Starting phenix.real_space_refine
on Sat Apr 26 23:10:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygu_39264/04_2025/8ygu_39264_neut.cif"
  }
  resolution = 3.13
  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=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      11      5.16       5
     C    2353      2.51       5
     N     617      2.21       5
     O     712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3693
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 117
          Classifications: {'peptide': 15}
          Link IDs: {'TRANS': 14}
    Chain: "B"
      Number of atoms: 1726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 216, 1726
          Classifications: {'peptide': 216}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 207}
    Chain: "C"
      Number of atoms: 152
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 152
          Classifications: {'peptide': 22}
          Link IDs: {'PTRANS': 2, 'TRANS': 19}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 880
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 818
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
  Residues with excluded nonbonded symmetry interactions: 9
    residue:
      pdb=" N   SER H  17 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  17 " occ=0.50
    residue:
      pdb=" N   SER H  61 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  61 " occ=0.50
    residue:
      pdb=" N   MET L  11 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET L  11 " occ=0.50
    residue:
      pdb=" N   ARG L  18 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  18 " occ=0.50
    residue:
      pdb=" N   GLN L  27 " occ=0.83
      ... (7 atoms not shown)
      pdb=" NE2 GLN L  27 " occ=0.83
    residue:
      pdb=" N   SER L  43 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  43 " occ=0.50
    residue:
      pdb=" N   SER L  50 " occ=0.90
      ... (4 atoms not shown)
      pdb=" OG  SER L  50 " occ=0.90
    residue:
      pdb=" N   SER L  67 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  67 " occ=0.50
    residue:
      pdb=" N   GLU L 105 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU L 105 " occ=0.50
  Time building chain proxies: 2.97, per 1000 atoms: 0.80
  Number of scatterers: 3693
  At special positions: 0
  Unit cell: (68.076, 90.036, 96.624, 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      11     16.00
     O     712      8.00
     N     617      7.00
     C    2353      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.05
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.04

  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: 0.69
  Conformation dependent library (CDL) restraints added in 418.1 milliseconds
  

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  866

  Finding SS restraints...
    Secondary structure from input PDB file:
      1 helices and 10 sheets defined
      1.1% alpha, 50.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'B' and resid 361 through 365
      removed outlier: 4.155A  pdb=" N   VAL B 365 " --> pdb=" O   PHE B 362 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 423
      removed outlier: 4.481A  pdb=" N   VAL B 409 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 4.969A  pdb=" N   ARG B 427 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   VAL B 409 " --> pdb=" O   ARG B 425 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ARG B 425 " --> pdb=" O   VAL B 409 " (cutoff:3.500A)
      removed outlier: 4.804A  pdb=" N   LEU B 411 " --> pdb=" O   SER B 423 " (cutoff:3.500A)
      removed outlier: 6.996A  pdb=" N   SER B 423 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   THR B 413 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 421 " --> pdb=" O   THR B 413 " (cutoff:3.500A)
      removed outlier: 12.048A  pdb=" N   ASN B 422 " --> pdb=" O   ASP B 357 " (cutoff:3.500A)
      removed outlier: 9.332A  pdb=" N   ASP B 357 " --> pdb=" O   ASN B 422 " (cutoff:3.500A)
      removed outlier: 4.583A  pdb=" N   LEU B 424 " --> pdb=" O   TYR B 355 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   VAL B 351 " --> pdb=" O   PHE B 428 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TRP B 356 " --> pdb=" O   HIS B 315 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 420 through 423
      removed outlier: 4.481A  pdb=" N   VAL B 409 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   VAL B 378 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 275
      removed outlier: 3.596A  pdb=" N   ILE B 271 " --> pdb=" O   GLY B 466 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   LEU B 473 " --> pdb=" O   VAL B 368 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   VAL B 368 " --> pdb=" O   LEU B 473 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 279 through 283
      removed outlier: 3.616A  pdb=" N   GLU B 293 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   GLU B 293 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   PHE B 342 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   SER B 295 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   VAL B 344 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   SER B 340 " --> pdb=" O   PHE B 328 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   PHE B 328 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 279 through 283
      removed outlier: 3.616A  pdb=" N   GLU B 293 " --> pdb=" O   ILE B 282 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   GLU B 293 " --> pdb=" O   SER B 340 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   PHE B 342 " --> pdb=" O   GLU B 293 " (cutoff:3.500A)
      removed outlier: 7.228A  pdb=" N   SER B 295 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 8.776A  pdb=" N   VAL B 344 " --> pdb=" O   SER B 295 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 384 through 386
    Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AA8, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.788A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   MET H  50 " --> pdb=" O   VAL H  34 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   VAL H  34 " --> pdb=" O   MET H  50 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6
      removed outlier: 6.152A  pdb=" N   THR L  69 " --> pdb=" O   ALA L  25 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.403A  pdb=" N   MET L  11 " --> pdb=" O   GLU L 105 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   TYR L  87 " --> pdb=" O   TYR L  36 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA L  34 " --> pdb=" O   GLN L  89 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)

