z= 0.424
  Chirality :  0.052   0.280   1395
  Planarity :  0.008   0.080   1569
  Dihedral  :  5.771  35.338   1173
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  6.61 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 25.35 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.95 (0.24), residues: 1089
  helix: -0.40 (0.36), residues: 188
  sheet: -0.73 (0.29), residues: 321
  loop : -1.97 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 544 
 TYR   0.016   0.002   TYR A 237 
 PHE   0.041   0.003   PHE B 291 
 TRP   0.028   0.003   TRP B 141 
 HIS   0.008   0.002   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00493 ( 9027)
  covalent geometry    : angle       0.83541 (12254)
  hydrogen bonds       : bond        0.04475 (  265)
  hydrogen bonds       : angle       6.44349 (  705)
  Misc. bond           : bond        0.00088 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 105
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLU cc_start: 0.3911 (mp0) cc_final: 0.3527 (mp0)
REVERT: A   80 MET cc_start: 0.0494 (mtt) cc_final: -0.0195 (ttm)
REVERT: A  208 MET cc_start: 0.3949 (mpp) cc_final: 0.3553 (mpp)
REVERT: A  369 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.5460 (t0)
REVERT: A  388 ASP cc_start: 0.3137 (OUTLIER) cc_final: 0.2497 (p0)
REVERT: A  441 ARG cc_start: 0.4110 (tmm160) cc_final: 0.3538 (mmt180)
REVERT: A  661 MET cc_start: -0.0648 (ptt) cc_final: -0.0879 (ptt)
REVERT: B  178 GLN cc_start: 0.4684 (mm-40) cc_final: 0.4482 (mm-40)
REVERT: B  292 ARG cc_start: 0.3648 (OUTLIER) cc_final: 0.3387 (ttt-90)
REVERT: B  441 ARG cc_start: 0.4261 (mtm180) cc_final: 0.1801 (mmm-85)
  outliers start: 56
  outliers final: 32
  residues processed: 149
  average time/residue: 0.0672
  time to fit residues: 14.5791
Evaluate side-chains
  127 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 92
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  150 LEU
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  266 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  595 HIS
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  264 LEU
Chi-restraints excluded: chain B residue  268 THR
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  288 SER
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  335 THR
Chi-restraints excluded: chain B residue  406 SER
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  475 PHE
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  537 GLU
Chi-restraints excluded: chain B residue  580 GLU
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 14 optimal weight:    8.9990
   chunk 23 optimal weight:    6.9990
   chunk 58 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0040
   chunk 48 optimal weight:    0.7980
   chunk 90 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
A 444 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5084 r_free = 0.5084 target = 0.209652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4803 r_free = 0.4803 target = 0.185778 restraints weight = 18533.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4852 r_free = 0.4852 target = 0.189697 restraints weight = 11764.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4885 r_free = 0.4885 target = 0.192497 restraints weight = 8393.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4910 r_free = 0.4910 target = 0.194494 restraints weight = 6487.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4922 r_free = 0.4922 target = 0.195619 restraints weight = 5305.294|
|-----------------------------------------------------------------------------|
r_work (final): 0.4903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4847
moved from start:          0.9056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9028  Z= 0.142
  Angle     :  0.708  10.003  12254  Z= 0.349
  Chirality :  0.046   0.196   1395
  Planarity :  0.007   0.099   1569
  Dihedral  :  5.219  34.605   1173
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.23 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 27.45 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.72 (0.24), residues: 1089
  helix: -0.05 (0.38), residues: 188
  sheet: -0.79 (0.30), residues: 296
  loop : -1.71 (0.24), residues: 605

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 651 
 TYR   0.011   0.001   TYR A 423 
 PHE   0.042   0.002   PHE B 291 
 TRP   0.030   0.002   TRP A 296 
 HIS   0.008   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 9027)
  covalent geometry    : angle       0.70848 (12254)
  hydrogen bonds       : bond        0.03591 (  265)
  hydrogen bonds       : angle       6.07355 (  705)
  Misc. bond           : bond        0.00107 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 106
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   12 GLU cc_start: 0.4034 (mp0) cc_final: 0.3686 (mp0)
REVERT: A   80 MET cc_start: 0.0283 (mtt) cc_final: -0.0354 (ttm)
REVERT: A  208 MET cc_start: 0.3749 (mpp) cc_final: 0.3224 (mpp)
REVERT: A  388 ASP cc_start: 0.3144 (OUTLIER) cc_final: 0.0979 (m-30)
REVERT: A  441 ARG cc_start: 0.4246 (tmm160) cc_final: 0.3652 (mmt180)
REVERT: B  441 ARG cc_start: 0.4052 (mtm180) cc_final: 0.1604 (mmm-85)
REVERT: B  475 PHE cc_start: 0.6276 (p90) cc_final: 0.5569 (p90)
  outliers start: 34
  outliers final: 21
  residues processed: 131
  average time/residue: 0.0764
  time to fit residues: 14.4733
Evaluate side-chains
  117 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  475 PHE
Chi-restraints excluded: chain A residue  498 TYR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  270 SER
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  587 VAL
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 65 optimal weight:    6.9990
   chunk 109 optimal weight:    7.9990
   chunk 36 optimal weight:   10.0000
   chunk 93 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0170
   chunk 35 optimal weight:    0.9980
   chunk 25 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:   10.0000
   overall best weight:    2.4024

