Starting phenix.real_space_refine
on Wed Mar  5 19:52:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lx5_23566/03_2025/7lx5_23566.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lx5_23566/03_2025/7lx5_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_2025/7lx5_23566.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2025/7lx5_23566.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2025/7lx5_23566.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lx5_23566/03_2025/7lx5_23566.cif"
  }
  resolution = 3.44
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.87, per 1000 atoms: 0.82
  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: 0.97
  Conformation dependent library (CDL) restraints added in 450.9 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: 0.57
  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: 1.00

  Time building geometry restraints manager: 0.96 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:             0.350
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.760
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
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   3575  Z= 0.315
  Angle     :  0.616   9.238   4848  Z= 0.336
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (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
 TRP   0.009   0.002   TRP B 436 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.020   0.002   PHE A 110 
 TYR   0.016   0.001   TYR C  80 
 ARG   0.002   0.000   ARG A 108 

*********************** 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  : 0.379 
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: 0.8133 (m110)
REVERT: C   59 LYS cc_start: 0.8706 (mtmt) cc_final: 0.8191 (mtpt)
REVERT: C   73 ASP cc_start: 0.8733 (m-30) cc_final: 0.7297 (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: 0.7734 (mmmt)
REVERT: A    3 GLN cc_start: 0.8205 (pt0) cc_final: 0.7772 (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: 0.6808 (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: 0.2060
  time to fit residues: 34.4201
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  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 18 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0970
   chunk 21 optimal weight:    7.9990
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0770
   chunk 20 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.6136

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

Flipped N/Q/H residues before XYZ refinement:
B 394 ASN
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.126707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.108014 restraints weight = 5634.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 3.50
r_work: 0.3181 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3575  Z= 0.174
  Angle     :  0.600   8.356   4848  Z= 0.317
  Chirality :  0.045   0.140    501
  Planarity :  0.004   0.029    633
  Dihedral  :  4.268  20.873    500
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 13.21 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.38), residues: 442
  helix: -3.13 (0.67), residues: 33
  sheet:  1.59 (0.45), residues: 131
  loop : -0.38 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 113 
 HIS   0.000   0.000   HIS C 114 
 PHE   0.014   0.001   PHE B 392 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.003   0.001   ARG B 408 

*********************** 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
  139 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8178 (mp0)
REVERT: B  357 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7676 (tmm-80)
REVERT: B  465 GLU cc_start: 0.8305 (tt0) cc_final: 0.8028 (tt0)
REVERT: B  469 SER cc_start: 0.9150 (t) cc_final: 0.8806 (p)
REVERT: B  472 ILE cc_start: 0.8768 (mm) cc_final: 0.8354 (tp)
REVERT: B  498 GLN cc_start: 0.8414 (mt0) cc_final: 0.8039 (mt0)
REVERT: B  501 ASN cc_start: 0.8528 (m110) cc_final: 0.7992 (m110)
REVERT: C    2 VAL cc_start: 0.7334 (OUTLIER) cc_final: 0.6865 (m)
REVERT: C   27 PHE cc_start: 0.8960 (m-80) cc_final: 0.8319 (m-80)
REVERT: C   31 TYR cc_start: 0.8373 (m-80) cc_final: 0.8163 (m-80)
REVERT: C   73 ASP cc_start: 0.8679 (m-30) cc_final: 0.7373 (m-30)
REVERT: C   76 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7877 (mtmm)
REVERT: C   80 TYR cc_start: 0.7959 (m-80) cc_final: 0.7660 (m-80)
REVERT: C   87 LYS cc_start: 0.8015 (mmtp) cc_final: 0.7699 (mmmt)
REVERT: C   91 THR cc_start: 0.8429 (p) cc_final: 0.8025 (p)
REVERT: C  124 THR cc_start: 0.8100 (p) cc_final: 0.7797 (p)
REVERT: A    3 GLN cc_start: 0.8128 (pt0) cc_final: 0.7839 (pm20)
REVERT: A  100 MET cc_start: 0.8193 (mmm) cc_final: 0.7255 (mtm)
  outliers start: 13
  outliers final: 4
  residues processed: 134
  average time/residue: 0.2073
  time to fit residues: 32.0329
Evaluate side-chains
  122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 117
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 16 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0040
   chunk 41 optimal weight:    0.0870
   chunk 36 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.5572

