Starting phenix.real_space_refine
on Tue Mar  3 11:41:38 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.44
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2026/7lx5_23566.cif"
  }
  resolution = 3.44
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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      19      5.16       5
     C    2206      2.51       5
     N     591      2.21       5
     O     669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  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: 3485
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "B"
      Number of atoms: 1552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1552
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 11, 'TRANS': 184}
    Chain: "C"
      Number of atoms: 982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 982
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 4, 'TRANS': 124}
    Chain: "A"
      Number of atoms: 951
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 951
          Classifications: {'peptide': 123}
          Link IDs: {'PTRANS': 4, 'TRANS': 118}
  Time building chain proxies: 0.92, per 1000 atoms: 0.26
  Number of scatterers: 3485
  At special positions: 0
  Unit cell: (61.92, 80.84, 99.76, 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      19     16.00
     O     669      8.00
     N     591      7.00
     C    2206      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 112 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  95 " 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: 0.21
  Conformation dependent library (CDL) restraints added in 139.5 milliseconds
  

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  802

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 9 sheets defined
      14.1% alpha, 47.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 365 through 370
      removed outlier: 3.526A  pdb=" N   TYR B 369 " --> pdb=" O   TYR B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.313A  pdb=" N   ASN B 388 " --> pdb=" O   PRO B 384 " (cutoff:3.500A)
      removed outlier: 4.347A  pdb=" N   ASP B 389 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.330A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 422
    Processing helix  chain 'B' and resid 438 through 443
      removed outlier: 3.776A  pdb=" N   SER B 443 " --> pdb=" O   ASN B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 505
    Processing helix  chain 'C' and resid 87 through 91
    Processing helix  chain 'C' and resid 113 through 117
      removed outlier: 3.577A  pdb=" N   MET C 117 " --> pdb=" O   HIS C 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.971A  pdb=" N   ARG A  31 " --> pdb=" O   THR A  28 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   TYR A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 28 through 32'
    Processing helix  chain 'A' and resid 86 through 90
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 7.537A  pdb=" N   ASN B 437 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   PHE B 374 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   SER B 375 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE A 110 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 112 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   THR A 117 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 5.531A  pdb=" N   GLY A  10 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358
      removed outlier: 7.537A  pdb=" N   ASN B 437 " --> pdb=" O   PHE B 374 " (cutoff:3.500A)
      removed outlier: 7.561A  pdb=" N   PHE B 374 " --> pdb=" O   ASN B 437 " (cutoff:3.500A)
      removed outlier: 7.913A  pdb=" N   SER B 375 " --> pdb=" O   PHE A 110 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE A 110 " --> pdb=" O   SER B 375 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   SER A 112 " --> pdb=" O   LYS A  97 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   VAL A  92 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 6.752A  pdb=" N   MET A  34 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   GLY A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'C' and resid 3 through 7
    Processing sheet with id=AA6, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.521A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   CYS C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE C  34 " --> pdb=" O   CYS C  50 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   SER C  52 " --> pdb=" O   TYR C  32 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   TYR C  32 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   TYR C 119 " --> pdb=" O   ALA C  98 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 58 through 60
      removed outlier: 6.521A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   CYS C  50 " --> pdb=" O   ILE C  34 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   ILE C  34 " --> pdb=" O   CYS C  50 " (cutoff:3.500A)
      removed outlier: 5.265A  pdb=" N   SER C  52 " --> pdb=" O   TYR C  32 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   TYR C  32 " --> pdb=" O   SER C  52 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 102 through 104
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.584A  pdb=" N   GLN A   3 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   SER A  25 " --> pdb=" O   GLN A   3 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN A   5 " --> pdb=" O   ALA A  23 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   ALA A  23 " --> pdb=" O   GLN A   5 " (cutoff:3.500A)

    159 hydrogen bonds defined for protein.
    399 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: 0.62