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 215 GLN
A 444 HIS
** A 539 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 457 GLN
B 505 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4966 r_free = 0.4966 target = 0.198547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.173495 restraints weight = 19451.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4696 r_free = 0.4696 target = 0.176864 restraints weight = 12852.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.179458 restraints weight = 9475.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4749 r_free = 0.4749 target = 0.181033 restraints weight = 7570.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4768 r_free = 0.4768 target = 0.182499 restraints weight = 6424.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5356
moved from start:          1.0842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.103   9028  Z= 0.263
  Angle     :  0.886  11.390  12254  Z= 0.456
  Chirality :  0.053   0.233   1395
  Planarity :  0.008   0.110   1569
  Dihedral  :  6.148  34.331   1173
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 20.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.08 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  5.79 %
    Allowed  : 25.15 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -2.21 (0.24), residues: 1089
  helix: -0.83 (0.35), residues: 182
  sheet: -0.79 (0.29), residues: 309
  loop : -2.09 (0.24), residues: 598

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 441 
 TYR   0.020   0.002   TYR B 435 
 PHE   0.040   0.003   PHE B 291 
 TRP   0.045   0.003   TRP B 296 
 HIS   0.007   0.002   HIS A 202 

Details of bonding type rmsd
  covalent geometry    : bond        0.00603 ( 9027)
  covalent geometry    : angle       0.88598 (12254)
  hydrogen bonds       : bond        0.04855 (  265)
  hydrogen bonds       : angle       6.86847 (  705)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 121
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.0959 (mtt) cc_final: 0.0199 (ptp)
REVERT: A  388 ASP cc_start: 0.3215 (OUTLIER) cc_final: 0.1236 (m-30)
REVERT: A  605 VAL cc_start: 0.3625 (OUTLIER) cc_final: 0.3420 (t)
REVERT: A  626 GLN cc_start: 0.6994 (tm-30) cc_final: 0.6136 (mt0)
REVERT: B  361 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6961 (p90)
REVERT: B  441 ARG cc_start: 0.4321 (mtm180) cc_final: 0.1847 (mmm-85)
  outliers start: 58
  outliers final: 29
  residues processed: 166
  average time/residue: 0.0729
  time to fit residues: 17.6893
Evaluate side-chains
  138 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  208 MET
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  366 VAL
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  595 HIS
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  611 CYS
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue   92 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  246 ASN
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  361 HIS
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  612 LEU
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 4 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    7.9990
   chunk 80 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9980
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
B 202 HIS
B 286 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5017 r_free = 0.5017 target = 0.202773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.177803 restraints weight = 18814.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.181430 restraints weight = 12096.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4796 r_free = 0.4796 target = 0.184182 restraints weight = 8825.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4820 r_free = 0.4820 target = 0.186103 restraints weight = 6913.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.187145 restraints weight = 5740.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.4804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5227
moved from start:          1.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.082   9028  Z= 0.157
  Angle     :  0.738  11.229  12254  Z= 0.365
  Chirality :  0.047   0.196   1395
  Planarity :  0.007   0.068   1569
  Dihedral  :  5.480  32.772   1173
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.88 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 27.15 %
    Favored  : 69.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.98 (0.25), residues: 1089
  helix: -0.42 (0.37), residues: 188
  sheet: -0.79 (0.30), residues: 308
  loop : -1.93 (0.24), residues: 593

