Starting phenix.real_space_refine
on Tue Jun 17 15:29:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tdd_25825/06_2025/7tdd_25825.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.016
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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     C    6690      2.51       5
     N    1549      2.21       5
     O    1721      1.98       5
     H   10025      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 20031
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10006
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 605, 10006
          Classifications: {'peptide': 605}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 586}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 10025
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 606, 10025
          Classifications: {'peptide': 606}
          Modifications used: {'NH1NOTPRO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 587}
          Chain breaks: 5
  Time building chain proxies: 10.90, per 1000 atoms: 0.54
  Number of scatterers: 20031
  At special positions: 0
  Unit cell: (125.25, 99.365, 105.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      46     16.00
     O    1721      8.00
     N    1549      7.00
     C    6690      6.00
     H   10025      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 101 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.98
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2322

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 0 sheets defined
      87.0% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 28
    Processing helix  chain 'A' and resid 29 through 43
    Processing helix  chain 'A' and resid 61 through 69
    Processing helix  chain 'A' and resid 70 through 84
    Processing helix  chain 'A' and resid 90 through 95
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 138 through 143
    Processing helix  chain 'A' and resid 143 through 150
    Processing helix  chain 'A' and resid 150 through 173
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 3.722A  pdb=" N   VAL A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 238
      removed outlier: 4.955A  pdb=" N   GLY A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ASN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.688A  pdb=" N   THR A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 270
      No H-bonds generated for 'chain 'A' and resid 268 through 270'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.070A  pdb=" N   PHE A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 333
      removed outlier: 3.782A  pdb=" N   GLY A 318 " --> pdb=" O   LYS A 314 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   MET A 319 " --> pdb=" O   GLN A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 345 through 355
    Processing helix  chain 'A' and resid 386 through 399
    Processing helix  chain 'A' and resid 411 through 416
      removed outlier: 3.528A  pdb=" N   HIS A 416 " --> pdb=" O   PRO A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 428
      removed outlier: 3.823A  pdb=" N   GLN A 421 " --> pdb=" O   SER A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 451
    Processing helix  chain 'A' and resid 462 through 493
      removed outlier: 3.960A  pdb=" N   VAL A 466 " --> pdb=" O   LYS A 462 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   PHE A 488 " --> pdb=" O   TYR A 484 " (cutoff:3.500A)
      removed outlier: 8.894A  pdb=" N   GLU A 489 " --> pdb=" O   THR A 485 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR A 491 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 515
    Processing helix  chain 'A' and resid 530 through 540
    Processing helix  chain 'A' and resid 541 through 547
      removed outlier: 4.233A  pdb=" N   LEU A 545 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 588
      removed outlier: 4.213A  pdb=" N   PHE A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      Proline residue:  A 563  - end of helix
      Proline residue:  A 567  - end of helix
    Processing helix  chain 'A' and resid 597 through 600
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 615 through 629
    Processing helix  chain 'A' and resid 632 through 644
      removed outlier: 3.833A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 661
      removed outlier: 4.183A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 661 " --> pdb=" O   VAL A 657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 690
    Processing helix  chain 'B' and resid 17 through 27
    Processing helix  chain 'B' and resid 29 through 43
    Processing helix  chain 'B' and resid 61 through 70
    Processing helix  chain 'B' and resid 70 through 88
      removed outlier: 4.614A  pdb=" N   ASN B  85 " --> pdb=" O   LEU B  81 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   PHE B  86 " --> pdb=" O   LEU B  82 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 90 through 96
      removed outlier: 3.620A  pdb=" N   ASN B  96 " --> pdb=" O   CYS B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 137
    Processing helix  chain 'B' and resid 137 through 143
      removed outlier: 4.544A  pdb=" N   TYR B 141 " --> pdb=" O   PHE B 137 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLY B 143 " --> pdb=" O   ILE B 139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 150
    Processing helix  chain 'B' and resid 150 through 173
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 3.931A  pdb=" N   VAL B 192 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 212
      removed outlier: 3.656A  pdb=" N   GLY B 211 " --> pdb=" O   VAL B 207 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   MET B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 238
      removed outlier: 4.008A  pdb=" N   ASN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 219 " --> pdb=" O   THR B 215 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 250 through 264
      removed outlier: 3.508A  pdb=" N   THR B 263 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 271 through 278
    Processing helix  chain 'B' and resid 280 through 295
      removed outlier: 4.313A  pdb=" N   PHE B 284 " --> pdb=" O   TRP B 280 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 333
    Processing helix  chain 'B' and resid 345 through 354
      removed outlier: 4.369A  pdb=" N   LEU B 350 " --> pdb=" O   GLN B 346 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLN B 353 " --> pdb=" O   LYS B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 398
      removed outlier: 3.612A  pdb=" N   LEU B 397 " --> pdb=" O   GLN B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 410
      removed outlier: 3.657A  pdb=" N   HIS B 410 " --> pdb=" O   LEU B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 417
    Processing helix  chain 'B' and resid 417 through 428
      removed outlier: 3.984A  pdb=" N   GLN B 421 " --> pdb=" O   SER B 417 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 455
    Processing helix  chain 'B' and resid 461 through 487
      removed outlier: 3.793A  pdb=" N   PHE B 469 " --> pdb=" O   GLN B 465 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   VAL B 470 " --> pdb=" O   VAL B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 488 through 493
    Processing helix  chain 'B' and resid 494 through 515
      removed outlier: 3.677A  pdb=" N   TRP B 505 " --> pdb=" O   PHE B 501 " (cutoff:3.500A)
      removed outlier: 4.334A  pdb=" N   VAL B 506 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 540
    Processing helix  chain 'B' and resid 542 through 547
      removed outlier: 3.754A  pdb=" N   MET B 546 " --> pdb=" O   ILE B 542 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 550 through 565
      removed outlier: 4.270A  pdb=" N   PHE B 554 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      Proline residue:  B 563  - end of helix
    Processing helix  chain 'B' and resid 565 through 588
    Processing helix  chain 'B' and resid 597 through 600
    Processing helix  chain 'B' and resid 601 through 606
    Processing helix  chain 'B' and resid 615 through 629
    Processing helix  chain 'B' and resid 632 through 644
      removed outlier: 3.801A  pdb=" N   MET B 636 " --> pdb=" O   TRP B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 645 through 647
      No H-bonds generated for 'chain 'B' and resid 645 through 647'
    Processing helix  chain 'B' and resid 648 through 660
      removed outlier: 4.097A  pdb=" N   PHE B 652 " --> pdb=" O   SER B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 690

    717 hydrogen bonds defined for protein.
