Starting phenix.real_space_refine
on Tue Mar  3 14:32:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7nqk_12528/03_2026/7nqk_12528.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7nqk_12528/03_2026/7nqk_12528.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/7nqk_12528/03_2026/7nqk_12528.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2026/7nqk_12528.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2026/7nqk_12528.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7nqk_12528/03_2026/7nqk_12528.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      37      5.16       5
     C    3998      2.51       5
     N    1014      2.21       5
     O    1090      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6139
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5173
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 658, 5173
          Classifications: {'peptide': 658}
          Link IDs: {'PTRANS': 24, 'TRANS': 633}
    Chain: "B"
      Number of atoms: 966
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 966
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
  Time building chain proxies: 1.37, per 1000 atoms: 0.22
  Number of scatterers: 6139
  At special positions: 0
  Unit cell: (103.168, 113.984, 93.184, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      37     16.00
     O    1090      8.00
     N    1014      7.00
     C    3998      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 211 " - pdb=" SG  CYS A 216 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " 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: 0.46
  Conformation dependent library (CDL) restraints added in 295.1 milliseconds
  

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1456

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 9 sheets defined
      46.1% alpha, 16.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 43 through 45
      No H-bonds generated for 'chain 'A' and resid 43 through 45'
    Processing helix  chain 'A' and resid 46 through 74
      removed outlier: 3.625A  pdb=" N   VAL A  51 " --> pdb=" O   ALA A  47 " (cutoff:3.500A)
      removed outlier: 5.395A  pdb=" N   ASN A  52 " --> pdb=" O   PHE A  48 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   SER A  59 " --> pdb=" O   CYS A  55 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   VAL A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A  67 " --> pdb=" O   MET A  63 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   THR A  68 " --> pdb=" O   LYS A  64 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU A  69 " --> pdb=" O   ALA A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 96
    Processing helix  chain 'A' and resid 96 through 106
      removed outlier: 4.042A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 130
      removed outlier: 3.572A  pdb=" N   TYR A 116 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
      removed outlier: 4.146A  pdb=" N   VAL A 120 " --> pdb=" O   TYR A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 171
      removed outlier: 3.533A  pdb=" N   SER A 146 " --> pdb=" O   HIS A 142 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   GLY A 159 " --> pdb=" O   LEU A 155 " (cutoff:3.500A)
      Proline residue:  A 162  - end of helix
      removed outlier: 3.757A  pdb=" N   ALA A 165 " --> pdb=" O   LYS A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 202
      removed outlier: 4.032A  pdb=" N   ARG A 182 " --> pdb=" O   GLU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 205
      No H-bonds generated for 'chain 'A' and resid 203 through 205'
    Processing helix  chain 'A' and resid 217 through 237
      Proline residue:  A 224  - end of helix
      removed outlier: 3.548A  pdb=" N   VAL A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 234 " --> pdb=" O   LEU A 230 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ALA A 236 " --> pdb=" O   LEU A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 238 through 241
    Processing helix  chain 'A' and resid 250 through 263
    Processing helix  chain 'A' and resid 289 through 306
      removed outlier: 3.635A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   ASP A 295 " --> pdb=" O   HIS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 318
      removed outlier: 3.763A  pdb=" N   PHE A 312 " --> pdb=" O   PRO A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 328
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 346 through 362
      removed outlier: 3.608A  pdb=" N   PHE A 350 " --> pdb=" O   VAL A 346 " (cutoff:3.500A)
      Proline residue:  A 357  - end of helix
    Processing helix  chain 'A' and resid 362 through 368
    Processing helix  chain 'A' and resid 377 through 402
    Processing helix  chain 'A' and resid 611 through 636
      removed outlier: 3.612A  pdb=" N   VAL A 627 " --> pdb=" O   VAL A 623 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   THR A 628 " --> pdb=" O   MET A 624 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 642
      removed outlier: 4.132A  pdb=" N   LYS A 642 " --> pdb=" O   SER A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 665
      removed outlier: 4.141A  pdb=" N   GLN A 665 " --> pdb=" O   LEU A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 670 through 695
      removed outlier: 3.685A  pdb=" N   TYR A 695 " --> pdb=" O   VAL A 691 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 28 through 30