    136 hydrogen bonds defined for protein.
    354 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: 0.90

  Time building geometry restraints manager: 0.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1163
        1.34 -     1.46: 975
        1.46 -     1.58: 1627
        1.58 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3781
  Sorted by residual:
  bond pdb=" C   GLN L  42 "
       pdb=" N   SER L  43 "
    ideal  model  delta    sigma   weight residual
    1.331  1.359 -0.028 1.59e-02 3.96e+03 3.11e+00
  bond pdb=" CG  ARG B 269 "
       pdb=" CD  ARG B 269 "
    ideal  model  delta    sigma   weight residual
    1.520  1.481  0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" CA  GLU B 347 "
       pdb=" C   GLU B 347 "
    ideal  model  delta    sigma   weight residual
    1.523  1.540 -0.017 1.34e-02 5.57e+03 1.67e+00
  bond pdb=" CB  PRO B 435 "
       pdb=" CG  PRO B 435 "
    ideal  model  delta    sigma   weight residual
    1.506  1.456  0.050 3.90e-02 6.57e+02 1.66e+00
  bond pdb=" CG  LEU B 375 "
       pdb=" CD1 LEU B 375 "
    ideal  model  delta    sigma   weight residual
    1.521  1.479  0.042 3.30e-02 9.18e+02 1.59e+00
  ... (remaining 3776 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 4983
        2.38 -     4.77: 127
        4.77 -     7.15: 17
        7.15 -     9.54: 1
        9.54 -    11.92: 1
  Bond angle restraints: 5129
  Sorted by residual:
  angle pdb=" C   GLN L  42 "
        pdb=" N   SER L  43 "
        pdb=" CA  SER L  43 "
      ideal   model   delta    sigma   weight residual
     122.38  134.30  -11.92 2.90e+00 1.19e-01 1.69e+01
  angle pdb=" N   GLY H  54 "
        pdb=" CA  GLY H  54 "
        pdb=" C   GLY H  54 "
      ideal   model   delta    sigma   weight residual
     112.82  107.98    4.84 1.38e+00 5.25e-01 1.23e+01
  angle pdb=" N   LYS B 346 "
        pdb=" CA  LYS B 346 "
        pdb=" C   LYS B 346 "
      ideal   model   delta    sigma   weight residual
     107.61  113.44   -5.83 1.74e+00 3.30e-01 1.12e+01
  angle pdb=" C   LYS B 346 "
        pdb=" N   GLU B 347 "
        pdb=" CA  GLU B 347 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" N   TYR L  55 "
        pdb=" CA  TYR L  55 "
        pdb=" C   TYR L  55 "
      ideal   model   delta    sigma   weight residual
     110.46  105.79    4.67 1.48e+00 4.57e-01 9.95e+00
  ... (remaining 5124 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.97: 2086
       13.97 -    27.93: 96
       27.93 -    41.90: 16
       41.90 -    55.87: 3
       55.87 -    69.83: 1
  Dihedral angle restraints: 2202
    sinusoidal: 845
      harmonic: 1357
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  145.02  -52.02     1      1.00e+01 1.00e-02 3.69e+01
  dihedral pdb=" CA  ASN B 456 "
           pdb=" C   ASN B 456 "
           pdb=" N   ASN B 457 "
           pdb=" CA  ASN B 457 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.23   24.77     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  LYS B 346 "
           pdb=" C   LYS B 346 "
           pdb=" N   GLU B 347 "
           pdb=" CA  GLU B 347 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 343
       0.041 -    0.082: 147
       0.082 -    0.123: 45
       0.123 -    0.164: 25
       0.164 -    0.205: 5
  Chirality restraints: 565
  Sorted by residual:
  chirality pdb=" CB  VAL B 320 "
            pdb=" CA  VAL B 320 "
            pdb=" CG1 VAL B 320 "
            pdb=" CG2 VAL B 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ILE B 294 "
            pdb=" N   ILE B 294 "
            pdb=" C   ILE B 294 "
            pdb=" CB  ILE B 294 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 8.83e-01
  chirality pdb=" CB  ILE B 271 "
            pdb=" CA  ILE B 271 "
            pdb=" CG1 ILE B 271 "
            pdb=" CG2 ILE B 271 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.00e-01
  ... (remaining 562 not shown)