    2124 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: 7.55

  Time building geometry restraints manager: 6.16 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 6804
        1.02 -     1.22: 3234
        1.22 -     1.42: 4881
        1.42 -     1.61: 5312
        1.61 -     1.81: 74
  Bond restraints: 20305
  Sorted by residual:
  bond pdb=" CB  THR B 264 "
       pdb=" OG1 THR B 264 "
    ideal  model  delta    sigma   weight residual
    1.433  1.269  0.164 1.60e-02 3.91e+03 1.05e+02
  bond pdb=" CA  ALA A 187 "
       pdb=" CB  ALA A 187 "
    ideal  model  delta    sigma   weight residual
    1.534  1.427  0.107 1.18e-02 7.18e+03 8.30e+01
  bond pdb=" CA  ALA B 187 "
       pdb=" CB  ALA B 187 "
    ideal  model  delta    sigma   weight residual
    1.534  1.427  0.107 1.18e-02 7.18e+03 8.27e+01
  bond pdb=" CZ  ARG B 191 "
       pdb=" NH2 ARG B 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.227  0.103 1.30e-02 5.92e+03 6.23e+01
  bond pdb=" CZ  ARG A 191 "
       pdb=" NH2 ARG A 191 "
    ideal  model  delta    sigma   weight residual
    1.330  1.228  0.102 1.30e-02 5.92e+03 6.21e+01
  ... (remaining 20300 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.37: 29979
        2.37 -     4.74: 4138
        4.74 -     7.10: 2017
        7.10 -     9.47: 414
        9.47 -    11.84: 42
  Bond angle restraints: 36590
  Sorted by residual:
  angle pdb=" N   ILE A 272 "
        pdb=" CA  ILE A 272 "
        pdb=" CB  ILE A 272 "
      ideal   model   delta    sigma   weight residual
     110.52  115.79   -5.27 6.70e-01 2.23e+00 6.19e+01
  angle pdb=" CA  PHE A  86 "
        pdb=" CB  PHE A  86 "
        pdb=" CG  PHE A  86 "
      ideal   model   delta    sigma   weight residual
     113.80  121.62   -7.82 1.00e+00 1.00e+00 6.11e+01
  angle pdb=" CA  ASN B 618 "
        pdb=" CB  ASN B 618 "
        pdb=" CG  ASN B 618 "
      ideal   model   delta    sigma   weight residual
     112.60  120.14   -7.54 1.00e+00 1.00e+00 5.69e+01
  angle pdb=" CA  ASN A  85 "
        pdb=" CB  ASN A  85 "
        pdb=" CG  ASN A  85 "
      ideal   model   delta    sigma   weight residual
     112.60  120.13   -7.53 1.00e+00 1.00e+00 5.67e+01
  angle pdb=" CA  ASP B 166 "
        pdb=" CB  ASP B 166 "
        pdb=" CG  ASP B 166 "
      ideal   model   delta    sigma   weight residual
     112.60  120.01   -7.41 1.00e+00 1.00e+00 5.50e+01
  ... (remaining 36585 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.77: 8826
       17.77 -    35.54: 444
       35.54 -    53.31: 133
       53.31 -    71.08: 160
       71.08 -    88.85: 9
  Dihedral angle restraints: 9572
    sinusoidal: 4945
      harmonic: 4627
  Sorted by residual:
  dihedral pdb=" C   MET A 629 "
           pdb=" N   MET A 629 "
           pdb=" CA  MET A 629 "
           pdb=" CB  MET A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.24   17.64     0      2.50e+00 1.60e-01 4.98e+01
  dihedral pdb=" N   MET A 629 "
           pdb=" C   MET A 629 "
           pdb=" CA  MET A 629 "
           pdb=" CB  MET A 629 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  138.06  -15.26     0      2.50e+00 1.60e-01 3.73e+01
  dihedral pdb=" CA  MET A 629 "
           pdb=" C   MET A 629 "
           pdb=" N   GLY A 630 "
           pdb=" CA  GLY A 630 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.07   27.93     0      5.00e+00 4.00e-02 3.12e+01
  ... (remaining 9569 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.148: 1160
       0.148 -    0.297: 28
       0.297 -    0.445: 33
       0.445 -    0.593: 218
       0.593 -    0.742: 147
  Chirality restraints: 1586
  Sorted by residual:
  chirality pdb=" CG  LEU B 623 "
            pdb=" CB  LEU B 623 "
            pdb=" CD1 LEU B 623 "
            pdb=" CD2 LEU B 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.38e+01
  chirality pdb=" CG  LEU A  84 "
            pdb=" CB  LEU A  84 "
            pdb=" CD1 LEU A  84 "
            pdb=" CD2 LEU A  84 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.37e+01
  chirality pdb=" CG  LEU A 623 "
            pdb=" CB  LEU A 623 "
            pdb=" CD1 LEU A 623 "
            pdb=" CD2 LEU A 623 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -1.85   -0.74 2.00e-01 2.50e+01 1.37e+01
  ... (remaining 1583 not shown)

  Planarity restraints: 2868
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  92 "   -0.183 2.00e-02 2.50e+03   6.12e-02 1.50e+02
        pdb=" CG  TRP A  92 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  92 "    0.049 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  92 "    0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  92 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  92 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  92 "    0.044 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  92 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  92 "    0.033 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  92 "   -0.009 2.00e-02 2.50e+03
        pdb=" HD1 TRP A  92 "    0.054 2.00e-02 2.50e+03
        pdb=" HE1 TRP A  92 "    0.031 2.00e-02 2.50e+03
        pdb=" HE3 TRP A  92 "    0.058 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A  92 "   -0.085 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A  92 "    0.033 2.00e-02 2.50e+03
        pdb=" HH2 TRP A  92 "   -0.051 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  92 "    0.153 2.00e-02 2.50e+03   5.03e-02 1.01e+02
        pdb=" CG  TRP B  92 "    0.008 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  92 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  92 "   -0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  92 "   -0.037 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  92 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  92 "   -0.039 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  92 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  92 "   -0.024 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  92 "    0.005 2.00e-02 2.50e+03