  Time building geometry restraints manager: 0.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1125
        1.34 -     1.46: 961
        1.46 -     1.58: 1465
        1.58 -     1.70: 0
        1.70 -     1.81: 24
  Bond restraints: 3575
  Sorted by residual:
  bond pdb=" CB  VAL B 350 "
       pdb=" CG1 VAL B 350 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.76e-01
  bond pdb=" CB  TRP C 120 "
       pdb=" CG  TRP C 120 "
    ideal  model  delta    sigma   weight residual
    1.498  1.470  0.028 3.10e-02 1.04e+03 7.91e-01
  bond pdb=" CG  LEU B 461 "
       pdb=" CD2 LEU B 461 "
    ideal  model  delta    sigma   weight residual
    1.521  1.492  0.029 3.30e-02 9.18e+02 7.71e-01
  bond pdb=" CB  TRP C  36 "
       pdb=" CG  TRP C  36 "
    ideal  model  delta    sigma   weight residual
    1.498  1.471  0.027 3.10e-02 1.04e+03 7.65e-01
  bond pdb=" CB  PRO A 106 "
       pdb=" CG  PRO A 106 "
    ideal  model  delta    sigma   weight residual
    1.492  1.535 -0.043 5.00e-02 4.00e+02 7.53e-01
  ... (remaining 3570 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 4753
        1.85 -     3.70: 87
        3.70 -     5.54: 6
        5.54 -     7.39: 1
        7.39 -     9.24: 1
  Bond angle restraints: 4848
  Sorted by residual:
  angle pdb=" CA  LEU B 461 "
        pdb=" CB  LEU B 461 "
        pdb=" CG  LEU B 461 "
      ideal   model   delta    sigma   weight residual
     116.30  125.54   -9.24 3.50e+00 8.16e-02 6.97e+00
  angle pdb=" CA  ARG A  30 "
        pdb=" CB  ARG A  30 "
        pdb=" CG  ARG A  30 "
      ideal   model   delta    sigma   weight residual
     114.10  108.92    5.18 2.00e+00 2.50e-01 6.70e+00
  angle pdb=" N   GLY B 485 "
        pdb=" CA  GLY B 485 "
        pdb=" C   GLY B 485 "
      ideal   model   delta    sigma   weight residual
     113.18  108.49    4.69 2.37e+00 1.78e-01 3.92e+00
  angle pdb=" C   ARG A  30 "
        pdb=" N   ARG A  31 "
        pdb=" CA  ARG A  31 "
      ideal   model   delta    sigma   weight residual
     123.24  120.36    2.88 1.54e+00 4.22e-01 3.49e+00
  angle pdb=" N   GLY A  15 "
        pdb=" CA  GLY A  15 "
        pdb=" C   GLY A  15 "
      ideal   model   delta    sigma   weight residual
     115.36  112.93    2.43 1.33e+00 5.65e-01 3.34e+00
  ... (remaining 4843 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.02: 1968
       16.02 -    32.04: 101
       32.04 -    48.06: 16
       48.06 -    64.07: 2
       64.07 -    80.09: 3
  Dihedral angle restraints: 2090
    sinusoidal: 810
      harmonic: 1280
  Sorted by residual:
  dihedral pdb=" CA  SER B 366 "
           pdb=" C   SER B 366 "
           pdb=" N   VAL B 367 "
           pdb=" CA  VAL B 367 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.01   17.99     0      5.00e+00 4.00e-02 1.30e+01
  dihedral pdb=" CA  TYR B 489 "
           pdb=" C   TYR B 489 "
           pdb=" N   PHE B 490 "
           pdb=" CA  PHE B 490 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.15   16.85     0      5.00e+00 4.00e-02 1.14e+01
  dihedral pdb=" CB  GLU B 471 "
           pdb=" CG  GLU B 471 "
           pdb=" CD  GLU B 471 "
           pdb=" OE1 GLU B 471 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   80.09  -80.09     1      3.00e+01 1.11e-03 8.83e+00
  ... (remaining 2087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 311
       0.031 -    0.063: 112
       0.063 -    0.094: 48
       0.094 -    0.126: 23
       0.126 -    0.157: 7
  Chirality restraints: 501
  Sorted by residual:
  chirality pdb=" CG  LEU B 461 "
            pdb=" CB  LEU B 461 "
            pdb=" CD1 LEU B 461 "
            pdb=" CD2 LEU B 461 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.75    0.16 2.00e-01 2.50e+01 6.17e-01
  chirality pdb=" CA  VAL A  40 "
            pdb=" N   VAL A  40 "
            pdb=" C   VAL A  40 "
            pdb=" CB  VAL A  40 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ARG A  30 "
            pdb=" N   ARG A  30 "
            pdb=" C   ARG A  30 "
            pdb=" CB  ARG A  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.43e-01
  ... (remaining 498 not shown)

  Planarity restraints: 633
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 110 "   -0.010 2.00e-02 2.50e+03   8.62e-03 1.30e+00
        pdb=" CG  PHE A 110 "    0.020 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 110 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 110 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 110 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 110 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C  80 "    0.007 2.00e-02 2.50e+03   6.42e-03 8.25e-01
        pdb=" CG  TYR C  80 "   -0.016 2.00e-02 2.50e+03
        pdb=" CD1 TYR C  80 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TYR C  80 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR C  80 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR C  80 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR C  80 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR C  80 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 467 "   -0.004 2.00e-02 2.50e+03   8.40e-03 7.06e-01
        pdb=" C   ASP B 467 "    0.015 2.00e-02 2.50e+03
        pdb=" O   ASP B 467 "   -0.005 2.00e-02 2.50e+03
        pdb=" N   ILE B 468 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 630 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 268
        2.74 -     3.28: 3134
        3.28 -     3.82: 5333
        3.82 -     4.36: 6330
        4.36 -     4.90: 11179
  Nonbonded interactions: 26244
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN B 498 "
            pdb=" OG1 THR C  28 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR A  52 "
            pdb=" O   TRP A 105 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   PHE A  29 "
            pdb=" NH2 ARG A  71 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" OE1 GLU B 406 "
            pdb=" OH  TYR B 495 "
     model   vdw
     2.292 3.040
  ... (remaining 26239 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.200
  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:             0.000
  Extract box with map and model:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.360
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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   0.043   3582  Z= 0.211
  Angle     :  0.617   9.238   4862  Z= 0.337
  Chirality :  0.045   0.157    501
  Planarity :  0.003   0.021    633
  Dihedral  : 10.099  80.092   1267
  Min Nonbonded Distance : 2.198