      No H-bonds generated for 'chain 'B' and resid 28 through 30'
    Processing helix  chain 'B' and resid 53 through 56
      removed outlier: 3.801A  pdb=" N   ARG B  56 " --> pdb=" O   TRP B  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 53 through 56'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 453 through 455
      removed outlier: 3.538A  pdb=" N   LEU A 416 " --> pdb=" O   SER A 453 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ILE A 414 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   PHE A 415 " --> pdb=" O   TYR A 487 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   LEU A 489 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLN A 417 " --> pdb=" O   LEU A 489 " (cutoff:3.500A)
      removed outlier: 8.033A  pdb=" N   ILE A 491 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 7.047A  pdb=" N   LEU A 419 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 8.814A  pdb=" N   GLN A 493 " --> pdb=" O   LEU A 419 " (cutoff:3.500A)
      removed outlier: 4.299A  pdb=" N   CYS A 486 " --> pdb=" O   ASP A 505 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 443
    Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 443
      removed outlier: 3.832A  pdb=" N   LEU A 464 " --> pdb=" O   HIS A 479 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   HIS A 479 " --> pdb=" O   LEU A 464 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.588A  pdb=" N   ASN A 521 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 545
      removed outlier: 3.588A  pdb=" N   ASN A 521 " --> pdb=" O   GLY A 544 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 554 through 556
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 562
    Processing sheet with id=AA8, first strand: chain 'B' and resid 20 through 23
    Processing sheet with id=AA9, first strand: chain 'B' and resid 58 through 60
      removed outlier: 5.360A  pdb=" N   PHE B  47 " --> pdb=" O   ARG B  38 " (cutoff:3.500A)
      removed outlier: 5.810A  pdb=" N   ARG B  38 " --> pdb=" O   PHE B  47 " (cutoff:3.500A)

    317 hydrogen bonds defined for protein.
    891 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: 0.84

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1908
        1.34 -     1.46: 1510
        1.46 -     1.58: 2816
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 6292
  Sorted by residual:
  bond pdb=" N   GLY B  10 "
       pdb=" CA  GLY B  10 "
    ideal  model  delta    sigma   weight residual
    1.443  1.485 -0.043 1.17e-02 7.31e+03 1.32e+01
  bond pdb=" CA  SER B   7 "
       pdb=" CB  SER B   7 "
    ideal  model  delta    sigma   weight residual
    1.535  1.485  0.049 1.58e-02 4.01e+03 9.80e+00
  bond pdb=" N   LEU B  11 "
       pdb=" CA  LEU B  11 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 1.32e-02 5.74e+03 8.91e+00
  bond pdb=" N   GLY B   9 "
       pdb=" CA  GLY B   9 "
    ideal  model  delta    sigma   weight residual
    1.449  1.486 -0.037 1.24e-02 6.50e+03 8.77e+00
  bond pdb=" N   GLU B   6 "
       pdb=" CA  GLU B   6 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.29e-02 6.01e+03 8.62e+00
  ... (remaining 6287 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 8328
        2.25 -     4.51: 183
        4.51 -     6.76: 27
        6.76 -     9.01: 4
        9.01 -    11.26: 3
  Bond angle restraints: 8545
  Sorted by residual:
  angle pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
        pdb=" N   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     114.48  120.99   -6.51 1.19e+00 7.06e-01 3.00e+01
  angle pdb=" CA  GLY B   9 "
        pdb=" C   GLY B   9 "
        pdb=" O   GLY B   9 "
      ideal   model   delta    sigma   weight residual
     121.87  116.39    5.48 1.02e+00 9.61e-01 2.88e+01
  angle pdb=" CA  THR B 124 "
        pdb=" C   THR B 124 "
        pdb=" O   THR B 124 "
      ideal   model   delta    sigma   weight residual
     121.60  115.98    5.62 1.21e+00 6.83e-01 2.15e+01
  angle pdb=" CA  CYS A 211 "
        pdb=" CB  CYS A 211 "
        pdb=" SG  CYS A 211 "
      ideal   model   delta    sigma   weight residual
     114.40  124.86  -10.46 2.30e+00 1.89e-01 2.07e+01
  angle pdb=" CA  VAL B   5 "
        pdb=" C   VAL B   5 "
        pdb=" O   VAL B   5 "
      ideal   model   delta    sigma   weight residual
     122.13  117.66    4.47 1.11e+00 8.12e-01 1.62e+01
  ... (remaining 8540 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.45: 3275
       17.45 -    34.90: 338
       34.90 -    52.35: 58
       52.35 -    69.80: 13
       69.80 -    87.24: 9
  Dihedral angle restraints: 3693
    sinusoidal: 1426
      harmonic: 2267
  Sorted by residual:
  dihedral pdb=" CA  LYS A 210 "
           pdb=" C   LYS A 210 "
           pdb=" N   CYS A 211 "
           pdb=" CA  CYS A 211 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -142.31  -37.69     0      5.00e+00 4.00e-02 5.68e+01
  dihedral pdb=" CA  VAL A 209 "
           pdb=" C   VAL A 209 "
           pdb=" N   LYS A 210 "
           pdb=" CA  LYS A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.85  -26.15     0      5.00e+00 4.00e-02 2.74e+01
  dihedral pdb=" CA  TRP A 283 "
           pdb=" C   TRP A 283 "
           pdb=" N   ALA A 284 "
           pdb=" CA  ALA A 284 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.02   24.98     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 3690 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 819