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

Flipped N/Q/H residues before XYZ refinement:
C  39 GLN
A  39 GLN
A 118 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.126803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.107795 restraints weight = 5574.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3305 rms_B_bonded: 3.62
r_work: 0.3170 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.3376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   3575  Z= 0.159
  Angle     :  0.574   7.434   4848  Z= 0.296
  Chirality :  0.043   0.149    501
  Planarity :  0.003   0.029    633
  Dihedral  :  3.949  16.875    500
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.02 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.39), residues: 442
  helix: -3.71 (0.87), residues: 20
  sheet:  1.79 (0.44), residues: 130
  loop : -0.35 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 436 
 HIS   0.001   0.000   HIS C 114 
 PHE   0.006   0.001   PHE B 392 
 TYR   0.018   0.001   TYR C  32 
 ARG   0.003   0.001   ARG B 408 

*********************** 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
  126 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8216 (mp0)
REVERT: B  357 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7789 (tmm160)
REVERT: B  465 GLU cc_start: 0.8297 (tt0) cc_final: 0.8019 (tt0)
REVERT: B  469 SER cc_start: 0.9195 (t) cc_final: 0.8897 (p)
REVERT: B  498 GLN cc_start: 0.8437 (mt0) cc_final: 0.8009 (mt0)
REVERT: B  501 ASN cc_start: 0.8583 (m110) cc_final: 0.8062 (m110)
REVERT: C   67 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8293 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8579 (m-30) cc_final: 0.7243 (m-30)
REVERT: C   76 LYS cc_start: 0.8259 (mmmt) cc_final: 0.7853 (mtmm)
REVERT: C   80 TYR cc_start: 0.7981 (m-80) cc_final: 0.7674 (m-80)
REVERT: C   87 LYS cc_start: 0.7991 (mmtp) cc_final: 0.7680 (mmmt)
REVERT: C   91 THR cc_start: 0.8393 (p) cc_final: 0.8054 (p)
REVERT: C  108 TYR cc_start: 0.8273 (m-80) cc_final: 0.8010 (m-80)
REVERT: A    3 GLN cc_start: 0.8142 (pt0) cc_final: 0.7882 (pm20)
REVERT: A   89 ASP cc_start: 0.8455 (m-30) cc_final: 0.7690 (t0)
  outliers start: 8
  outliers final: 7
  residues processed: 124
  average time/residue: 0.2083
  time to fit residues: 30.0557
Evaluate side-chains
  120 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
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  478 THR
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 24 optimal weight:    6.9990
   chunk 30 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 33 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN
** A  39 GLN ** 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 = 0.3516 r_free = 0.3516 target = 0.122704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.103811 restraints weight = 5709.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3253 rms_B_bonded: 3.60
r_work: 0.3117 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3575  Z= 0.222
  Angle     :  0.589   9.015   4848  Z= 0.304
  Chirality :  0.044   0.183    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.975  16.911    500
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.17 %
    Favored  : 80.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.39), residues: 442
  helix: -3.27 (1.08), residues: 21
  sheet:  1.83 (0.44), residues: 128
  loop : -0.42 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.007   0.001   PHE B 392 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.003   0.000   ARG A  99 

*********************** 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: 11
    poor density    : 116
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8220 (mp0)
REVERT: B  357 ARG cc_start: 0.8254 (ttp80) cc_final: 0.7730 (tmm160)
REVERT: B  406 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8299 (mt-10)
REVERT: B  466 ARG cc_start: 0.8002 (ptm160) cc_final: 0.7766 (ptm160)
REVERT: B  469 SER cc_start: 0.9206 (t) cc_final: 0.8991 (p)
REVERT: B  472 ILE cc_start: 0.8697 (mm) cc_final: 0.8337 (tp)
REVERT: B  498 GLN cc_start: 0.8415 (mt0) cc_final: 0.8073 (mt0)
REVERT: B  501 ASN cc_start: 0.8618 (m110) cc_final: 0.8115 (m110)
REVERT: C   59 LYS cc_start: 0.7693 (mtpt) cc_final: 0.7480 (mtpt)
REVERT: C   67 ARG cc_start: 0.8643 (mtm-85) cc_final: 0.8364 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8593 (m-30) cc_final: 0.7351 (m-30)
REVERT: C   76 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7918 (mtmm)
REVERT: C   80 TYR cc_start: 0.8061 (m-80) cc_final: 0.7783 (m-80)
REVERT: C   87 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7709 (mmmt)
REVERT: C   91 THR cc_start: 0.8513 (p) cc_final: 0.8220 (p)
REVERT: C  125 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8570 (tm-30)
REVERT: A    3 GLN cc_start: 0.8179 (pt0) cc_final: 0.7673 (pm20)
REVERT: A    5 GLN cc_start: 0.7608 (mp10) cc_final: 0.7090 (mp10)
REVERT: A   19 ARG cc_start: 0.8553 (mpp80) cc_final: 0.8219 (mpp80)
REVERT: A   89 ASP cc_start: 0.8560 (m-30) cc_final: 0.7817 (t0)
REVERT: A  100 MET cc_start: 0.8316 (mmm) cc_final: 0.7234 (mtm)
  outliers start: 11
  outliers final: 11
  residues processed: 124
  average time/residue: 0.2232
  time to fit residues: 31.8368
Evaluate side-chains
  122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  349 SER
Chi-restraints excluded: chain B residue  383 SER
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
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain A residue   53 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 16 optimal weight:    0.1980
   chunk 33 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0470
   chunk 38 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   chunk 7 optimal weight:    4.9990
   chunk 26 optimal weight:    0.3980
   overall best weight:    0.4680