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  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: -0.46 (0.38), residues: 442
  helix: -4.06 (0.60), residues: 27
  sheet:  0.79 (0.46), residues: 132
  loop : -0.43 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 108 
 TYR   0.016   0.001   TYR C  80 
 PHE   0.020   0.002   PHE A 110 
 TRP   0.009   0.002   TRP B 436 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 3575)
  covalent geometry    : angle       0.61584 ( 4848)
  SS BOND              : bond        0.00341 (    7)
  SS BOND              : angle       0.87374 (   14)
  hydrogen bonds       : bond        0.25654 (  115)
  hydrogen bonds       : angle       9.50671 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
REVERT: B  357 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7165 (tmm-80)
REVERT: B  469 SER cc_start: 0.8965 (t) cc_final: 0.8593 (p)
REVERT: B  501 ASN cc_start: 0.8483 (m110) cc_final: 0.8132 (m110)
REVERT: C   59 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8192 (mtpt)
REVERT: C   73 ASP cc_start: 0.8733 (m-30) cc_final: 0.7298 (m-30)
REVERT: C   76 LYS cc_start: 0.8240 (mmmt) cc_final: 0.8016 (mtmm)
REVERT: C   80 TYR cc_start: 0.7863 (m-80) cc_final: 0.7638 (m-80)
REVERT: C   87 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7735 (mmmt)
REVERT: A    3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7771 (pm20)
REVERT: A   36 TRP cc_start: 0.8333 (m100) cc_final: 0.7580 (m100)
REVERT: A   75 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7687 (mtpt)
REVERT: A   84 SER cc_start: 0.7257 (m) cc_final: 0.6807 (p)
REVERT: A  121 VAL cc_start: 0.8394 (t) cc_final: 0.8149 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0827
  time to fit residues: 13.9396
Evaluate side-chains
  115 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 24 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    5.9990
   chunk 16 optimal weight:    7.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0970
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.9982