       0.063 -    0.126: 132
       0.126 -    0.188: 17
       0.188 -    0.251: 2
       0.251 -    0.314: 1
  Chirality restraints: 971
  Sorted by residual:
  chirality pdb=" CB  VAL B   5 "
            pdb=" CA  VAL B   5 "
            pdb=" CG1 VAL B   5 "
            pdb=" CG2 VAL B   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.32   -0.31 2.00e-01 2.50e+01 2.47e+00
  chirality pdb=" CB  VAL B 123 "
            pdb=" CA  VAL B 123 "
            pdb=" CG1 VAL B 123 "
            pdb=" CG2 VAL B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ASP B  90 "
            pdb=" N   ASP B  90 "
            pdb=" C   ASP B  90 "
            pdb=" CB  ASP B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.94e-01
  ... (remaining 968 not shown)

  Planarity restraints: 1067
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 280 "   -0.020 2.00e-02 2.50e+03   2.18e-02 1.19e+01
        pdb=" CG  TRP A 280 "    0.058 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 280 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 280 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 280 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 280 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 280 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 280 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 280 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 280 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 210 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.93e+00
        pdb=" C   LYS A 210 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LYS A 210 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   CYS A 211 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B  89 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.75e+00
        pdb=" C   ARG B  89 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG B  89 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP B  90 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1064 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 76
        2.61 -     3.18: 5686
        3.18 -     3.75: 9220
        3.75 -     4.33: 12704
        4.33 -     4.90: 20703
  Nonbonded interactions: 48389
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 423 "
            pdb=" OH  TYR A 470 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" NH1 ARG A 322 "
            pdb=" OE2 GLU A 674 "
     model   vdw
     2.122 3.120
  nonbonded pdb=" OG1 THR A 533 "
            pdb=" OD2 ASP B  73 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   SER A 321 "
            pdb=" OG1 THR A 324 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OH  TYR A 306 "
            pdb=" OG  SER A 633 "
     model   vdw
     2.207 3.040
  ... (remaining 48384 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             3.400
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6294  Z= 0.253
  Angle     :  0.842  11.263   8549  Z= 0.481
  Chirality :  0.049   0.314    971
  Planarity :  0.004   0.043   1067
  Dihedral  : 14.925  87.244   2231
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 16.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  0.75 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.31), residues: 777
  helix:  0.17 (0.29), residues: 332
  sheet: -1.51 (0.40), residues: 166
  loop : -2.63 (0.39), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  56 
 TYR   0.022   0.002   TYR A 121 
 PHE   0.019   0.002   PHE A 355 
 TRP   0.058   0.002   TRP A 280 
 HIS   0.006   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00498 ( 6292)
  covalent geometry    : angle       0.84128 ( 8545)
  SS BOND              : bond        0.01065 (    2)
  SS BOND              : angle       2.00353 (    4)
  hydrogen bonds       : bond        0.18199 (  304)
  hydrogen bonds       : angle       7.39106 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 159
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8070 (tp30) cc_final: 0.7626 (tp30)
REVERT: A  105 ASP cc_start: 0.8431 (m-30) cc_final: 0.8105 (m-30)
REVERT: A  147 LEU cc_start: 0.9140 (mm) cc_final: 0.8927 (mm)
REVERT: A  228 MET cc_start: 0.8136 (tmm) cc_final: 0.7803 (tmm)
REVERT: B   11 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7358 (tt)
  outliers start: 6
  outliers final: 2
  residues processed: 165
  average time/residue: 0.0673
  time to fit residues: 15.2882
Evaluate side-chains
  127 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0170
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.4824

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 GLN
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 521 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.103920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.091802 restraints weight = 14771.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.094264 restraints weight = 6383.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.095769 restraints weight = 3635.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.096779 restraints weight = 2445.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.097344 restraints weight = 1831.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3411
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6294  Z= 0.191
  Angle     :  0.707   8.534   8549  Z= 0.371