  Planarity restraints: 653
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 333 "   -0.036 5.00e-02 4.00e+02   5.38e-02 4.63e+00
        pdb=" N   PRO C 334 "    0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 334 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO C 334 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L  43 "   -0.032 5.00e-02 4.00e+02   4.87e-02 3.79e+00
        pdb=" N   PRO L  44 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO L  44 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO L  44 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS L  39 "   -0.031 5.00e-02 4.00e+02   4.74e-02 3.60e+00
        pdb=" N   PRO L  40 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO L  40 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO L  40 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 650 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 195
        2.72 -     3.27: 2952
        3.27 -     3.81: 5378
        3.81 -     4.36: 6219
        4.36 -     4.90: 11619
  Nonbonded interactions: 26363
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG L  54 "
            pdb=" OD1 ASP L  60 "
     model   vdw
     2.179 3.120
  nonbonded pdb=" OD2 ASP B 270 "
            pdb=" OG1 THR L  94 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" O   ASN H  53 "
            pdb=" NZ  LYS H  71 "
     model   vdw
     2.324 3.120
  nonbonded pdb=" NZ  LYS H   5 "
            pdb=" OE1 GLN H 109 "
     model   vdw
     2.378 3.120
  nonbonded pdb=" O   SER B 476 "
            pdb=" OG  SER B 476 "
     model   vdw
     2.458 3.040
  ... (remaining 26358 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=0.50 max=1.00 mean=0.99
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:             1.990
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     12.800
  Find NCS groups from input model:        0.040
  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:2.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7549
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      :  0.006   0.055   3783  Z= 0.258
  Angle     :  0.923  11.923   5133  Z= 0.513
  Chirality :  0.057   0.205    565
  Planarity :  0.007   0.054    653
  Dihedral  :  8.810  69.834   1330
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 1.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -3.27 (0.34), residues: 460
  helix: -5.53 (0.22), residues: 9
  sheet: -0.96 (0.35), residues: 221
  loop : -3.38 (0.28), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.004   TRP H  52 
 HIS   0.007   0.002   HIS L  91 
 PHE   0.031   0.003   PHE B 362 
 TYR   0.020   0.002   TYR H  93 
 ARG   0.005   0.001   ARG B 274 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.29186 (  122)
  hydrogen bonds       : angle       9.02655 (  354)
  SS BOND              : bond        0.01342 (    2)
  SS BOND              : angle       1.48630 (    4)
  covalent geometry    : bond        0.00574 ( 3781)
  covalent geometry    : angle       0.92291 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: B  280 THR cc_start: 0.8341 (m) cc_final: 0.7951 (p)
REVERT: H   50 MET cc_start: 0.8136 (ttt) cc_final: 0.7816 (ttp)
REVERT: H  112 THR cc_start: 0.8145 (t) cc_final: 0.7721 (m)
REVERT: L   45 LYS cc_start: 0.7018 (mmtp) cc_final: 0.6760 (mmtp)
  outliers start: 0
  outliers final: 0
  residues processed: 91
  average time/residue: 0.1692
  time to fit residues: 18.7298
Evaluate side-chains
  67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 18 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 35 optimal weight:    0.0010
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.3980
   chunk 26 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 22 optimal weight:    0.8980
   overall best weight:    0.4986