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.121716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.103200 restraints weight = 5766.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.3234 rms_B_bonded: 3.55
r_work: 0.3098 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3582  Z= 0.189
  Angle     :  0.661   8.981   4862  Z= 0.350
  Chirality :  0.046   0.197    501
  Planarity :  0.004   0.027    633
  Dihedral  :  4.553  20.394    500
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.48 %
    Favored  : 82.75 %
  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: -0.16 (0.38), residues: 442
  helix: -4.19 (0.56), residues: 27
  sheet:  1.49 (0.45), residues: 131
  loop : -0.47 (0.34), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  38 
 TYR   0.020   0.001   TYR A  58 
 PHE   0.009   0.001   PHE B 392 
 TRP   0.014   0.002   TRP A 113 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 3575)
  covalent geometry    : angle       0.63997 ( 4848)
  SS BOND              : bond        0.00454 (    7)
  SS BOND              : angle       3.17866 (   14)
  hydrogen bonds       : bond        0.04356 (  115)
  hydrogen bonds       : angle       5.24169 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 126
  time to evaluate  : 0.105 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8252 (mp0)
REVERT: B  357 ARG cc_start: 0.8291 (ttp80) cc_final: 0.7802 (tmm160)
REVERT: B  465 GLU cc_start: 0.8269 (tt0) cc_final: 0.8011 (tt0)
REVERT: B  469 SER cc_start: 0.9188 (t) cc_final: 0.8870 (p)
REVERT: B  498 GLN cc_start: 0.8414 (mt0) cc_final: 0.8146 (mt0)
REVERT: B  501 ASN cc_start: 0.8648 (m110) cc_final: 0.8138 (m110)
REVERT: C    2 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.6910 (m)
REVERT: C   27 PHE cc_start: 0.8985 (m-80) cc_final: 0.8368 (m-10)
REVERT: C   31 TYR cc_start: 0.8487 (m-80) cc_final: 0.8218 (m-80)
REVERT: C   59 LYS cc_start: 0.8242 (mtmt) cc_final: 0.8000 (mtpt)
REVERT: C   73 ASP cc_start: 0.8833 (m-30) cc_final: 0.7140 (m-30)
REVERT: C   76 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7960 (mtmm)
REVERT: C   78 THR cc_start: 0.8789 (m) cc_final: 0.8030 (t)
REVERT: C   80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7530 (m-80)
REVERT: C   81 LEU cc_start: 0.8195 (tt) cc_final: 0.7945 (tt)
REVERT: C   87 LYS cc_start: 0.8087 (mmtp) cc_final: 0.7790 (mmmt)
REVERT: C   91 THR cc_start: 0.8541 (p) cc_final: 0.8135 (p)
REVERT: C  124 THR cc_start: 0.8134 (p) cc_final: 0.7810 (p)
REVERT: A    3 GLN cc_start: 0.8171 (pt0) cc_final: 0.7732 (pm20)
REVERT: A   36 TRP cc_start: 0.8528 (m100) cc_final: 0.7772 (m100)
REVERT: A  100 MET cc_start: 0.8284 (mmm) cc_final: 0.7293 (mtm)
  outliers start: 14
  outliers final: 8
  residues processed: 134
  average time/residue: 0.0911
  time to fit residues: 14.1288
Evaluate side-chains
  129 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain C residue    2 VAL
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   50 CYS
Chi-restraints excluded: chain A residue   53 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 41 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    1.9990
   chunk 29 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0970
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN
A   1 GLN
A  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.124654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.106043 restraints weight = 5660.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 3.60
r_work: 0.3147 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.3147
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3582  Z= 0.110
  Angle     :  0.591   7.188   4862  Z= 0.308
  Chirality :  0.043   0.147    501
  Planarity :  0.003   0.027    633
  Dihedral  :  4.070  17.584    500
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 15.09 %
    Favored  : 82.48 %
  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:  0.08 (0.38), residues: 442
  helix: -4.10 (0.56), residues: 28
  sheet:  1.96 (0.44), residues: 127
  loop : -0.41 (0.34), residues: 287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.015   0.001   TYR A  94 
 PHE   0.007   0.001   PHE C  68 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 3575)
  covalent geometry    : angle       0.57064 ( 4848)
  SS BOND              : bond        0.00229 (    7)
  SS BOND              : angle       2.95504 (   14)
  hydrogen bonds       : bond        0.03684 (  115)
  hydrogen bonds       : angle       4.50250 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8230 (mp0)
REVERT: B  357 ARG cc_start: 0.8238 (ttp80) cc_final: 0.7765 (tmm160)
REVERT: B  457 ARG cc_start: 0.7890 (ttt-90) cc_final: 0.7649 (ttt-90)
REVERT: B  465 GLU cc_start: 0.8318 (tt0) cc_final: 0.8083 (tt0)
REVERT: B  469 SER cc_start: 0.9213 (t) cc_final: 0.8906 (p)
REVERT: B  498 GLN cc_start: 0.8413 (mt0) cc_final: 0.8082 (mt0)
REVERT: B  501 ASN cc_start: 0.8577 (m110) cc_final: 0.8035 (m110)
REVERT: B  505 TYR cc_start: 0.8515 (m-10) cc_final: 0.8099 (m-80)
REVERT: C   67 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8275 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8644 (m-30) cc_final: 0.7388 (m-30)
REVERT: C   76 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7854 (mtmm)
REVERT: C   80 TYR cc_start: 0.8012 (m-80) cc_final: 0.7697 (m-80)
REVERT: C   87 LYS cc_start: 0.8016 (mmtp) cc_final: 0.7696 (mmmt)
REVERT: C   91 THR cc_start: 0.8488 (p) cc_final: 0.8155 (p)
REVERT: A    3 GLN cc_start: 0.8192 (pt0) cc_final: 0.7718 (pm20)
  outliers start: 9
  outliers final: 6
  residues processed: 129
  average time/residue: 0.0935
  time to fit residues: 13.9735
Evaluate side-chains
  117 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 111
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   53 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 7 optimal weight:    0.9980
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 17 optimal weight:    4.9990
   chunk 3 optimal weight:    0.0070
   chunk 4 optimal weight:    5.9990
   chunk 26 optimal weight:    0.0570
   chunk 18 optimal weight:    5.9990
   chunk 0 optimal weight:    0.8980
   chunk 31 optimal weight:    9.9990
   overall best weight:    0.4516

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

Flipped N/Q/H residues before XYZ refinement:
A 118 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.125936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.107577 restraints weight = 5603.032|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 3.46
r_work: 0.3173 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3582  Z= 0.100
  Angle     :  0.589   8.244   4862  Z= 0.298
  Chirality :  0.043   0.155    501
  Planarity :  0.003   0.029    633
  Dihedral  :  3.766  12.873    500
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 18.06 %
    Favored  : 79.78 %
  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:  0.25 (0.39), residues: 442
  helix: -3.78 (0.84), residues: 21
  sheet:  1.91 (0.44), residues: 128
  loop : -0.34 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  19 
 TYR   0.014   0.001   TYR C 103 
 PHE   0.007   0.001   PHE C  68 
 TRP   0.009   0.001   TRP B 436 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00231 ( 3575)
  covalent geometry    : angle       0.57213 ( 4848)
  SS BOND              : bond        0.00304 (    7)
  SS BOND              : angle       2.65333 (   14)
  hydrogen bonds       : bond        0.03339 (  115)
  hydrogen bonds       : angle       4.31382 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 119
  time to evaluate  : 0.132 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8201 (mp0)
REVERT: B  357 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7744 (tmm160)
REVERT: B  465 GLU cc_start: 0.8323 (tt0) cc_final: 0.8112 (tt0)
REVERT: B  469 SER cc_start: 0.9238 (t) cc_final: 0.9014 (p)
REVERT: B  472 ILE cc_start: 0.8735 (mm) cc_final: 0.8380 (tp)
REVERT: B  498 GLN cc_start: 0.8425 (mt0) cc_final: 0.8051 (mt0)
REVERT: B  501 ASN cc_start: 0.8588 (m110) cc_final: 0.8070 (m110)
REVERT: B  505 TYR cc_start: 0.8486 (m-10) cc_final: 0.8142 (m-80)
REVERT: C   67 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8392 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8578 (m-30) cc_final: 0.7412 (m-30)
REVERT: C   76 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7892 (mtmm)
REVERT: C   80 TYR cc_start: 0.7973 (m-10) cc_final: 0.7634 (m-80)
REVERT: C   87 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7678 (mmmt)
REVERT: C   91 THR cc_start: 0.8470 (p) cc_final: 0.8181 (p)
REVERT: A    3 GLN cc_start: 0.8169 (pt0) cc_final: 0.7725 (pm20)
REVERT: A   19 ARG cc_start: 0.8465 (mpp80) cc_final: 0.8190 (mpp80)
REVERT: A   89 ASP cc_start: 0.8492 (m-30) cc_final: 0.7801 (t0)
REVERT: A  100 MET cc_start: 0.8267 (mmm) cc_final: 0.7213 (mtm)
  outliers start: 8
  outliers final: 7
  residues processed: 123
  average time/residue: 0.0913
  time to fit residues: 13.0188
Evaluate side-chains
  119 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 112
  time to evaluate  : 0.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  391 CYS
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue   11 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 1 optimal weight:    0.0370
   chunk 28 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 31 optimal weight:   10.0000
   chunk 12 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    3.2066