  Chirality :  0.045   0.183    971
  Planarity :  0.005   0.052   1067
  Dihedral  :  6.485  51.435    844
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.27 %
    Favored  : 90.73 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.08 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.31), residues: 777
  helix:  0.65 (0.29), residues: 332
  sheet: -1.57 (0.39), residues: 168
  loop : -2.52 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  56 
 TYR   0.015   0.001   TYR A 121 
 PHE   0.013   0.001   PHE A 111 
 TRP   0.020   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 ( 6292)
  covalent geometry    : angle       0.70621 ( 8545)
  SS BOND              : bond        0.00662 (    2)
  SS BOND              : angle       1.35264 (    4)
  hydrogen bonds       : bond        0.04187 (  304)
  hydrogen bonds       : angle       5.29076 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 141
  time to evaluate  : 0.226 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8371 (tp30) cc_final: 0.7784 (tp30)
REVERT: A  105 ASP cc_start: 0.8614 (m-30) cc_final: 0.8190 (m-30)
REVERT: A  147 LEU cc_start: 0.9178 (mm) cc_final: 0.8900 (mm)
REVERT: A  228 MET cc_start: 0.8186 (tmm) cc_final: 0.7841 (tmm)
REVERT: B   43 LYS cc_start: 0.8262 (tmtt) cc_final: 0.7990 (tmtt)
  outliers start: 19
  outliers final: 17
  residues processed: 152
  average time/residue: 0.0674
  time to fit residues: 14.1304
Evaluate side-chains
  151 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 134
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  151 SER
Chi-restraints excluded: chain A residue  160 ILE
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 34 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 49 optimal weight:    5.9990
   chunk 55 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 269 ASN
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.105548 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.093345 restraints weight = 14545.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.095820 restraints weight = 6389.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.097391 restraints weight = 3630.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.098404 restraints weight = 2419.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.099082 restraints weight = 1796.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6294  Z= 0.133
  Angle     :  0.644   8.835   8549  Z= 0.333
  Chirality :  0.043   0.163    971
  Planarity :  0.005   0.054   1067
  Dihedral  :  5.746  46.662    842
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.56 %
    Allowed  : 18.35 %
    Favored  : 79.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.32), residues: 777
  helix:  0.89 (0.29), residues: 333
  sheet: -1.44 (0.39), residues: 167
  loop : -2.34 (0.40), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  56 
 TYR   0.010   0.001   TYR A 121 
 PHE   0.011   0.001   PHE A 111 
 TRP   0.013   0.001   TRP A 280 
 HIS   0.003   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6292)
  covalent geometry    : angle       0.64345 ( 8545)
  SS BOND              : bond        0.00283 (    2)
  SS BOND              : angle       0.91661 (    4)
  hydrogen bonds       : bond        0.03732 (  304)
  hydrogen bonds       : angle       4.86876 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8353 (tp30) cc_final: 0.7642 (tp30)
REVERT: A  105 ASP cc_start: 0.8634 (m-30) cc_final: 0.8203 (m-30)
REVERT: A  147 LEU cc_start: 0.9158 (mm) cc_final: 0.8886 (mm)
REVERT: A  204 MET cc_start: 0.7809 (tpt) cc_final: 0.6879 (tmm)
REVERT: A  228 MET cc_start: 0.8248 (tmm) cc_final: 0.8046 (tmm)
REVERT: B   43 LYS cc_start: 0.8252 (tmtt) cc_final: 0.8033 (tmtt)
REVERT: B  109 ASN cc_start: 0.9067 (p0) cc_final: 0.8762 (p0)
  outliers start: 17
  outliers final: 17
  residues processed: 157
  average time/residue: 0.0651
  time to fit residues: 14.1016
Evaluate side-chains
  156 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  241 MET
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  660 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 74 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0670
   chunk 40 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   chunk 60 optimal weight:    0.0770
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0770
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.3234

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.108403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.096056 restraints weight = 14716.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.098576 restraints weight = 6407.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.100146 restraints weight = 3624.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.101180 restraints weight = 2408.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.101894 restraints weight = 1792.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6294  Z= 0.114
  Angle     :  0.613   9.449   8549  Z= 0.315
  Chirality :  0.042   0.159    971
  Planarity :  0.005   0.054   1067
  Dihedral  :  5.251  35.973    842
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 20.30 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.32), residues: 777
  helix:  1.13 (0.29), residues: 327
  sheet: -1.35 (0.40), residues: 174