        pdb=" HD1 TRP B  92 "   -0.032 2.00e-02 2.50e+03
        pdb=" HE1 TRP B  92 "   -0.011 2.00e-02 2.50e+03
        pdb=" HE3 TRP B  92 "   -0.043 2.00e-02 2.50e+03
        pdb=" HZ2 TRP B  92 "    0.070 2.00e-02 2.50e+03
        pdb=" HZ3 TRP B  92 "   -0.018 2.00e-02 2.50e+03
        pdb=" HH2 TRP B  92 "    0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 185 "   -0.153 9.50e-02 1.11e+02   7.50e-02 7.08e+01
        pdb=" NE  ARG B 185 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 185 "   -0.037 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 185 "   -0.060 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 185 "   -0.014 2.00e-02 2.50e+03
        pdb="HH11 ARG B 185 "    0.122 2.00e-02 2.50e+03
        pdb="HH12 ARG B 185 "   -0.055 2.00e-02 2.50e+03
        pdb="HH21 ARG B 185 "    0.049 2.00e-02 2.50e+03
        pdb="HH22 ARG B 185 "    0.031 2.00e-02 2.50e+03
  ... (remaining 2865 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 704
        2.15 -     2.77: 37286
        2.77 -     3.38: 56753
        3.38 -     3.99: 70376
        3.99 -     4.60: 110325
  Nonbonded interactions: 275444
  Sorted by model distance:
  nonbonded pdb=" O   THR A 263 "
            pdb=" HG1 THR A 264 "
     model   vdw
     1.543 2.450
  nonbonded pdb=" O   VAL A 449 "
            pdb=" HG1 THR A 452 "
     model   vdw
     1.547 2.450
  nonbonded pdb=" O   GLU A 352 "
            pdb=" HG1 THR A 355 "
     model   vdw
     1.581 2.450
  nonbonded pdb=" O   SER B 278 "
            pdb=" HG  SER B 281 "
     model   vdw
     1.583 2.450
  nonbonded pdb=" HH  TYR A 305 "
            pdb=" OE2 GLU A 673 "
     model   vdw
     1.591 2.450
  ... (remaining 275439 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and (resid 16 through 454 or resid 459 through 690))
}

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:             5.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.340
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.130
  Set scattering table:                    0.180
  Process input model:                     44.720
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6454
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      :  0.029   0.164  10282  Z= 1.418
  Angle     :  2.072  11.838  13983  Z= 1.394
  Chirality :  0.294   0.742   1586
  Planarity :  0.010   0.104   1709
  Dihedral  : 12.649  88.847   3595
  Min Nonbonded Distance : 2.192

Molprobity Statistics.
  All-atom Clashscore : 1.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.52 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  3.23 %
    Favored  : 96.21 %
  Cbeta Deviations : 15.76 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.23), residues: 1187
  helix: -0.32 (0.15), residues: 926
  sheet:  None (None), residues: 0
  loop :  0.24 (0.42), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.109   0.011   TRP A  92 
 HIS   0.013   0.004   HIS A 134 
 PHE   0.080   0.008   PHE A 599 
 TYR   0.097   0.011   TYR A 106 
 ARG   0.016   0.002   ARG B 540 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11888 (  717)
  hydrogen bonds       : angle       5.84845 ( 2124)
  SS BOND              : bond        0.00456 (    2)
  SS BOND              : angle       0.80965 (    4)
  covalent geometry    : bond        0.02881 (10280)
  covalent geometry    : angle       2.07216 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 262
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.7049 (t0)
REVERT: A  260 ILE cc_start: 0.7258 (mt) cc_final: 0.7042 (mt)
REVERT: A  465 GLN cc_start: 0.7415 (mt0) cc_final: 0.6684 (mt0)
REVERT: A  468 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: A  490 ASN cc_start: 0.7660 (m-40) cc_final: 0.7251 (m110)
REVERT: A  563 PRO cc_start: 0.7130 (Cg_endo) cc_final: 0.6903 (Cg_exo)
REVERT: A  637 GLU cc_start: 0.7020 (mm-30) cc_final: 0.6810 (mm-30)
REVERT: B  322 MET cc_start: 0.7012 (tpp) cc_final: 0.6628 (tpp)
REVERT: B  438 PHE cc_start: 0.7489 (t80) cc_final: 0.7217 (t80)
REVERT: B  671 VAL cc_start: 0.7748 (t) cc_final: 0.7462 (p)
REVERT: B  679 LEU cc_start: 0.8030 (mt) cc_final: 0.7808 (mt)
  outliers start: 6
  outliers final: 2
  residues processed: 268
  average time/residue: 0.5236
  time to fit residues: 191.1214
Evaluate side-chains
  236 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 233
  time to evaluate  : 1.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  690 GLN
Chi-restraints excluded: chain B residue  160 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 90 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 94 optimal weight:    3.9990
   chunk 36 optimal weight:    2.9990
   chunk 57 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 108 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
A 665 ASN
A 690 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.187769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.153035 restraints weight = 45192.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.158926 restraints weight = 18813.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.162452 restraints weight = 10819.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6661
moved from start:          0.2490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  10282  Z= 0.220
  Angle     :  0.600   5.868  13983  Z= 0.331
  Chirality :  0.040   0.179   1586
  Planarity :  0.004   0.037   1709
  Dihedral  :  5.639  87.305   1323
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  0.76 %
    Favored  : 99.16 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  :  9.05 %
    Favored  : 89.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.24), residues: 1187
  helix:  1.15 (0.16), residues: 925
  sheet:  None (None), residues: 0
  loop :  0.66 (0.43), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 271 
 HIS   0.011   0.002   HIS B  27 
 PHE   0.023   0.002   PHE B 624 
 TYR   0.025   0.002   TYR B 294 