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

Flipped N/Q/H residues before XYZ refinement:
C   3 GLN
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.117400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.099092 restraints weight = 5812.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.3167 rms_B_bonded: 3.51
r_work: 0.3032 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   3582  Z= 0.280
  Angle     :  0.710  10.004   4862  Z= 0.372
  Chirality :  0.047   0.188    501
  Planarity :  0.004   0.026    633
  Dihedral  :  4.583  17.146    500
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 16.44 %
    Favored  : 78.98 %
  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: -0.03 (0.39), residues: 442
  helix: -3.62 (0.97), residues: 21
  sheet:  1.54 (0.43), residues: 138
  loop : -0.55 (0.35), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  38 
 TYR   0.020   0.002   TYR A  58 
 PHE   0.010   0.002   PHE A  29 
 TRP   0.012   0.002   TRP B 436 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 3575)
  covalent geometry    : angle       0.68679 ( 4848)
  SS BOND              : bond        0.00543 (    7)
  SS BOND              : angle       3.42418 (   14)
  hydrogen bonds       : bond        0.04376 (  115)
  hydrogen bonds       : angle       4.89160 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8263 (mp0)
REVERT: B  357 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7607 (tmm-80)
REVERT: B  406 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: B  461 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7273 (tt)
REVERT: B  501 ASN cc_start: 0.8696 (m110) cc_final: 0.8348 (m110)
REVERT: C   59 LYS cc_start: 0.7672 (mtpt) cc_final: 0.7384 (mtpt)
REVERT: C   73 ASP cc_start: 0.8762 (m-30) cc_final: 0.7339 (m-30)
REVERT: C   76 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8182 (mtmm)
REVERT: C   78 THR cc_start: 0.8817 (m) cc_final: 0.8071 (t)
REVERT: C   87 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7871 (mmmt)
REVERT: C   91 THR cc_start: 0.8717 (p) cc_final: 0.8456 (p)
REVERT: C  125 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8628 (tm-30)
REVERT: A    5 GLN cc_start: 0.7622 (mp10) cc_final: 0.7357 (mp10)
REVERT: A   64 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8851 (mtpt)
REVERT: A   88 GLU cc_start: 0.8953 (tt0) cc_final: 0.7786 (tm-30)
REVERT: A  121 VAL cc_start: 0.8995 (t) cc_final: 0.8700 (m)
  outliers start: 17
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0944
  time to fit residues: 14.2650
Evaluate side-chains
  132 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.126 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   89 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9990
   chunk 9 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
B 498 GLN
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.122337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.103747 restraints weight = 5684.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 3.58
r_work: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.4042