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

Flipped N/Q/H residues before XYZ refinement:
B 474 GLN
C   3 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 = 0.3578 r_free = 0.3578 target = 0.127988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.109512 restraints weight = 5681.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 3.57
r_work: 0.3183 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3183
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   3575  Z= 0.144
  Angle     :  0.546   8.116   4848  Z= 0.277
  Chirality :  0.042   0.148    501
  Planarity :  0.003   0.029    633
  Dihedral  :  3.668  14.371    500
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 16.71 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.39), residues: 442
  helix: -2.94 (1.07), residues: 21
  sheet:  1.91 (0.44), residues: 128
  loop : -0.37 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 436 
 HIS   0.001   0.001   HIS B 519 
 PHE   0.010   0.001   PHE B 392 
 TYR   0.018   0.001   TYR C  32 
 ARG   0.002   0.000   ARG A  31 

*********************** 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
  128 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8209 (mp0)
REVERT: B  357 ARG cc_start: 0.8233 (ttp80) cc_final: 0.7762 (tmm160)
REVERT: B  457 ARG cc_start: 0.8058 (ttt180) cc_final: 0.7789 (ttt-90)
REVERT: B  469 SER cc_start: 0.9164 (t) cc_final: 0.8932 (p)
REVERT: B  472 ILE cc_start: 0.8648 (mm) cc_final: 0.8297 (tp)
REVERT: B  498 GLN cc_start: 0.8355 (mt0) cc_final: 0.7986 (mt0)
REVERT: B  501 ASN cc_start: 0.8508 (m110) cc_final: 0.7980 (m110)
REVERT: C   27 PHE cc_start: 0.8955 (m-80) cc_final: 0.8704 (m-80)
REVERT: C   67 ARG cc_start: 0.8608 (mtm-85) cc_final: 0.8344 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8445 (m-30) cc_final: 0.7286 (m-30)
REVERT: C   76 LYS cc_start: 0.8275 (mmmt) cc_final: 0.7846 (mtmm)
REVERT: C   80 TYR cc_start: 0.7973 (m-10) cc_final: 0.7710 (m-80)
REVERT: C   87 LYS cc_start: 0.7946 (mmtp) cc_final: 0.7586 (mmmt)
REVERT: C   91 THR cc_start: 0.8521 (p) cc_final: 0.8260 (p)
REVERT: A    3 GLN cc_start: 0.8190 (pt0) cc_final: 0.7713 (pm20)
REVERT: A   19 ARG cc_start: 0.8474 (mpp80) cc_final: 0.8181 (mpp80)
REVERT: A   89 ASP cc_start: 0.8504 (m-30) cc_final: 0.7825 (t0)
REVERT: A  100 MET cc_start: 0.8195 (mmm) cc_final: 0.7046 (mtm)
  outliers start: 11
  outliers final: 8
  residues processed: 124
  average time/residue: 0.2012
  time to fit residues: 29.0510
Evaluate side-chains
  120 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 112
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  375 SER
Chi-restraints excluded: chain B residue  420 ASP
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  124 THR
Chi-restraints excluded: chain A residue   53 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 37 optimal weight:    0.4980
   chunk 36 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 28 optimal weight:   10.0000
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
B 460 ASN
A  39 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.125457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.106590 restraints weight = 5762.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 3.65
r_work: 0.3154 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.4053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   3575  Z= 0.161
  Angle     :  0.552   7.178   4848  Z= 0.281
  Chirality :  0.042   0.147    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.603  12.959    500
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 17.52 %
    Favored  : 78.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.39), residues: 442
  helix: -2.83 (1.09), residues: 21
  sheet:  2.01 (0.44), residues: 127
  loop : -0.35 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 436 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.007   0.001   PHE B 392 
 TYR   0.016   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A  99 