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 292 
 TYR   0.017   0.001   TYR A  97 
 PHE   0.040   0.002   PHE B 291 
 TRP   0.069   0.004   TRP A 658 
 HIS   0.008   0.002   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9027)
  covalent geometry    : angle       0.73792 (12254)
  hydrogen bonds       : bond        0.03949 (  265)
  hydrogen bonds       : angle       6.31887 (  705)
  Misc. bond           : bond        0.00084 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 106
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.0842 (mtt) cc_final: 0.0081 (ptp)
REVERT: A  239 MET cc_start: 0.7025 (tmm) cc_final: 0.6737 (tpp)
REVERT: A  388 ASP cc_start: 0.3017 (OUTLIER) cc_final: 0.1304 (m-30)
REVERT: A  626 GLN cc_start: 0.6908 (tm-30) cc_final: 0.6445 (mt0)
REVERT: B  194 PHE cc_start: 0.6593 (m-10) cc_final: 0.6186 (m-80)
REVERT: B  441 ARG cc_start: 0.3968 (mtm180) cc_final: 0.1868 (mmm-85)
REVERT: B  443 MET cc_start: 0.3709 (pmm) cc_final: 0.2963 (ptt)
  outliers start: 35
  outliers final: 25
  residues processed: 136
  average time/residue: 0.0699
  time to fit residues: 14.3074
Evaluate side-chains
  128 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 102
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 CYS
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain A residue  595 HIS
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   74 VAL
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 109 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 89 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 4 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    8.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4963 r_free = 0.4963 target = 0.197111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.172128 restraints weight = 19095.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4698 r_free = 0.4698 target = 0.175482 restraints weight = 12698.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.178049 restraints weight = 9439.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4753 r_free = 0.4753 target = 0.179741 restraints weight = 7541.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4767 r_free = 0.4767 target = 0.180859 restraints weight = 6391.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.4741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5374
moved from start:          1.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.091   9028  Z= 0.195
  Angle     :  0.784  10.326  12254  Z= 0.392
  Chirality :  0.050   0.395   1395
  Planarity :  0.007   0.072   1569
  Dihedral  :  5.676  33.503   1173
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 18.52
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  8.08 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 26.85 %
    Favored  : 69.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -2.05 (0.24), residues: 1089
  helix: -0.57 (0.36), residues: 182
  sheet: -0.83 (0.30), residues: 298
  loop : -1.93 (0.24), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 292 
 TYR   0.013   0.002   TYR A 498 
 PHE   0.039   0.002   PHE B 291 
 TRP   0.046   0.003   TRP A 658 
 HIS   0.008   0.002   HIS A 444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00463 ( 9027)
  covalent geometry    : angle       0.78441 (12254)
  hydrogen bonds       : bond        0.04300 (  265)
  hydrogen bonds       : angle       6.51046 (  705)
  Misc. bond           : bond        0.00017 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 113
  time to evaluate  : 0.207 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.0871 (mtt) cc_final: 0.0318 (ptp)
REVERT: A  139 TRP cc_start: 0.4974 (OUTLIER) cc_final: 0.4267 (t60)
REVERT: A  388 ASP cc_start: 0.2915 (OUTLIER) cc_final: 0.1396 (m-30)
REVERT: A  623 LEU cc_start: 0.5661 (tt) cc_final: 0.5446 (tt)
REVERT: A  626 GLN cc_start: 0.7047 (tm-30) cc_final: 0.6817 (mt0)
REVERT: B  307 GLU cc_start: 0.3735 (tp30) cc_final: 0.3316 (tp30)
REVERT: B  441 ARG cc_start: 0.4005 (mtm180) cc_final: 0.1741 (mmm-85)
REVERT: B  443 MET cc_start: 0.3741 (pmm) cc_final: 0.3076 (ptt)
  outliers start: 40
  outliers final: 27
  residues processed: 144
  average time/residue: 0.0766
  time to fit residues: 15.8097
Evaluate side-chains
  135 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 106
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain A residue  139 TRP
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  565 ILE
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  472 VAL
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9980
   chunk 14 optimal weight:    0.2980
   chunk 47 optimal weight:    6.9990
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 457 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.5012 r_free = 0.5012 target = 0.202609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.177608 restraints weight = 18942.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4758 r_free = 0.4758 target = 0.181276 restraints weight = 12140.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4793 r_free = 0.4793 target = 0.184043 restraints weight = 8830.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4812 r_free = 0.4812 target = 0.185554 restraints weight = 6900.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4832 r_free = 0.4832 target = 0.187133 restraints weight = 5838.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.4806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5265
moved from start:          1.2060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   9028  Z= 0.142
  Angle     :  0.737  10.925  12254  Z= 0.362
  Chirality :  0.047   0.259   1395
  Planarity :  0.006   0.064   1569
  Dihedral  :  5.349  32.713   1173
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 15.11
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.23 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 27.74 %
    Favored  : 69.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.85 (0.25), residues: 1089
  helix: -0.21 (0.38), residues: 183
  sheet: -0.74 (0.29), residues: 306
  loop : -1.86 (0.25), residues: 600