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3582  Z= 0.121
  Angle     :  0.619   7.379   4862  Z= 0.319
  Chirality :  0.043   0.148    501
  Planarity :  0.003   0.025    633
  Dihedral  :  4.017  15.804    500
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 17.79 %
    Favored  : 77.90 %
  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:  0.10 (0.39), residues: 442
  helix: -3.38 (0.97), residues: 21
  sheet:  1.86 (0.45), residues: 126
  loop : -0.51 (0.34), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.017   0.001   TYR A  32 
 PHE   0.005   0.001   PHE A  67 
 TRP   0.010   0.001   TRP A 105 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 3575)
  covalent geometry    : angle       0.60440 ( 4848)
  SS BOND              : bond        0.00243 (    7)
  SS BOND              : angle       2.56280 (   14)
  hydrogen bonds       : bond        0.03372 (  115)
  hydrogen bonds       : angle       4.50108 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 112
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8838 (mm-30) cc_final: 0.8233 (mp0)
REVERT: B  357 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7748 (tmm160)
REVERT: B  461 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.8031 (tt)
REVERT: B  501 ASN cc_start: 0.8756 (m110) cc_final: 0.8230 (m110)
REVERT: C   67 ARG cc_start: 0.8703 (mtm-85) cc_final: 0.8296 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8614 (m-30) cc_final: 0.7474 (m-30)
REVERT: C   76 LYS cc_start: 0.8364 (mmmt) cc_final: 0.7949 (mtmm)
REVERT: C   80 TYR cc_start: 0.8158 (m-80) cc_final: 0.7910 (m-80)
REVERT: C   87 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7769 (mmmt)
REVERT: C   91 THR cc_start: 0.8715 (p) cc_final: 0.8485 (p)
REVERT: A    5 GLN cc_start: 0.7737 (mp10) cc_final: 0.7285 (mp10)
REVERT: A   19 ARG cc_start: 0.8565 (mpp80) cc_final: 0.8282 (mpp80)
REVERT: A   64 LYS cc_start: 0.9143 (ttmt) cc_final: 0.8812 (mtpt)
REVERT: A   89 ASP cc_start: 0.8533 (m-30) cc_final: 0.7852 (t0)
REVERT: A  100 MET cc_start: 0.8289 (mmm) cc_final: 0.7209 (mtm)
  outliers start: 16
  outliers final: 13
  residues processed: 120
  average time/residue: 0.0869
  time to fit residues: 12.1219
Evaluate side-chains
  123 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 109
  time to evaluate  : 0.097 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 15 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 37 optimal weight:    0.0470
   chunk 36 optimal weight:    4.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    3.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.124448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.105743 restraints weight = 5711.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 3.59
r_work: 0.3121 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3582  Z= 0.110
  Angle     :  0.601   8.331   4862  Z= 0.307
  Chirality :  0.042   0.148    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.798  15.159    500
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 18.06 %
    Favored  : 77.09 %
  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:  0.17 (0.39), residues: 442
  helix: -3.08 (1.01), residues: 21
  sheet:  1.75 (0.46), residues: 128
  loop : -0.41 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  99 
 TYR   0.010   0.001   TYR A  94 
 PHE   0.021   0.001   PHE C  68 
 TRP   0.029   0.002   TRP A 105 
 HIS   0.001   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 3575)
  covalent geometry    : angle       0.58757 ( 4848)
  SS BOND              : bond        0.00236 (    7)
  SS BOND              : angle       2.43124 (   14)
  hydrogen bonds       : bond        0.03296 (  115)
  hydrogen bonds       : angle       4.38119 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.091 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8269 (mp0)
REVERT: B  357 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7754 (tmm160)
REVERT: B  461 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7992 (tt)
REVERT: B  466 ARG cc_start: 0.7873 (ptm160) cc_final: 0.7345 (ptm160)
REVERT: B  501 ASN cc_start: 0.8685 (m110) cc_final: 0.8135 (m110)
REVERT: C   67 ARG cc_start: 0.8678 (mtm-85) cc_final: 0.8357 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8565 (m-30) cc_final: 0.7532 (m-30)
REVERT: C   76 LYS cc_start: 0.8289 (mmmt) cc_final: 0.7870 (mtmm)
REVERT: C   87 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7689 (mmmt)
REVERT: C   91 THR cc_start: 0.8676 (p) cc_final: 0.8466 (p)
REVERT: A    3 GLN cc_start: 0.8446 (pt0) cc_final: 0.8198 (pt0)
REVERT: A    5 GLN cc_start: 0.7809 (mp10) cc_final: 0.7336 (mp10)
REVERT: A   19 ARG cc_start: 0.8526 (mpp80) cc_final: 0.8227 (mpp80)
REVERT: A   64 LYS cc_start: 0.9127 (ttmt) cc_final: 0.8789 (mtpt)
REVERT: A   89 ASP cc_start: 0.8540 (m-30) cc_final: 0.7881 (t0)
REVERT: A  100 MET cc_start: 0.8181 (mmm) cc_final: 0.7046 (mtm)
REVERT: A  101 ASP cc_start: 0.9068 (p0) cc_final: 0.8844 (p0)
  outliers start: 18
  outliers final: 16
  residues processed: 123
  average time/residue: 0.0830
  time to fit residues: 11.9145
Evaluate side-chains
  127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0770
   chunk 6 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.5744