*********************** 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
  127 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8203 (mp0)
REVERT: B  357 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7620 (ttp80)
REVERT: B  472 ILE cc_start: 0.8670 (mm) cc_final: 0.8336 (tp)
REVERT: B  498 GLN cc_start: 0.8373 (mt0) cc_final: 0.8012 (mt0)
REVERT: B  501 ASN cc_start: 0.8558 (m110) cc_final: 0.8078 (m110)
REVERT: C   73 ASP cc_start: 0.8431 (m-30) cc_final: 0.7725 (m-30)
REVERT: C   87 LYS cc_start: 0.7979 (mmtp) cc_final: 0.7640 (mmmt)
REVERT: C   91 THR cc_start: 0.8532 (p) cc_final: 0.8297 (p)
REVERT: A    3 GLN cc_start: 0.8216 (pt0) cc_final: 0.7675 (pm20)
REVERT: A    5 GLN cc_start: 0.7539 (mp10) cc_final: 0.7010 (mp10)
REVERT: A   19 ARG cc_start: 0.8492 (mpp80) cc_final: 0.8179 (mpp80)
REVERT: A   64 LYS cc_start: 0.9130 (ttmt) cc_final: 0.8786 (mtpt)
REVERT: A   89 ASP cc_start: 0.8542 (m-30) cc_final: 0.7863 (t0)
  outliers start: 14
  outliers final: 13
  residues processed: 122
  average time/residue: 0.2056
  time to fit residues: 29.1667
Evaluate side-chains
  120 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  420 ASP
Chi-restraints excluded: chain B residue  430 THR
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   24 VAL
Chi-restraints excluded: chain C residue  124 THR
Chi-restraints excluded: chain A residue   53 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 22 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   overall best weight:    1.3788

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.122848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.104117 restraints weight = 5684.876|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 3.56
r_work: 0.3122 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.4192

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   3575  Z= 0.228
  Angle     :  0.642  11.571   4848  Z= 0.320
  Chirality :  0.043   0.148    501
  Planarity :  0.004   0.051    633
  Dihedral  :  4.032  22.609    500
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 17.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.39), residues: 442
  helix: -2.74 (1.15), residues: 21
  sheet:  1.95 (0.45), residues: 127
  loop : -0.42 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 105 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.007   0.001   PHE C  68 
 TYR   0.017   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A  99 

*********************** 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
  126 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8249 (mp0)
REVERT: B  357 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7746 (tmm160)
REVERT: B  498 GLN cc_start: 0.8365 (mt0) cc_final: 0.8073 (mt0)
REVERT: B  501 ASN cc_start: 0.8616 (m110) cc_final: 0.8158 (m110)
REVERT: C   67 ARG cc_start: 0.8585 (mtm-85) cc_final: 0.8096 (mtm-85)
REVERT: C   73 ASP cc_start: 0.8461 (m-30) cc_final: 0.7875 (m-30)
REVERT: C   76 LYS cc_start: 0.8318 (mmmt) cc_final: 0.7899 (mtmm)
REVERT: C   87 LYS cc_start: 0.8021 (mmtp) cc_final: 0.7685 (mmmt)
REVERT: C   91 THR cc_start: 0.8617 (p) cc_final: 0.8394 (p)
REVERT: A    5 GLN cc_start: 0.7593 (mp10) cc_final: 0.7062 (mp10)
REVERT: A   19 ARG cc_start: 0.8544 (mpp80) cc_final: 0.8238 (mpp80)
REVERT: A   64 LYS cc_start: 0.9144 (ttmt) cc_final: 0.8798 (mtpt)
REVERT: A   89 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7905 (t0)
REVERT: A  100 MET cc_start: 0.8359 (mmm) cc_final: 0.7252 (mtm)
  outliers start: 17
  outliers final: 13
  residues processed: 120
  average time/residue: 0.2363
  time to fit residues: 33.6498
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  : 0.507 
-------------------------------------------------------------------------------
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  420 ASP
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 43
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0770
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    6.9990
   chunk 5 optimal weight:    4.9990
   chunk 6 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
A   3 GLN
** A  39 GLN ** 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 = 0.3528 r_free = 0.3528 target = 0.124174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.105047 restraints weight = 5725.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 3.65
r_work: 0.3134 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.4333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3575  Z= 0.196
  Angle     :  0.615   8.941   4848  Z= 0.308
  Chirality :  0.043   0.148    501
  Planarity :  0.003   0.033    633
  Dihedral  :  3.942  22.747    500
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 18.60 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.26 (0.40), residues: 442
  helix: -2.91 (1.06), residues: 21
  sheet:  1.89 (0.46), residues: 128
  loop : -0.40 (0.36), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 105 
 HIS   0.001   0.001   HIS C 114 
 PHE   0.009   0.001   PHE C  68 
 TYR   0.015   0.001   TYR C  32 
 ARG   0.006   0.000   ARG A  99 