  loop : -2.08 (0.40), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  56 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 350 
 TRP   0.012   0.001   TRP A 280 
 HIS   0.002   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 6292)
  covalent geometry    : angle       0.61253 ( 8545)
  SS BOND              : bond        0.00251 (    2)
  SS BOND              : angle       0.80595 (    4)
  hydrogen bonds       : bond        0.03289 (  304)
  hydrogen bonds       : angle       4.48061 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8279 (tp30) cc_final: 0.7618 (tp30)
REVERT: A  147 LEU cc_start: 0.9087 (mm) cc_final: 0.8844 (mm)
REVERT: A  228 MET cc_start: 0.8225 (tmm) cc_final: 0.7983 (tmm)
REVERT: A  350 PHE cc_start: 0.8294 (t80) cc_final: 0.8068 (t80)
REVERT: A  406 HIS cc_start: 0.5270 (OUTLIER) cc_final: 0.4676 (p90)
REVERT: A  622 GLU cc_start: 0.7977 (tp30) cc_final: 0.7692 (tp30)
REVERT: B  109 ASN cc_start: 0.8980 (p0) cc_final: 0.8637 (p0)
  outliers start: 19
  outliers final: 10
  residues processed: 162
  average time/residue: 0.0697
  time to fit residues: 15.2937
Evaluate side-chains
  150 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.223 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 26 optimal weight:    0.2980
   chunk 72 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 67 optimal weight:    5.9990
   chunk 69 optimal weight:    2.9990
   chunk 57 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 46 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
A 171 GLN
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.102971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.091217 restraints weight = 15107.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.094450 restraints weight = 6733.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.095959 restraints weight = 3242.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.096567 restraints weight = 1939.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.096952 restraints weight = 1605.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.2078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   6294  Z= 0.225
  Angle     :  0.690   9.979   8549  Z= 0.360
  Chirality :  0.045   0.184    971
  Planarity :  0.005   0.072   1067
  Dihedral  :  5.593  33.535    842
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.40 %
    Favored  : 90.60 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 19.70 %
    Favored  : 75.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.00 (0.32), residues: 777
  helix:  1.06 (0.29), residues: 327
  sheet: -1.54 (0.38), residues: 179
  loop : -2.13 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B  56 
 TYR   0.010   0.002   TYR B  95 
 PHE   0.010   0.001   PHE A 111 
 TRP   0.013   0.001   TRP A 280 
 HIS   0.006   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 6292)
  covalent geometry    : angle       0.69006 ( 8545)
  SS BOND              : bond        0.00310 (    2)
  SS BOND              : angle       0.58463 (    4)
  hydrogen bonds       : bond        0.03720 (  304)
  hydrogen bonds       : angle       4.59992 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 137
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8451 (tp30) cc_final: 0.7826 (tp30)
REVERT: A   57 ARG cc_start: 0.8789 (mmm160) cc_final: 0.8542 (tpp-160)
REVERT: A  147 LEU cc_start: 0.9179 (mm) cc_final: 0.8916 (mm)
REVERT: A  204 MET cc_start: 0.7783 (tpt) cc_final: 0.6779 (tmm)
REVERT: A  212 PHE cc_start: 0.6381 (m-80) cc_final: 0.6181 (m-10)
REVERT: A  406 HIS cc_start: 0.5383 (OUTLIER) cc_final: 0.4650 (p90)
REVERT: A  534 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7431 (p0)
REVERT: A  622 GLU cc_start: 0.8026 (tp30) cc_final: 0.7724 (tp30)
  outliers start: 30
  outliers final: 23
  residues processed: 156
  average time/residue: 0.0638
  time to fit residues: 13.8244
Evaluate side-chains
  155 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   98 ILE
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  126 VAL
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  356 ILE
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  663 VAL
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue   53 TRP
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  124 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 43 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0030
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 345 GLN
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.106398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.094766 restraints weight = 14562.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.097923 restraints weight = 6433.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.099508 restraints weight = 3139.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.100091 restraints weight = 1832.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.100713 restraints weight = 1521.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6294  Z= 0.126
  Angle     :  0.637  10.628   8549  Z= 0.326
  Chirality :  0.043   0.182    971
  Planarity :  0.005   0.050   1067
  Dihedral  :  5.300  24.187    842
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.46 %
    Favored  : 92.54 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 20.75 %
    Favored  : 75.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.32), residues: 777
  helix:  1.09 (0.29), residues: 327