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 292 
 TYR   0.013   0.001   TYR A  97 
 PHE   0.038   0.002   PHE B 291 
 TRP   0.043   0.003   TRP A 658 
 HIS   0.009   0.001   HIS A 444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00331 ( 9027)
  covalent geometry    : angle       0.73713 (12254)
  hydrogen bonds       : bond        0.03848 (  265)
  hydrogen bonds       : angle       6.13502 (  705)
  Misc. bond           : bond        0.00063 (    1)

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

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

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2178 Ramachandran restraints generated.
    1089 Oldfield, 0 Emsley, 1089 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 114
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 MET cc_start: 0.1083 (mtt) cc_final: 0.0238 (ptp)
REVERT: A  352 MET cc_start: 0.7246 (ppp) cc_final: 0.6677 (mmt)
REVERT: A  388 ASP cc_start: 0.3005 (OUTLIER) cc_final: 0.1508 (m-30)
REVERT: A  623 LEU cc_start: 0.5591 (OUTLIER) cc_final: 0.5355 (tt)
REVERT: B  307 GLU cc_start: 0.3548 (tp30) cc_final: 0.3232 (tp30)
REVERT: B  441 ARG cc_start: 0.3749 (mtm180) cc_final: 0.1950 (mmm-85)
REVERT: B  443 MET cc_start: 0.3456 (pmm) cc_final: 0.2691 (ptt)
REVERT: B  592 LEU cc_start: 0.6857 (mm) cc_final: 0.6168 (mt)
  outliers start: 30
  outliers final: 25
  residues processed: 138
  average time/residue: 0.0730
  time to fit residues: 14.8898
Evaluate side-chains
  132 residues out of total 1005 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue   79 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain A residue  388 ASP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  451 LEU
Chi-restraints excluded: chain A residue  506 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  623 LEU
Chi-restraints excluded: chain B residue   38 THR
Chi-restraints excluded: chain B residue   80 MET
Chi-restraints excluded: chain B residue  111 THR
Chi-restraints excluded: chain B residue  139 TRP
Chi-restraints excluded: chain B residue  180 MET
Chi-restraints excluded: chain B residue  200 VAL
Chi-restraints excluded: chain B residue  251 VAL
Chi-restraints excluded: chain B residue  284 VAL
Chi-restraints excluded: chain B residue  291 PHE
Chi-restraints excluded: chain B residue  299 THR
Chi-restraints excluded: chain B residue  456 VAL
Chi-restraints excluded: chain B residue  504 GLN
Chi-restraints excluded: chain B residue  595 HIS
Chi-restraints excluded: chain B residue  596 LEU
Chi-restraints excluded: chain B residue  623 LEU
Chi-restraints excluded: chain B residue  647 THR
Chi-restraints excluded: chain B residue  662 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 84 optimal weight:    6.9990
   chunk 65 optimal weight:    3.9990
   chunk 94 optimal weight:    0.0050
   chunk 30 optimal weight:    2.9990
   chunk 78 optimal weight:    0.8980
   chunk 40 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 5 optimal weight:    9.9990
   chunk 43 optimal weight:    4.9990
   chunk 4 optimal weight:   10.0000
   chunk 7 optimal weight:    0.7980
   overall best weight:    1.0996

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

Flipped N/Q/H residues before XYZ refinement:
A 215 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4988 r_free = 0.4988 target = 0.199415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4688 r_free = 0.4688 target = 0.174931 restraints weight = 18893.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4731 r_free = 0.4731 target = 0.178217 restraints weight = 12530.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4763 r_free = 0.4763 target = 0.180703 restraints weight = 9342.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4785 r_free = 0.4785 target = 0.182467 restraints weight = 7439.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4797 r_free = 0.4797 target = 0.183405 restraints weight = 6283.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.4771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5343
moved from start:          1.2399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   9028  Z= 0.155
  Angle     :  0.742  10.461  12254  Z= 0.367
  Chirality :  0.047   0.222   1395
  Planarity :  0.006   0.059   1569
  Dihedral  :  5.336  33.276   1173
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.53 %
    Favored  : 92.38 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 28.14 %
    Favored  : 68.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

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 are not related in a simple way.
  whole: -1.77 (0.25), residues: 1089
  helix: -0.00 (0.38), residues: 176
  sheet: -0.73 (0.30), residues: 304
  loop : -1.80 (0.25), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 292 
 TYR   0.016   0.001   TYR A 435 
 PHE   0.036   0.002   PHE B 291 
 TRP   0.036   0.003   TRP A 658 
 HIS   0.009   0.001   HIS A 444 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 9027)
  covalent geometry    : angle       0.74249 (12254)
  hydrogen bonds       : bond        0.03886 (  265)
  hydrogen bonds       : angle       6.14701 (  705)
  Misc. bond           : bond        0.00041 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1551.29 seconds
wall clock time: 27 minutes 28.61 seconds (1648.61 seconds total)