 ARG   0.005   0.001   ARG A 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04948 (  717)
  hydrogen bonds       : angle       4.97625 ( 2124)
  SS BOND              : bond        0.00139 (    2)
  SS BOND              : angle       1.38688 (    4)
  covalent geometry    : bond        0.00495 (10280)
  covalent geometry    : angle       0.60004 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 252
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.7560 (OUTLIER) cc_final: 0.7359 (t0)
REVERT: A  251 TYR cc_start: 0.7666 (t80) cc_final: 0.6712 (t80)
REVERT: A  451 THR cc_start: 0.7609 (t) cc_final: 0.7377 (m)
REVERT: A  465 GLN cc_start: 0.7301 (mt0) cc_final: 0.6714 (mt0)
REVERT: A  490 ASN cc_start: 0.7627 (m-40) cc_final: 0.7391 (m-40)
REVERT: B  136 PHE cc_start: 0.7701 (m-10) cc_final: 0.7498 (m-80)
REVERT: B  212 MET cc_start: 0.6957 (ptm) cc_final: 0.6650 (ptp)
REVERT: B  294 TYR cc_start: 0.7116 (m-80) cc_final: 0.6868 (m-80)
REVERT: B  438 PHE cc_start: 0.7533 (t80) cc_final: 0.7250 (t80)
REVERT: B  621 VAL cc_start: 0.7048 (t) cc_final: 0.6628 (m)
REVERT: B  648 SER cc_start: 0.8215 (p) cc_final: 0.7994 (t)
REVERT: B  649 ILE cc_start: 0.8308 (mt) cc_final: 0.8086 (mm)
REVERT: B  656 TYR cc_start: 0.7695 (t80) cc_final: 0.7373 (t80)
  outliers start: 14
  outliers final: 10
  residues processed: 260
  average time/residue: 0.5163
  time to fit residues: 184.7447
Evaluate side-chains
  255 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 244
  time to evaluate  : 1.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 ASN
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  601 THR
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  679 LEU
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  300 ILE
Chi-restraints excluded: chain B residue  677 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    0.5980
   chunk 22 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 24 optimal weight:    0.0870
   chunk 50 optimal weight:    0.4980
   chunk 75 optimal weight:    0.0870
   chunk 31 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 81 optimal weight:    0.3980
   chunk 41 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
B 153 ASN
B 353 GLN
B 625 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.187567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.151792 restraints weight = 44433.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.157704 restraints weight = 18372.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.161228 restraints weight = 10661.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6683
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10282  Z= 0.133
  Angle     :  0.519   6.385  13983  Z= 0.282
  Chirality :  0.036   0.180   1586
  Planarity :  0.004   0.049   1709
  Dihedral  :  4.467  26.883   1319
  Min Nonbonded Distance : 2.295

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  0.84 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 10.16 %
    Favored  : 88.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.24), residues: 1187
  helix:  1.63 (0.16), residues: 931
  sheet:  None (None), residues: 0
  loop :  0.81 (0.45), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 223 
 HIS   0.007   0.001   HIS B  27 
 PHE   0.028   0.001   PHE B  31 
 TYR   0.016   0.001   TYR B 256 
 ARG   0.003   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04412 (  717)
  hydrogen bonds       : angle       4.59996 ( 2124)
  SS BOND              : bond        0.00235 (    2)
  SS BOND              : angle       0.36763 (    4)
  covalent geometry    : bond        0.00279 (10280)
  covalent geometry    : angle       0.51932 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 237
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   85 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7329 (t0)
REVERT: A  308 PHE cc_start: 0.7746 (t80) cc_final: 0.7507 (t80)
REVERT: A  465 GLN cc_start: 0.7233 (mt0) cc_final: 0.6949 (mt0)
REVERT: A  490 ASN cc_start: 0.7666 (m-40) cc_final: 0.7446 (m-40)
REVERT: A  597 LYS cc_start: 0.8096 (mttt) cc_final: 0.7790 (tttt)
REVERT: A  606 ASP cc_start: 0.7168 (m-30) cc_final: 0.6883 (m-30)
REVERT: A  637 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7027 (tp30)
REVERT: B  166 ASP cc_start: 0.6892 (t0) cc_final: 0.6659 (m-30)
REVERT: B  189 TYR cc_start: 0.8376 (m-80) cc_final: 0.7469 (m-80)
REVERT: B  212 MET cc_start: 0.6942 (ptm) cc_final: 0.6649 (ptp)
REVERT: B  264 THR cc_start: 0.7998 (p) cc_final: 0.6886 (m)
REVERT: B  319 MET cc_start: 0.5756 (tmm) cc_final: 0.5496 (tmm)
REVERT: B  326 MET cc_start: 0.6385 (ttm) cc_final: 0.6023 (ttm)
REVERT: B  438 PHE cc_start: 0.7550 (t80) cc_final: 0.7278 (t80)
REVERT: B  607 ASP cc_start: 0.7794 (t0) cc_final: 0.7449 (t0)
REVERT: B  621 VAL cc_start: 0.6889 (t) cc_final: 0.6522 (m)
REVERT: B  648 SER cc_start: 0.8187 (p) cc_final: 0.7980 (t)
  outliers start: 14
  outliers final: 8
  residues processed: 243
  average time/residue: 0.5731
  time to fit residues: 190.7904
Evaluate side-chains
  240 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 231
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  566 MET
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  298 ASN
Chi-restraints excluded: chain B residue  677 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 77 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 99 optimal weight:    0.7980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.181389 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.145942 restraints weight = 44722.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.151806 restraints weight = 17940.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.155158 restraints weight = 10305.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.064  10282  Z= 0.275
  Angle     :  0.593   6.147  13983  Z= 0.328
  Chirality :  0.040   0.174   1586
  Planarity :  0.004   0.052   1709
  Dihedral  :  4.692  29.786   1319