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.120774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.101676 restraints weight = 5758.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3210 rms_B_bonded: 3.66
r_work: 0.3076 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3076
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
moved from start:          0.4342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   3582  Z= 0.162
  Angle     :  0.681  12.008   4862  Z= 0.347
  Chirality :  0.043   0.148    501
  Planarity :  0.004   0.047    633
  Dihedral  :  4.228  21.520    500
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 18.06 %
    Favored  : 76.01 %
  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:  0.06 (0.40), residues: 442
  helix: -2.97 (1.08), residues: 21
  sheet:  1.66 (0.46), residues: 128
  loop : -0.50 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  99 
 TYR   0.011   0.001   TYR B 453 
 PHE   0.012   0.001   PHE C  68 
 TRP   0.020   0.002   TRP A 105 
 HIS   0.001   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 3575)
  covalent geometry    : angle       0.66210 ( 4848)
  SS BOND              : bond        0.00274 (    7)
  SS BOND              : angle       3.06614 (   14)
  hydrogen bonds       : bond        0.03683 (  115)
  hydrogen bonds       : angle       4.43690 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8899 (mm-30) cc_final: 0.8285 (mp0)
REVERT: B  357 ARG cc_start: 0.8249 (ttp80) cc_final: 0.7725 (tmm160)
REVERT: B  406 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8341 (mt-10)
REVERT: B  420 ASP cc_start: 0.7818 (OUTLIER) cc_final: 0.7270 (m-30)
REVERT: B  461 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7910 (tt)
REVERT: B  466 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7384 (ptm160)
REVERT: B  501 ASN cc_start: 0.8662 (m110) cc_final: 0.8155 (m110)
REVERT: C   60 TYR cc_start: 0.8191 (m-80) cc_final: 0.7916 (m-80)
REVERT: C   67 ARG cc_start: 0.8689 (mtm-85) cc_final: 0.8445 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8524 (m-30) cc_final: 0.7405 (m-30)
REVERT: C   76 LYS cc_start: 0.8368 (mmmt) cc_final: 0.7905 (mtmm)
REVERT: C   87 LYS cc_start: 0.8096 (mmtp) cc_final: 0.7762 (mmmt)
REVERT: C   91 THR cc_start: 0.8724 (p) cc_final: 0.8513 (p)
REVERT: A    5 GLN cc_start: 0.7891 (mp10) cc_final: 0.7460 (mp10)
REVERT: A   19 ARG cc_start: 0.8610 (mpp80) cc_final: 0.8311 (mpp80)
REVERT: A   64 LYS cc_start: 0.9146 (ttmt) cc_final: 0.8816 (mtpt)
REVERT: A   88 GLU cc_start: 0.8928 (tt0) cc_final: 0.7966 (tm-30)
REVERT: A   89 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7926 (t0)
REVERT: A  100 MET cc_start: 0.8226 (mmm) cc_final: 0.8026 (mmm)
REVERT: A  121 VAL cc_start: 0.8866 (t) cc_final: 0.8651 (p)
  outliers start: 22
  outliers final: 16
  residues processed: 122
  average time/residue: 0.0859
  time to fit residues: 12.2596
Evaluate side-chains
  129 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue    6 GLU
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   89 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 36 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.121440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.102156 restraints weight = 5722.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3215 rms_B_bonded: 3.63
r_work: 0.3083 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   3582  Z= 0.137
  Angle     :  0.646   8.357   4862  Z= 0.330
  Chirality :  0.043   0.149    501
  Planarity :  0.003   0.032    633
  Dihedral  :  4.164  22.336    500
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 17.79 %
    Favored  : 76.82 %
  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: -0.05 (0.40), residues: 442
  helix: -3.22 (0.89), residues: 27
  sheet:  1.67 (0.46), residues: 126
  loop : -0.52 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.010   0.001   TYR B 453 
 PHE   0.014   0.001   PHE C  68 
 TRP   0.019   0.001   TRP A 105 
 HIS   0.001   0.001   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 3575)
  covalent geometry    : angle       0.62844 ( 4848)
  SS BOND              : bond        0.00242 (    7)
  SS BOND              : angle       2.88402 (   14)
  hydrogen bonds       : bond        0.03584 (  115)
  hydrogen bonds       : angle       4.40566 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8897 (mm-30) cc_final: 0.8292 (mp0)
REVERT: B  357 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7720 (tmm160)
REVERT: B  406 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8348 (mt-10)
REVERT: B  420 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7260 (m-30)
REVERT: B  461 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7896 (tt)
REVERT: B  466 ARG cc_start: 0.8006 (ptm160) cc_final: 0.7429 (ptm160)
REVERT: B  501 ASN cc_start: 0.8675 (m110) cc_final: 0.8134 (m110)
REVERT: C   27 PHE cc_start: 0.8885 (m-80) cc_final: 0.8657 (m-80)
REVERT: C   60 TYR cc_start: 0.8225 (m-80) cc_final: 0.8002 (m-80)
REVERT: C   67 ARG cc_start: 0.8720 (mtm-85) cc_final: 0.8495 (mtm-85)
REVERT: C   68 PHE cc_start: 0.9198 (m-10) cc_final: 0.8933 (m-10)
REVERT: C   73 ASP cc_start: 0.8469 (m-30) cc_final: 0.7298 (m-30)
REVERT: C   76 LYS cc_start: 0.8330 (mmmt) cc_final: 0.7850 (mtmm)
REVERT: C   87 LYS cc_start: 0.8029 (mmtp) cc_final: 0.7691 (mmmt)
REVERT: C   91 THR cc_start: 0.8725 (p) cc_final: 0.8524 (p)
REVERT: A    5 GLN cc_start: 0.7854 (mp10) cc_final: 0.7402 (mp10)
REVERT: A   19 ARG cc_start: 0.8619 (mpp80) cc_final: 0.8309 (mpp80)
REVERT: A   64 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8786 (mtpt)
REVERT: A   89 ASP cc_start: 0.8615 (OUTLIER) cc_final: 0.7963 (t0)
REVERT: A  100 MET cc_start: 0.8188 (mmm) cc_final: 0.7985 (mmm)
REVERT: A  121 VAL cc_start: 0.8858 (t) cc_final: 0.8646 (p)
  outliers start: 20
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0866
  time to fit residues: 12.2249
Evaluate side-chains
  127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  383 SER
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   89 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 42 optimal weight:    9.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    0.8988