  sheet: -1.41 (0.39), residues: 179
  loop : -2.11 (0.41), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  56 
 TYR   0.012   0.001   TYR A 183 
 PHE   0.011   0.001   PHE A 111 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6292)
  covalent geometry    : angle       0.63727 ( 8545)
  SS BOND              : bond        0.00231 (    2)
  SS BOND              : angle       0.70147 (    4)
  hydrogen bonds       : bond        0.03341 (  304)
  hydrogen bonds       : angle       4.48397 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 144
  time to evaluate  : 0.179 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8387 (tp30) cc_final: 0.7701 (tp30)
REVERT: A  130 LEU cc_start: 0.9117 (tp) cc_final: 0.8916 (tp)
REVERT: A  147 LEU cc_start: 0.9096 (mm) cc_final: 0.8851 (mm)
REVERT: A  212 PHE cc_start: 0.6334 (m-80) cc_final: 0.6118 (m-10)
REVERT: A  228 MET cc_start: 0.8089 (tmm) cc_final: 0.7712 (tmm)
REVERT: A  406 HIS cc_start: 0.5229 (OUTLIER) cc_final: 0.4632 (p90)
REVERT: A  534 ASP cc_start: 0.7660 (OUTLIER) cc_final: 0.7373 (p0)
REVERT: A  550 THR cc_start: 0.9308 (OUTLIER) cc_final: 0.8965 (t)
REVERT: A  622 GLU cc_start: 0.7988 (tp30) cc_final: 0.7659 (tp30)
  outliers start: 27
  outliers final: 16
  residues processed: 159
  average time/residue: 0.0651
  time to fit residues: 14.0871
Evaluate side-chains
  156 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  229 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 30 optimal weight:    0.5980
   chunk 71 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0870
   chunk 43 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 61 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.107000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.094863 restraints weight = 14703.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.097344 restraints weight = 6429.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.098934 restraints weight = 3673.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.099963 restraints weight = 2433.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.100688 restraints weight = 1800.641|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6294  Z= 0.125
  Angle     :  0.653  11.340   8549  Z= 0.329
  Chirality :  0.043   0.191    971
  Planarity :  0.004   0.046   1067
  Dihedral  :  5.191  22.006    841
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 22.26 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.85 (0.32), residues: 777
  helix:  1.15 (0.29), residues: 327
  sheet: -1.36 (0.39), residues: 178
  loop : -2.10 (0.40), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  56 
 TYR   0.011   0.001   TYR A 183 
 PHE   0.017   0.001   PHE A 350 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6292)
  covalent geometry    : angle       0.65287 ( 8545)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       0.74394 (    4)
  hydrogen bonds       : bond        0.03257 (  304)
  hydrogen bonds       : angle       4.43776 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 146
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8396 (tp30) cc_final: 0.7833 (tp30)
REVERT: A   57 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8531 (tpp-160)
REVERT: A  147 LEU cc_start: 0.9075 (mm) cc_final: 0.8822 (mm)
REVERT: A  204 MET cc_start: 0.7670 (tpt) cc_final: 0.6642 (tmm)
REVERT: A  228 MET cc_start: 0.8112 (tmm) cc_final: 0.7723 (tmm)
REVERT: A  350 PHE cc_start: 0.8384 (t80) cc_final: 0.8053 (t80)
REVERT: A  406 HIS cc_start: 0.5163 (OUTLIER) cc_final: 0.4587 (p90)
REVERT: A  534 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7409 (p0)
REVERT: A  550 THR cc_start: 0.9295 (OUTLIER) cc_final: 0.8989 (t)
REVERT: B   76 LYS cc_start: 0.8679 (ptmt) cc_final: 0.8403 (pttm)
  outliers start: 20
  outliers final: 11
  residues processed: 159
  average time/residue: 0.0640
  time to fit residues: 13.8762
Evaluate side-chains
  157 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 3 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 46 optimal weight:    6.9990
   chunk 49 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.106947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.094706 restraints weight = 14773.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.097229 restraints weight = 6505.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.098821 restraints weight = 3703.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.099856 restraints weight = 2456.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.100584 restraints weight = 1816.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6294  Z= 0.134
  Angle     :  0.659  12.094   8549  Z= 0.333
  Chirality :  0.044   0.193    971
  Planarity :  0.004   0.043   1067
  Dihedral  :  5.159  21.053    841
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.76 %
    Favored  : 73.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.84 (0.32), residues: 777
  helix:  1.20 (0.29), residues: 327
  sheet: -1.37 (0.39), residues: 179
  loop : -2.14 (0.40), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  56 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.014   0.001   PHE A 350 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6292)
  covalent geometry    : angle       0.65897 ( 8545)
  SS BOND              : bond        0.00258 (    2)
  SS BOND              : angle       0.72715 (    4)