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 10.90 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (0.24), residues: 1187
  helix:  1.35 (0.16), residues: 944
  sheet:  None (None), residues: 0
  loop :  0.39 (0.44), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 223 
 HIS   0.006   0.002   HIS B  27 
 PHE   0.029   0.002   PHE A 675 
 TYR   0.027   0.002   TYR B 294 
 ARG   0.005   0.001   ARG A 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05050 (  717)
  hydrogen bonds       : angle       4.79820 ( 2124)
  SS BOND              : bond        0.00436 (    2)
  SS BOND              : angle       0.99165 (    4)
  covalent geometry    : bond        0.00615 (10280)
  covalent geometry    : angle       0.59256 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 239
  time to evaluate  : 1.585 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  269 ASP cc_start: 0.7307 (m-30) cc_final: 0.7103 (m-30)
REVERT: A  465 GLN cc_start: 0.7305 (mt0) cc_final: 0.6988 (mt0)
REVERT: A  490 ASN cc_start: 0.7823 (m-40) cc_final: 0.7561 (m-40)
REVERT: A  500 ASP cc_start: 0.7649 (m-30) cc_final: 0.7223 (m-30)
REVERT: A  597 LYS cc_start: 0.8142 (mttt) cc_final: 0.7734 (tttt)
REVERT: A  606 ASP cc_start: 0.7347 (m-30) cc_final: 0.7062 (m-30)
REVERT: B  126 ILE cc_start: 0.8104 (mm) cc_final: 0.7806 (mt)
REVERT: B  166 ASP cc_start: 0.7021 (t0) cc_final: 0.6735 (m-30)
REVERT: B  212 MET cc_start: 0.7323 (ptm) cc_final: 0.7101 (ptp)
REVERT: B  294 TYR cc_start: 0.7378 (m-80) cc_final: 0.7094 (m-80)
REVERT: B  319 MET cc_start: 0.5921 (tmm) cc_final: 0.5656 (tmm)
REVERT: B  320 ASP cc_start: 0.6435 (m-30) cc_final: 0.5729 (m-30)
REVERT: B  438 PHE cc_start: 0.7630 (t80) cc_final: 0.7385 (t80)
REVERT: B  534 LEU cc_start: 0.7012 (OUTLIER) cc_final: 0.6788 (tt)
REVERT: B  547 ASN cc_start: 0.6844 (m-40) cc_final: 0.6616 (m-40)
REVERT: B  584 VAL cc_start: 0.8148 (p) cc_final: 0.7785 (t)
REVERT: B  607 ASP cc_start: 0.7842 (t0) cc_final: 0.7558 (t0)
REVERT: B  629 MET cc_start: 0.7670 (mmm) cc_final: 0.7284 (mmt)
REVERT: B  648 SER cc_start: 0.8190 (p) cc_final: 0.7922 (t)
REVERT: B  673 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7241 (mm-30)
  outliers start: 18
  outliers final: 10
  residues processed: 246
  average time/residue: 0.5346
  time to fit residues: 181.0559
Evaluate side-chains
  244 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 233
  time to evaluate  : 1.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  534 LEU
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 50 optimal weight:    0.1980
   chunk 102 optimal weight:    5.9990
   chunk 66 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 105 optimal weight:    4.9990
   chunk 117 optimal weight:    0.8980
   chunk 109 optimal weight:    0.2980
   chunk 112 optimal weight:    0.5980
   chunk 56 optimal weight:    0.9980
   chunk 85 optimal weight:    0.4980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
B 665 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.183095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.147886 restraints weight = 44486.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.153753 restraints weight = 17680.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.157240 restraints weight = 10063.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6768
moved from start:          0.4293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10282  Z= 0.141
  Angle     :  0.508   6.060  13983  Z= 0.276
  Chirality :  0.035   0.150   1586
  Planarity :  0.003   0.038   1709
  Dihedral  :  4.307  22.043   1317
  Min Nonbonded Distance : 2.338

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.52 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.91 %
    Favored  : 86.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.15 (0.24), residues: 1187
  helix:  1.72 (0.16), residues: 942
  sheet:  None (None), residues: 0
  loop :  0.49 (0.45), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.024   0.001   PHE B 624 
 TYR   0.014   0.001   TYR B 107 
 ARG   0.005   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04373 (  717)
  hydrogen bonds       : angle       4.49172 ( 2124)
  SS BOND              : bond        0.00381 (    2)
  SS BOND              : angle       0.45120 (    4)
  covalent geometry    : bond        0.00304 (10280)
  covalent geometry    : angle       0.50846 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 236
  time to evaluate  : 1.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  204 ASP cc_start: 0.6538 (m-30) cc_final: 0.6093 (m-30)
REVERT: A  269 ASP cc_start: 0.7251 (m-30) cc_final: 0.7047 (m-30)
REVERT: A  465 GLN cc_start: 0.7181 (mt0) cc_final: 0.6934 (mt0)
REVERT: A  490 ASN cc_start: 0.7760 (m-40) cc_final: 0.7484 (m-40)
REVERT: A  597 LYS cc_start: 0.8045 (mttt) cc_final: 0.7717 (tttt)
REVERT: A  606 ASP cc_start: 0.7377 (m-30) cc_final: 0.7096 (m-30)
REVERT: B  109 LEU cc_start: 0.8434 (mp) cc_final: 0.8127 (mm)
REVERT: B  126 ILE cc_start: 0.8103 (mm) cc_final: 0.7824 (mt)
REVERT: B  189 TYR cc_start: 0.8352 (m-80) cc_final: 0.7566 (m-80)
REVERT: B  294 TYR cc_start: 0.7340 (m-80) cc_final: 0.7052 (m-80)
REVERT: B  319 MET cc_start: 0.5898 (tmm) cc_final: 0.5638 (tmm)
REVERT: B  320 ASP cc_start: 0.6480 (m-30) cc_final: 0.5771 (m-30)
REVERT: B  438 PHE cc_start: 0.7592 (t80) cc_final: 0.7339 (t80)
REVERT: B  547 ASN cc_start: 0.7118 (m-40) cc_final: 0.6824 (m-40)
REVERT: B  584 VAL cc_start: 0.8018 (p) cc_final: 0.7671 (t)
REVERT: B  607 ASP cc_start: 0.7823 (t0) cc_final: 0.7550 (t0)
REVERT: B  629 MET cc_start: 0.7474 (mmm) cc_final: 0.7188 (mmt)
REVERT: B  648 SER cc_start: 0.8215 (p) cc_final: 0.7903 (t)
  outliers start: 15
  outliers final: 12
  residues processed: 241
  average time/residue: 0.5490
  time to fit residues: 183.3638
Evaluate side-chains
  246 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 234
  time to evaluate  : 1.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  306 ASP