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

Flipped N/Q/H residues before XYZ refinement:
A 414 GLN
B 266 GLN
B 302 GLN
B 324 ASN
B 374 ASN
B 414 GLN
C 329 ASN
H  73 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.112006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.094094 restraints weight = 5738.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3105 rms_B_bonded: 1.84
r_work: 0.3008 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2874 r_free = 0.2874    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2874
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3783  Z= 0.165
  Angle     :  0.625   6.070   5133  Z= 0.336
  Chirality :  0.047   0.187    565
  Planarity :  0.005   0.039    653
  Dihedral  :  5.777  30.886    511
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  7.09 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.37), residues: 460
  helix:  None (None), residues: 0
  sheet: -0.10 (0.35), residues: 234
  loop : -2.96 (0.33), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP H 107 
 HIS   0.005   0.002   HIS L   8 
 PHE   0.019   0.002   PHE C 337 
 TYR   0.015   0.002   TYR B 305 
 ARG   0.004   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04706 (  122)
  hydrogen bonds       : angle       5.56220 (  354)
  SS BOND              : bond        0.00904 (    2)
  SS BOND              : angle       1.37679 (    4)
  covalent geometry    : bond        0.00401 ( 3781)
  covalent geometry    : angle       0.62402 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 70
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8119 (t0) cc_final: 0.7807 (t0)
REVERT: H    4 LEU cc_start: 0.7928 (mp) cc_final: 0.7671 (mt)
REVERT: H   20 ILE cc_start: 0.7453 (OUTLIER) cc_final: 0.7245 (mt)
REVERT: H   50 MET cc_start: 0.8415 (ttt) cc_final: 0.8195 (ttp)
REVERT: H  105 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7948 (m-30)
REVERT: H  112 THR cc_start: 0.8411 (t) cc_final: 0.8019 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 73
  average time/residue: 0.1409
  time to fit residues: 12.9860
Evaluate side-chains
  67 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 61
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue  105 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   chunk 41 optimal weight:    3.9990
   chunk 38 optimal weight:    0.3980
   chunk 44 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 34 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 414 GLN
L  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.090135 restraints weight = 5714.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 1.93
r_work: 0.2938 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2812
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2812 r_free = 0.2812    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2812
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3783  Z= 0.192
  Angle     :  0.633   5.073   5133  Z= 0.340
  Chirality :  0.047   0.146    565
  Planarity :  0.005   0.037    653
  Dihedral  :  5.703  31.743    511
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  :  8.07 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.19 (0.33), residues: 239
  loop : -2.74 (0.36), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 356 
 HIS   0.005   0.002   HIS L  91 
 PHE   0.020   0.002   PHE C 337 
 TYR   0.016   0.002   TYR L  86 
 ARG   0.003   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04945 (  122)
  hydrogen bonds       : angle       5.23541 (  354)
  SS BOND              : bond        0.00893 (    2)
  SS BOND              : angle       1.34138 (    4)
  covalent geometry    : bond        0.00470 ( 3781)
  covalent geometry    : angle       0.63187 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 66
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8114 (t0) cc_final: 0.7646 (t0)
REVERT: B  388 SER cc_start: 0.8788 (t) cc_final: 0.8516 (p)
REVERT: B  414 GLN cc_start: 0.8413 (tt0) cc_final: 0.8201 (tt0)
REVERT: H    4 LEU cc_start: 0.7955 (mp) cc_final: 0.7667 (mt)
REVERT: H   50 MET cc_start: 0.8430 (ttt) cc_final: 0.8155 (ttp)
REVERT: H  105 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7915 (m-30)
REVERT: H  112 THR cc_start: 0.8313 (t) cc_final: 0.7943 (m)
REVERT: L   45 LYS cc_start: 0.7459 (mmtp) cc_final: 0.7148 (mmtp)
  outliers start: 14
  outliers final: 11
  residues processed: 73
  average time/residue: 0.1498
  time to fit residues: 13.7735
Evaluate side-chains
  78 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue  105 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 26 optimal weight:    0.5980
   chunk 31 optimal weight:    0.6980
   chunk 13 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.2980
   chunk 36 optimal weight:    0.0770
   overall best weight:    0.3538