  hydrogen bonds       : bond        0.03250 (  304)
  hydrogen bonds       : angle       4.39325 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8410 (tp30) cc_final: 0.7838 (tp30)
REVERT: A   57 ARG cc_start: 0.8758 (mmm160) cc_final: 0.8536 (tpp-160)
REVERT: A  147 LEU cc_start: 0.9084 (mm) cc_final: 0.8837 (mm)
REVERT: A  204 MET cc_start: 0.7651 (tpt) cc_final: 0.6704 (tmm)
REVERT: A  350 PHE cc_start: 0.8394 (t80) cc_final: 0.8017 (t80)
REVERT: A  365 ARG cc_start: 0.7681 (tpt90) cc_final: 0.6734 (mtp180)
REVERT: A  406 HIS cc_start: 0.5176 (OUTLIER) cc_final: 0.4587 (p90)
REVERT: A  534 ASP cc_start: 0.7628 (OUTLIER) cc_final: 0.7401 (p0)
REVERT: A  550 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8982 (t)
  outliers start: 18
  outliers final: 12
  residues processed: 154
  average time/residue: 0.0677
  time to fit residues: 14.0890
Evaluate side-chains
  153 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 138
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 32 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 69 optimal weight:    4.9990
   chunk 72 optimal weight:    0.0060
   chunk 57 optimal weight:    0.9990
   chunk 31 optimal weight:    0.3980
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.108035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.095768 restraints weight = 14786.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.098286 restraints weight = 6468.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.099899 restraints weight = 3683.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.100712 restraints weight = 2436.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.101549 restraints weight = 1889.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3483
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6294  Z= 0.123
  Angle     :  0.659  11.213   8549  Z= 0.330
  Chirality :  0.043   0.190    971
  Planarity :  0.004   0.041   1067
  Dihedral  :  5.064  20.365    841
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 23.31 %
    Favored  : 73.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.76 (0.32), residues: 777
  helix:  1.27 (0.29), residues: 327
  sheet: -1.28 (0.40), residues: 179
  loop : -2.15 (0.40), residues: 271

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  56 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.014   0.001   PHE A 350 
 TRP   0.007   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 6292)
  covalent geometry    : angle       0.65878 ( 8545)
  SS BOND              : bond        0.00232 (    2)
  SS BOND              : angle       0.82568 (    4)
  hydrogen bonds       : bond        0.03195 (  304)
  hydrogen bonds       : angle       4.34542 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 145
  time to evaluate  : 0.273 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8377 (tp30) cc_final: 0.7813 (tp30)
REVERT: A   57 ARG cc_start: 0.8744 (mmm160) cc_final: 0.8519 (tpp-160)
REVERT: A  147 LEU cc_start: 0.9052 (mm) cc_final: 0.8832 (mm)
REVERT: A  228 MET cc_start: 0.7954 (tmm) cc_final: 0.7535 (tmm)
REVERT: A  350 PHE cc_start: 0.8384 (t80) cc_final: 0.8000 (t80)
REVERT: A  365 ARG cc_start: 0.7640 (tpt90) cc_final: 0.6521 (ttt-90)
REVERT: A  406 HIS cc_start: 0.5030 (OUTLIER) cc_final: 0.4528 (p90)
REVERT: A  450 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8540 (t)
REVERT: A  550 THR cc_start: 0.9188 (OUTLIER) cc_final: 0.8949 (t)
  outliers start: 19
  outliers final: 13
  residues processed: 157
  average time/residue: 0.0641
  time to fit residues: 13.9075
Evaluate side-chains
  156 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  450 THR
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 125 HIS
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.107578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.095218 restraints weight = 14952.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.097753 restraints weight = 6582.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.099360 restraints weight = 3742.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100363 restraints weight = 2482.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.101104 restraints weight = 1855.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6294  Z= 0.133
  Angle     :  0.669  12.099   8549  Z= 0.335
  Chirality :  0.044   0.194    971
  Planarity :  0.004   0.040   1067
  Dihedral  :  5.042  20.134    841
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 23.31 %
    Favored  : 73.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.32), residues: 777
  helix:  1.23 (0.29), residues: 333
  sheet: -1.21 (0.40), residues: 179
  loop : -2.16 (0.40), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  56 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.014   0.001   PHE A 212 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.004   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6292)
  covalent geometry    : angle       0.66928 ( 8545)
  SS BOND              : bond        0.00227 (    2)
  SS BOND              : angle       0.86850 (    4)
  hydrogen bonds       : bond        0.03253 (  304)
  hydrogen bonds       : angle       4.34979 (  891)

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

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

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1554 Ramachandran restraints generated.