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  658 ILE
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 66 optimal weight:    0.1980
   chunk 72 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0980
   chunk 82 optimal weight:    0.9990
   chunk 29 optimal weight:    4.9990
   chunk 38 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.182938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.148156 restraints weight = 44385.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.153970 restraints weight = 17472.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.157369 restraints weight = 9894.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6771
moved from start:          0.4511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10282  Z= 0.150
  Angle     :  0.501   8.196  13983  Z= 0.270
  Chirality :  0.035   0.147   1586
  Planarity :  0.003   0.038   1709
  Dihedral  :  4.164  20.367   1317
  Min Nonbonded Distance : 2.333

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  1.85 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 12.00 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.24), residues: 1187
  helix:  1.88 (0.16), residues: 939
  sheet:  None (None), residues: 0
  loop :  0.53 (0.44), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.020   0.001   PHE B 624 
 TYR   0.014   0.001   TYR B 107 
 ARG   0.003   0.000   ARG A 200 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  717)
  hydrogen bonds       : angle       4.38964 ( 2124)
  SS BOND              : bond        0.00328 (    2)
  SS BOND              : angle       0.37593 (    4)
  covalent geometry    : bond        0.00323 (10280)
  covalent geometry    : angle       0.50102 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 232
  time to evaluate  : 2.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.7351 (t80) cc_final: 0.7099 (t80)
REVERT: A  240 ASP cc_start: 0.7011 (t0) cc_final: 0.6724 (t0)
REVERT: A  465 GLN cc_start: 0.7206 (mt0) cc_final: 0.6952 (mt0)
REVERT: A  490 ASN cc_start: 0.7789 (m-40) cc_final: 0.7507 (m-40)
REVERT: A  500 ASP cc_start: 0.7554 (m-30) cc_final: 0.7304 (m-30)
REVERT: A  597 LYS cc_start: 0.8032 (mttt) cc_final: 0.7707 (tttt)
REVERT: A  606 ASP cc_start: 0.7408 (m-30) cc_final: 0.7112 (m-30)
REVERT: A  637 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7078 (tp30)
REVERT: B  109 LEU cc_start: 0.8469 (mp) cc_final: 0.8206 (mm)
REVERT: B  189 TYR cc_start: 0.8342 (m-80) cc_final: 0.7520 (m-80)
REVERT: B  311 GLN cc_start: 0.7650 (mm-40) cc_final: 0.7441 (mm-40)
REVERT: B  319 MET cc_start: 0.5900 (tmm) cc_final: 0.5685 (tmm)
REVERT: B  320 ASP cc_start: 0.6505 (m-30) cc_final: 0.5792 (m-30)
REVERT: B  438 PHE cc_start: 0.7607 (t80) cc_final: 0.7363 (t80)
REVERT: B  547 ASN cc_start: 0.7149 (m-40) cc_final: 0.6845 (m-40)
REVERT: B  607 ASP cc_start: 0.7813 (t0) cc_final: 0.7555 (t0)
REVERT: B  648 SER cc_start: 0.8268 (p) cc_final: 0.7978 (t)
  outliers start: 11
  outliers final: 10
  residues processed: 236
  average time/residue: 0.6446
  time to fit residues: 212.0830
Evaluate side-chains
  238 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 228
  time to evaluate  : 2.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ILE
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  479 MET
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 54 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 66 optimal weight:    0.1980
   chunk 42 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
B 243 GLN
B 454 ASN
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.179714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144536 restraints weight = 43885.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.150243 restraints weight = 17354.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.153601 restraints weight = 9908.128|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6826
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10282  Z= 0.221
  Angle     :  0.545   7.359  13983  Z= 0.298
  Chirality :  0.037   0.156   1586
  Planarity :  0.004   0.051   1709
  Dihedral  :  4.289  22.714   1317
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.70 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 12.00 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.24), residues: 1187
  helix:  1.74 (0.16), residues: 935
  sheet:  None (None), residues: 0
  loop :  0.30 (0.42), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.021   0.001   PHE B 351 
 TYR   0.019   0.002   TYR B 123 
 ARG   0.008   0.001   ARG B 145 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04660 (  717)
  hydrogen bonds       : angle       4.54481 ( 2124)
  SS BOND              : bond        0.00402 (    2)
  SS BOND              : angle       0.73886 (    4)
  covalent geometry    : bond        0.00489 (10280)
  covalent geometry    : angle       0.54525 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 241
  time to evaluate  : 1.472 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.7372 (t80) cc_final: 0.7142 (t80)
REVERT: A  240 ASP cc_start: 0.7067 (t0) cc_final: 0.6815 (t0)
REVERT: A  269 ASP cc_start: 0.7419 (m-30) cc_final: 0.7081 (m-30)
REVERT: A  465 GLN cc_start: 0.7235 (mt0) cc_final: 0.7015 (mt0)
REVERT: A  490 ASN cc_start: 0.7893 (m-40) cc_final: 0.7570 (m-40)
REVERT: A  606 ASP cc_start: 0.7422 (m-30) cc_final: 0.7147 (m-30)
REVERT: A  637 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7089 (tp30)
REVERT: B  109 LEU cc_start: 0.8502 (mp) cc_final: 0.8220 (mm)
REVERT: B  126 ILE cc_start: 0.8088 (tp) cc_final: 0.7857 (tt)
REVERT: B  168 LEU cc_start: 0.7988 (tp) cc_final: 0.7768 (tp)
REVERT: B  189 TYR cc_start: 0.8338 (m-80) cc_final: 0.7505 (m-80)
REVERT: B  320 ASP cc_start: 0.6700 (m-30) cc_final: 0.6082 (m-30)
REVERT: B  547 ASN cc_start: 0.7200 (m-40) cc_final: 0.6945 (m-40)
REVERT: B  584 VAL cc_start: 0.8034 (p) cc_final: 0.7697 (t)