*********************** 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
  126 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8255 (mp0)
REVERT: B  357 ARG cc_start: 0.8256 (ttp80) cc_final: 0.7612 (ttp80)
REVERT: B  466 ARG cc_start: 0.8165 (ptm160) cc_final: 0.7596 (ptm160)
REVERT: B  498 GLN cc_start: 0.8325 (mt0) cc_final: 0.8040 (mt0)
REVERT: B  501 ASN cc_start: 0.8592 (m110) cc_final: 0.8061 (m110)
REVERT: C   73 ASP cc_start: 0.8411 (m-30) cc_final: 0.7743 (m-30)
REVERT: C   87 LYS cc_start: 0.8002 (mmtp) cc_final: 0.7657 (mmmt)
REVERT: C   91 THR cc_start: 0.8657 (p) cc_final: 0.8452 (p)
REVERT: A    3 GLN cc_start: 0.8459 (pt0) cc_final: 0.7755 (pm20)
REVERT: A    5 GLN cc_start: 0.7620 (mp10) cc_final: 0.7082 (mp10)
REVERT: A   19 ARG cc_start: 0.8537 (mpp80) cc_final: 0.8217 (mpp80)
REVERT: A   64 LYS cc_start: 0.9128 (ttmt) cc_final: 0.8791 (mtpt)
REVERT: A   89 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7914 (t0)
REVERT: A  100 MET cc_start: 0.8308 (mmm) cc_final: 0.7192 (mtm)
  outliers start: 18
  outliers final: 15
  residues processed: 119
  average time/residue: 0.2104
  time to fit residues: 29.4888
Evaluate side-chains
  122 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
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  385 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  445 VAL
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 C residue   11 LEU
Chi-restraints excluded: chain C residue   24 VAL
Chi-restraints excluded: chain C residue  124 THR
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 29 optimal weight:    1.9990
   chunk 40 optimal weight:    6.9990
   chunk 26 optimal weight:    5.9990
   chunk 7 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0270
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.3844

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.121723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102959 restraints weight = 5776.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 3.56
r_work: 0.3087 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.4343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3575  Z= 0.220
  Angle     :  0.620   8.534   4848  Z= 0.314
  Chirality :  0.043   0.148    501
  Planarity :  0.003   0.025    633
  Dihedral  :  3.877  15.346    500
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.85 %
    Allowed  : 17.79 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.18 (0.40), residues: 442
  helix: -2.89 (1.09), residues: 21
  sheet:  1.76 (0.46), residues: 128
  loop : -0.41 (0.35), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 105 
 HIS   0.001   0.001   HIS C 114 
 PHE   0.013   0.001   PHE C  68 
 TYR   0.014   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A  99 