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.111368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.092031 restraints weight = 5723.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.98
r_work: 0.2963 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2841
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2841 r_free = 0.2841    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2841
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   3783  Z= 0.124
  Angle     :  0.547   4.908   5133  Z= 0.293
  Chirality :  0.044   0.143    565
  Planarity :  0.004   0.032    653
  Dihedral  :  5.219  28.453    511
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  :  8.56 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.37), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.25 (0.33), residues: 231
  loop : -2.33 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 356 
 HIS   0.004   0.002   HIS L  91 
 PHE   0.013   0.002   PHE B 437 
 TYR   0.012   0.001   TYR B 305 
 ARG   0.002   0.000   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03919 (  122)
  hydrogen bonds       : angle       4.87851 (  354)
  SS BOND              : bond        0.00708 (    2)
  SS BOND              : angle       0.89344 (    4)
  covalent geometry    : bond        0.00289 ( 3781)
  covalent geometry    : angle       0.54666 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 62
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8036 (t0) cc_final: 0.7664 (t0)
REVERT: B  388 SER cc_start: 0.8794 (t) cc_final: 0.8524 (p)
REVERT: H   50 MET cc_start: 0.8388 (ttt) cc_final: 0.8128 (ttp)
REVERT: H  112 THR cc_start: 0.8283 (t) cc_final: 0.7914 (m)
  outliers start: 14
  outliers final: 10
  residues processed: 70
  average time/residue: 0.1553
  time to fit residues: 13.6225
Evaluate side-chains
  73 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0370
   chunk 0 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0970
   chunk 15 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9980
   chunk 14 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5256

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.090976 restraints weight = 5846.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.3047 rms_B_bonded: 1.94
r_work: 0.2952 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3783  Z= 0.165
  Angle     :  0.603   6.930   5133  Z= 0.320
  Chirality :  0.046   0.148    565
  Planarity :  0.004   0.033    653
  Dihedral  :  5.368  29.771    511
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  :  9.78 %
    Favored  : 86.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.20 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.47 (0.33), residues: 240
  loop : -2.38 (0.37), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 356 
 HIS   0.004   0.002   HIS B 315 
 PHE   0.014   0.002   PHE C 337 
 TYR   0.015   0.002   TYR L  86 
 ARG   0.003   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04342 (  122)
  hydrogen bonds       : angle       4.90377 (  354)
  SS BOND              : bond        0.00813 (    2)
  SS BOND              : angle       1.17014 (    4)
  covalent geometry    : bond        0.00400 ( 3781)
  covalent geometry    : angle       0.60199 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8024 (t0) cc_final: 0.7722 (t0)
REVERT: B  388 SER cc_start: 0.8795 (t) cc_final: 0.8534 (p)
REVERT: B  427 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8118 (ttp-170)
REVERT: H   50 MET cc_start: 0.8454 (ttt) cc_final: 0.8195 (ttp)
REVERT: H  112 THR cc_start: 0.8273 (t) cc_final: 0.7953 (m)
REVERT: L   45 LYS cc_start: 0.7454 (mmtp) cc_final: 0.7174 (mmtp)
  outliers start: 14
  outliers final: 13
  residues processed: 71
  average time/residue: 0.1495
  time to fit residues: 13.4991
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0170
   chunk 37 optimal weight:    0.6980
   chunk 34 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 2 optimal weight:    0.6980
   overall best weight:    0.5618