REVERT: B  607 ASP cc_start: 0.7794 (t0) cc_final: 0.7539 (t0)
REVERT: B  648 SER cc_start: 0.8247 (p) cc_final: 0.7896 (t)
  outliers start: 17
  outliers final: 13
  residues processed: 246
  average time/residue: 0.5802
  time to fit residues: 199.4892
Evaluate side-chains
  248 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 235
  time to evaluate  : 2.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  497 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  629 MET
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 72 optimal weight:    0.4980
   chunk 96 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 116 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 321 GLN
B 625 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.179809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.145055 restraints weight = 44252.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.150754 restraints weight = 17280.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.154132 restraints weight = 9801.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6823
moved from start:          0.5187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  10282  Z= 0.216
  Angle     :  0.533   7.008  13983  Z= 0.291
  Chirality :  0.037   0.144   1586
  Planarity :  0.004   0.057   1709
  Dihedral  :  4.239  21.430   1317
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 5.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.74 %
    Favored  : 85.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.24), residues: 1187
  helix:  1.75 (0.16), residues: 937
  sheet:  None (None), residues: 0
  loop :  0.15 (0.41), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.018   0.001   PHE B 624 
 TYR   0.025   0.002   TYR B  78 
 ARG   0.005   0.000   ARG B 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04575 (  717)
  hydrogen bonds       : angle       4.50154 ( 2124)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       0.58051 (    4)
  covalent geometry    : bond        0.00475 (10280)
  covalent geometry    : angle       0.53322 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 231
  time to evaluate  : 1.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 PHE cc_start: 0.7427 (t80) cc_final: 0.7186 (t80)
REVERT: A  240 ASP cc_start: 0.7071 (t0) cc_final: 0.6809 (t0)
REVERT: A  269 ASP cc_start: 0.7403 (m-30) cc_final: 0.7075 (m-30)
REVERT: A  465 GLN cc_start: 0.7229 (mt0) cc_final: 0.6968 (mt0)
REVERT: A  490 ASN cc_start: 0.7958 (m-40) cc_final: 0.7612 (m-40)
REVERT: A  500 ASP cc_start: 0.7643 (m-30) cc_final: 0.7390 (m-30)
REVERT: A  600 GLU cc_start: 0.7701 (pt0) cc_final: 0.7369 (pm20)
REVERT: A  606 ASP cc_start: 0.7452 (m-30) cc_final: 0.7175 (m-30)
REVERT: A  637 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7037 (tp30)
REVERT: B  126 ILE cc_start: 0.8102 (tp) cc_final: 0.7853 (tt)
REVERT: B  168 LEU cc_start: 0.7981 (tp) cc_final: 0.7751 (tp)
REVERT: B  189 TYR cc_start: 0.8322 (m-80) cc_final: 0.7579 (m-80)
REVERT: B  311 GLN cc_start: 0.7457 (mm-40) cc_final: 0.7242 (mm-40)
REVERT: B  320 ASP cc_start: 0.6711 (m-30) cc_final: 0.6309 (m-30)
REVERT: B  547 ASN cc_start: 0.7112 (m-40) cc_final: 0.6905 (m-40)
REVERT: B  584 VAL cc_start: 0.8025 (p) cc_final: 0.7694 (t)
REVERT: B  607 ASP cc_start: 0.7790 (t0) cc_final: 0.7528 (t0)
REVERT: B  648 SER cc_start: 0.8256 (p) cc_final: 0.7894 (t)
  outliers start: 16
  outliers final: 13
  residues processed: 233
  average time/residue: 0.7455
  time to fit residues: 247.8821
Evaluate side-chains
  240 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 227
  time to evaluate  : 3.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  497 ASN
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 84 optimal weight:    0.5980
   chunk 3 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 33 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0070
   chunk 80 optimal weight:    0.2980
   chunk 44 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 112 optimal weight:    0.9980
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.180340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.145961 restraints weight = 43955.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.151654 restraints weight = 17109.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.155033 restraints weight = 9685.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6808
moved from start:          0.5300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10282  Z= 0.165
  Angle     :  0.517   8.353  13983  Z= 0.278
  Chirality :  0.035   0.132   1586
  Planarity :  0.004   0.052   1709
  Dihedral  :  4.163  22.154   1317
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.19 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.30 %
    Favored  : 85.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.24), residues: 1187
  helix:  1.88 (0.16), residues: 938
  sheet:  None (None), residues: 0
  loop :  0.25 (0.42), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 632 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.018   0.001   PHE B 624 
 TYR   0.023   0.001   TYR B  78 
 ARG   0.007   0.000   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04301 (  717)
  hydrogen bonds       : angle       4.39347 ( 2124)
  SS BOND              : bond        0.00332 (    2)
  SS BOND              : angle       0.44562 (    4)
  covalent geometry    : bond        0.00362 (10280)
  covalent geometry    : angle       0.51673 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 231
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4350 (m-80) cc_final: 0.4111 (m-80)
REVERT: A  229 PHE cc_start: 0.7418 (t80) cc_final: 0.7197 (t80)
REVERT: A  240 ASP cc_start: 0.7134 (t0) cc_final: 0.6848 (t0)
REVERT: A  326 MET cc_start: 0.7515 (ttm) cc_final: 0.7304 (ttm)
REVERT: A  465 GLN cc_start: 0.7197 (mt0) cc_final: 0.6916 (mt0)
REVERT: A  490 ASN cc_start: 0.7981 (m-40) cc_final: 0.7674 (m-40)