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.123297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.104433 restraints weight = 5867.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.61
r_work: 0.3098 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3582  Z= 0.119
  Angle     :  0.619   7.934   4862  Z= 0.316
  Chirality :  0.043   0.150    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.873  17.913    500
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.62 %
    Favored  : 96.38 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 18.60 %
    Favored  : 76.28 %
  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: -0.09 (0.40), residues: 442
  helix: -3.20 (0.89), residues: 27
  sheet:  1.59 (0.46), residues: 126
  loop : -0.52 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  99 
 TYR   0.009   0.001   TYR B 453 
 PHE   0.011   0.001   PHE C  68 
 TRP   0.018   0.001   TRP A 105 
 HIS   0.000   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 3575)
  covalent geometry    : angle       0.60517 ( 4848)
  SS BOND              : bond        0.00195 (    7)
  SS BOND              : angle       2.48349 (   14)
  hydrogen bonds       : bond        0.03447 (  115)
  hydrogen bonds       : angle       4.36758 (  399)

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

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

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  884 Ramachandran restraints generated.
    442 Oldfield, 0 Emsley, 442 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8279 (mp0)
REVERT: B  357 ARG cc_start: 0.8229 (ttp80) cc_final: 0.7746 (tmm160)
REVERT: B  406 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8307 (mt-10)
REVERT: B  420 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7235 (m-30)
REVERT: B  461 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7836 (tt)
REVERT: B  466 ARG cc_start: 0.8038 (ptm160) cc_final: 0.7491 (ptm160)
REVERT: B  501 ASN cc_start: 0.8678 (m110) cc_final: 0.8119 (m110)
REVERT: C   27 PHE cc_start: 0.8885 (m-80) cc_final: 0.8652 (m-80)
REVERT: C   59 LYS cc_start: 0.7575 (mtpt) cc_final: 0.7207 (mtpt)
REVERT: C   60 TYR cc_start: 0.8318 (m-80) cc_final: 0.8079 (m-80)
REVERT: C   67 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8468 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8468 (m-30) cc_final: 0.8143 (m-30)
REVERT: C   87 LYS cc_start: 0.8011 (mmtp) cc_final: 0.7668 (mmmt)
REVERT: A    5 GLN cc_start: 0.7903 (mp10) cc_final: 0.7466 (mp10)
REVERT: A   19 ARG cc_start: 0.8585 (mpp80) cc_final: 0.8274 (mpp80)
REVERT: A   64 LYS cc_start: 0.9129 (ttmt) cc_final: 0.8791 (mtpt)
REVERT: A   75 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8623 (mtpt)
REVERT: A   89 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.7957 (t0)
REVERT: A  100 MET cc_start: 0.8197 (mmm) cc_final: 0.7981 (mmm)
  outliers start: 19
  outliers final: 16
  residues processed: 121
  average time/residue: 0.0833
  time to fit residues: 11.7708
Evaluate side-chains
  129 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  371 SER
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  420 ASP
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  461 LEU
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  478 THR
Chi-restraints excluded: chain B residue  506 GLN
Chi-restraints excluded: chain B residue  525 CYS
Chi-restraints excluded: chain C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   39 GLN
Chi-restraints excluded: chain A residue   53 SER
Chi-restraints excluded: chain A residue   57 THR
Chi-restraints excluded: chain A residue   89 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 18 optimal weight:    5.9990
   chunk 9 optimal weight:    0.0570
   chunk 41 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.8102

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

Flipped N/Q/H residues before XYZ refinement:
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.123581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.104772 restraints weight = 5826.604|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 3.62
r_work: 0.3102 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.4609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3582  Z= 0.116
  Angle     :  0.623   7.661   4862  Z= 0.318
  Chirality :  0.043   0.153    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.804  16.283    500
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 6.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.66 %
    Allowed  : 19.14 %
    Favored  : 75.20 %
  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: -0.11 (0.40), residues: 442
  helix: -3.22 (0.89), residues: 27
  sheet:  1.58 (0.47), residues: 126
  loop : -0.53 (0.36), residues: 289

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  99 
 TYR   0.009   0.001   TYR A  94 
 PHE   0.021   0.001   PHE C  68 
 TRP   0.018   0.001   TRP A 105 
 HIS   0.000   0.000   HIS C 114 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 3575)
  covalent geometry    : angle       0.61034 ( 4848)
  SS BOND              : bond        0.00172 (    7)
  SS BOND              : angle       2.40499 (   14)
  hydrogen bonds       : bond        0.03478 (  115)
  hydrogen bonds       : angle       4.35844 (  399)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1005.95 seconds
wall clock time: 17 minutes 49.21 seconds (1069.21 seconds total)