    777 Oldfield, 0 Emsley, 777 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.155 
Fit side-chains
REVERT: A   53 GLU cc_start: 0.8383 (tp30) cc_final: 0.7821 (tp30)
REVERT: A   57 ARG cc_start: 0.8763 (mmm160) cc_final: 0.8502 (tpp-160)
REVERT: A  147 LEU cc_start: 0.9048 (mm) cc_final: 0.8818 (mm)
REVERT: A  204 MET cc_start: 0.7646 (tpt) cc_final: 0.6706 (tmm)
REVERT: A  350 PHE cc_start: 0.8412 (t80) cc_final: 0.8017 (t80)
REVERT: A  365 ARG cc_start: 0.7654 (tpt90) cc_final: 0.6765 (mtp180)
REVERT: A  406 HIS cc_start: 0.5055 (OUTLIER) cc_final: 0.4486 (p90)
REVERT: A  501 MET cc_start: 0.7285 (ttt) cc_final: 0.6969 (ttt)
REVERT: A  534 ASP cc_start: 0.7746 (OUTLIER) cc_final: 0.7470 (p0)
REVERT: A  550 THR cc_start: 0.9248 (OUTLIER) cc_final: 0.8962 (t)
REVERT: B   64 MET cc_start: 0.7190 (ttp) cc_final: 0.6901 (ptt)
  outliers start: 18
  outliers final: 13
  residues processed: 154
  average time/residue: 0.0594
  time to fit residues: 12.5620
Evaluate side-chains
  157 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   91 SER
Chi-restraints excluded: chain A residue   99 LEU
Chi-restraints excluded: chain A residue  200 PHE
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  309 LEU
Chi-restraints excluded: chain A residue  358 LEU
Chi-restraints excluded: chain A residue  401 ILE
Chi-restraints excluded: chain A residue  406 HIS
Chi-restraints excluded: chain A residue  475 VAL
Chi-restraints excluded: chain A residue  534 ASP
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  684 VAL
Chi-restraints excluded: chain A residue  687 LEU
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain B residue  123 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9980
   chunk 71 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.106874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.094587 restraints weight = 14861.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.097097 restraints weight = 6566.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.098674 restraints weight = 3739.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.099721 restraints weight = 2486.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.100399 restraints weight = 1845.161|
|-----------------------------------------------------------------------------|
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6294  Z= 0.141
  Angle     :  0.671  11.576   8549  Z= 0.337
  Chirality :  0.044   0.193    971
  Planarity :  0.004   0.040   1067
  Dihedral  :  5.053  20.798    841
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.75 %
    Favored  : 91.25 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 24.21 %
    Favored  : 73.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.32), residues: 777
  helix:  1.26 (0.29), residues: 334
  sheet: -1.16 (0.40), residues: 179
  loop : -2.14 (0.40), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  56 
 TYR   0.010   0.001   TYR A 183 
 PHE   0.013   0.001   PHE A 212 
 TRP   0.008   0.001   TRP A 280 
 HIS   0.005   0.001   HIS A 492 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6292)
  covalent geometry    : angle       0.67105 ( 8545)
  SS BOND              : bond        0.00250 (    2)
  SS BOND              : angle       0.78429 (    4)
  hydrogen bonds       : bond        0.03277 (  304)
  hydrogen bonds       : angle       4.35189 (  891)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1200.81 seconds
wall clock time: 21 minutes 20.96 seconds (1280.96 seconds total)