REVERT: A  600 GLU cc_start: 0.7728 (pt0) cc_final: 0.7404 (pm20)
REVERT: A  606 ASP cc_start: 0.7447 (m-30) cc_final: 0.7163 (m-30)
REVERT: B  109 LEU cc_start: 0.8449 (mp) cc_final: 0.8238 (mm)
REVERT: B  126 ILE cc_start: 0.8115 (tp) cc_final: 0.7883 (tt)
REVERT: B  168 LEU cc_start: 0.7947 (tp) cc_final: 0.7712 (tp)
REVERT: B  189 TYR cc_start: 0.8299 (m-80) cc_final: 0.7555 (m-80)
REVERT: B  320 ASP cc_start: 0.6585 (m-30) cc_final: 0.6245 (m-30)
REVERT: B  547 ASN cc_start: 0.7130 (m-40) cc_final: 0.6927 (m-40)
REVERT: B  607 ASP cc_start: 0.7777 (t0) cc_final: 0.7527 (t0)
REVERT: B  648 SER cc_start: 0.8249 (p) cc_final: 0.7891 (t)
  outliers start: 13
  outliers final: 11
  residues processed: 234
  average time/residue: 0.6567
  time to fit residues: 219.7754
Evaluate side-chains
  240 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 229
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  535 LEU
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  479 MET
Chi-restraints excluded: chain B residue  664 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 118 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 70 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 105 optimal weight:    5.9990
   chunk 93 optimal weight:    0.0770
   chunk 119 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.180069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.145494 restraints weight = 44022.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.151178 restraints weight = 17151.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.154557 restraints weight = 9731.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
moved from start:          0.5427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10282  Z= 0.166
  Angle     :  0.522   7.201  13983  Z= 0.280
  Chirality :  0.035   0.132   1586
  Planarity :  0.004   0.046   1709
  Dihedral  :  4.099  18.230   1317
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 13.57 %
    Favored  : 85.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.24), residues: 1187
  helix:  2.00 (0.16), residues: 934
  sheet:  None (None), residues: 0
  loop :  0.36 (0.42), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.018   0.001   PHE B 624 
 TYR   0.020   0.001   TYR B  78 
 ARG   0.005   0.000   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04252 (  717)
  hydrogen bonds       : angle       4.39535 ( 2124)
  SS BOND              : bond        0.00347 (    2)
  SS BOND              : angle       0.43863 (    4)
  covalent geometry    : bond        0.00365 (10280)
  covalent geometry    : angle       0.52166 (13979)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 229
  time to evaluate  : 2.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 TYR cc_start: 0.4367 (m-80) cc_final: 0.4131 (m-80)
REVERT: A  240 ASP cc_start: 0.7135 (t0) cc_final: 0.6876 (t0)
REVERT: A  326 MET cc_start: 0.7484 (ttm) cc_final: 0.7275 (ttm)
REVERT: A  465 GLN cc_start: 0.7190 (mt0) cc_final: 0.6943 (mt0)
REVERT: A  490 ASN cc_start: 0.8091 (m-40) cc_final: 0.7615 (m-40)
REVERT: A  606 ASP cc_start: 0.7439 (m-30) cc_final: 0.7165 (m-30)
REVERT: A  637 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7039 (tp30)
REVERT: B  126 ILE cc_start: 0.8117 (tp) cc_final: 0.7887 (tt)
REVERT: B  168 LEU cc_start: 0.7892 (tp) cc_final: 0.7659 (tp)
REVERT: B  189 TYR cc_start: 0.8302 (m-80) cc_final: 0.7564 (m-80)
REVERT: B  320 ASP cc_start: 0.6646 (m-30) cc_final: 0.6304 (m-30)
REVERT: B  607 ASP cc_start: 0.7756 (t0) cc_final: 0.7507 (t0)
REVERT: B  648 SER cc_start: 0.8256 (p) cc_final: 0.7899 (t)
  outliers start: 14
  outliers final: 11
  residues processed: 233
  average time/residue: 0.8079
  time to fit residues: 277.7810
Evaluate side-chains
  237 residues out of total 1083 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 226
  time to evaluate  : 2.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  468 GLU
Chi-restraints excluded: chain A residue  631 ASN
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain B residue  184 PHE
Chi-restraints excluded: chain B residue  186 ILE
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  310 GLU
Chi-restraints excluded: chain B residue  479 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 83 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 108 optimal weight:    0.5980
   chunk 73 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
B 665 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.179676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.144923 restraints weight = 44093.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.150600 restraints weight = 17209.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.154018 restraints weight = 9779.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.5585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  10282  Z= 0.219
  Angle     :  0.550   8.669  13983  Z= 0.298
  Chirality :  0.037   0.161   1586
  Planarity :  0.004   0.053   1709
  Dihedral  :  4.172  17.949   1317
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.22 %
    Favored  : 84.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 11.11 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1187
  helix:  1.90 (0.16), residues: 928
  sheet:  None (None), residues: 0
  loop :  0.29 (0.41), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 148 
 HIS   0.005   0.001   HIS B  27 
 PHE   0.017   0.001   PHE B 624 
 TYR   0.017   0.002   TYR B 123 
 ARG   0.007   0.000   ARG B 324 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04488 (  717)
  hydrogen bonds       : angle       4.49414 ( 2124)
  SS BOND              : bond        0.00414 (    2)
  SS BOND              : angle       0.57876 (    4)
  covalent geometry    : bond        0.00486 (10280)
  covalent geometry    : angle       0.55004 (13979)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9060.85 seconds
wall clock time: 164 minutes 36.79 seconds (9876.79 seconds total)