*********************** 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
  124 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 0.371 
Fit side-chains
REVERT: B  340 GLU cc_start: 0.8890 (mm-30) cc_final: 0.8254 (mp0)
REVERT: B  357 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7752 (tmm160)
REVERT: B  406 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8269 (mt-10)
REVERT: B  501 ASN cc_start: 0.8597 (m110) cc_final: 0.8078 (m110)
REVERT: C   59 LYS cc_start: 0.7719 (mtpt) cc_final: 0.7389 (mtpt)
REVERT: C   67 ARG cc_start: 0.8588 (mtm-85) cc_final: 0.8058 (ptp90)
REVERT: C   73 ASP cc_start: 0.8461 (m-30) cc_final: 0.7706 (m-30)
REVERT: C   87 LYS cc_start: 0.8028 (mmtp) cc_final: 0.7688 (mmmt)
REVERT: A    5 GLN cc_start: 0.7694 (mp10) cc_final: 0.7400 (mp10)
REVERT: A   19 ARG cc_start: 0.8550 (mpp80) cc_final: 0.8238 (mpp80)
REVERT: A   64 LYS cc_start: 0.9156 (ttmt) cc_final: 0.8828 (mtpt)
REVERT: A   89 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7914 (t0)
REVERT: A  100 MET cc_start: 0.8352 (mmm) cc_final: 0.7246 (mtm)
  outliers start: 18
  outliers final: 16
  residues processed: 116
  average time/residue: 0.2060
  time to fit residues: 27.6883
Evaluate side-chains
  123 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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  385 THR
Chi-restraints excluded: chain B residue  392 PHE
Chi-restraints excluded: chain B residue  445 VAL
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  124 THR
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 37 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    5.9990
   chunk 13 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 30 optimal weight:    0.4980
   chunk 36 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
C  39 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 = 0.3510 r_free = 0.3510 target = 0.123148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.104104 restraints weight = 5797.262|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 3.65
r_work: 0.3118 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3575  Z= 0.180
  Angle     :  0.617   8.345   4848  Z= 0.313
  Chirality :  0.042   0.148    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.742  15.721    500
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.14 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.40), residues: 442
  helix: -3.33 (0.83), residues: 27
  sheet:  1.65 (0.46), residues: 130
  loop : -0.40 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 105 
 HIS   0.000   0.000   HIS B 519 
 PHE   0.007   0.001   PHE B 392 
 TYR   0.014   0.001   TYR C  32 
 ARG   0.008   0.000   ARG A  99 

********************** 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
  126 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 110
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  340 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8266 (mp0)
REVERT: B  357 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7660 (ttp80)
REVERT: B  406 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8235 (mt-10)
REVERT: B  466 ARG cc_start: 0.7957 (ptm160) cc_final: 0.7699 (ptm160)
REVERT: B  501 ASN cc_start: 0.8629 (m110) cc_final: 0.8081 (m110)
REVERT: C   59 LYS cc_start: 0.7689 (mtpt) cc_final: 0.7452 (mtpt)
REVERT: C   60 TYR cc_start: 0.8266 (m-80) cc_final: 0.8001 (m-80)
REVERT: C   67 ARG cc_start: 0.8634 (mtm-85) cc_final: 0.8108 (ptp90)
REVERT: C   68 PHE cc_start: 0.9241 (m-10) cc_final: 0.9034 (m-10)
REVERT: C   73 ASP cc_start: 0.8444 (m-30) cc_final: 0.8107 (m-30)
REVERT: C   87 LYS cc_start: 0.8041 (mmtp) cc_final: 0.7697 (mmmt)
REVERT: A    5 GLN cc_start: 0.7784 (mp10) cc_final: 0.7306 (mp10)
REVERT: A   19 ARG cc_start: 0.8516 (mpp80) cc_final: 0.8196 (mpp80)
REVERT: A   64 LYS cc_start: 0.9148 (ttmt) cc_final: 0.8817 (mtpt)
REVERT: A   75 LYS cc_start: 0.8881 (mtpt) cc_final: 0.8518 (mtpt)
REVERT: A   89 ASP cc_start: 0.8526 (OUTLIER) cc_final: 0.7866 (t0)
REVERT: A  100 MET cc_start: 0.8270 (mmm) cc_final: 0.7195 (mtm)
  outliers start: 16
  outliers final: 14
  residues processed: 119
  average time/residue: 0.2092
  time to fit residues: 28.9035
Evaluate side-chains
  125 residues out of total 371 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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  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   24 VAL
Chi-restraints excluded: chain C residue  124 THR
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 0 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    9.9990
   chunk 6 optimal weight:    6.9990
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9990
   chunk 11 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 41 optimal weight:    0.6980
   chunk 14 optimal weight:    7.9990
   overall best weight:    1.2184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.122326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.103624 restraints weight = 5843.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 3.59
r_work: 0.3094 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.4413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3575  Z= 0.207
  Angle     :  0.617   8.332   4848  Z= 0.313
  Chirality :  0.043   0.152    501
  Planarity :  0.003   0.027    633
  Dihedral  :  3.779  15.282    500
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  4.58 %
    Allowed  : 18.87 %
    Favored  : 76.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.40), residues: 442
  helix: -3.30 (0.85), residues: 27
  sheet:  1.64 (0.47), residues: 130
  loop : -0.44 (0.36), residues: 285

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 105 
 HIS   0.001   0.000   HIS C 114 
 PHE   0.007   0.001   PHE A  29 
 TYR   0.014   0.001   TYR C  32 
 ARG   0.004   0.000   ARG A  99 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2213.01 seconds
wall clock time: 38 minutes 52.02 seconds (2332.02 seconds total)