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.110223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.090992 restraints weight = 5827.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 1.92
r_work: 0.2952 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2826 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2826
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2825
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2825 r_free = 0.2825    target_work(ls_wunit_k1) = 0.078         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2825
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3783  Z= 0.173
  Angle     :  0.611   7.194   5133  Z= 0.323
  Chirality :  0.046   0.146    565
  Planarity :  0.004   0.035    653
  Dihedral  :  5.384  30.510    511
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  :  9.54 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.37), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.64 (0.33), residues: 233
  loop : -2.39 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.005   0.002   HIS L  91 
 PHE   0.014   0.002   PHE B 437 
 TYR   0.014   0.002   TYR B 305 
 ARG   0.003   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04312 (  122)
  hydrogen bonds       : angle       4.88846 (  354)
  SS BOND              : bond        0.00856 (    2)
  SS BOND              : angle       1.14318 (    4)
  covalent geometry    : bond        0.00421 ( 3781)
  covalent geometry    : angle       0.61043 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8083 (t0) cc_final: 0.7751 (t0)
REVERT: B  388 SER cc_start: 0.8783 (t) cc_final: 0.8536 (p)
REVERT: B  427 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8144 (ttp-170)
REVERT: H   50 MET cc_start: 0.8461 (ttt) cc_final: 0.8198 (ttp)
REVERT: H  112 THR cc_start: 0.8269 (t) cc_final: 0.7955 (m)
REVERT: L   90 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7791 (pp30)
  outliers start: 14
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1554
  time to fit residues: 13.2508
Evaluate side-chains
  74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 3 optimal weight:    0.4980
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 4 optimal weight:    0.2980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 8 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.109855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.090532 restraints weight = 5768.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.91
r_work: 0.2944 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2819 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2810
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2810 r_free = 0.2810    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2810
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   3783  Z= 0.187
  Angle     :  0.628   7.578   5133  Z= 0.331
  Chirality :  0.046   0.158    565
  Planarity :  0.004   0.035    653
  Dihedral  :  5.416  31.652    511
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 10.27 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.70 (0.33), residues: 233
  loop : -2.37 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.004   0.002   HIS L  91 
 PHE   0.015   0.002   PHE B 437 
 TYR   0.014   0.002   TYR L  86 
 ARG   0.003   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04440 (  122)
  hydrogen bonds       : angle       4.90505 (  354)
  SS BOND              : bond        0.00901 (    2)
  SS BOND              : angle       1.17260 (    4)
  covalent geometry    : bond        0.00459 ( 3781)
  covalent geometry    : angle       0.62697 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: B  358 ASP cc_start: 0.8051 (t0) cc_final: 0.7811 (t0)
REVERT: B  388 SER cc_start: 0.8788 (t) cc_final: 0.8528 (p)
REVERT: B  427 ARG cc_start: 0.8389 (ttp80) cc_final: 0.8142 (ttp-170)
REVERT: H   50 MET cc_start: 0.8471 (ttt) cc_final: 0.8204 (ttp)
REVERT: H  112 THR cc_start: 0.8266 (t) cc_final: 0.7959 (m)
REVERT: L   45 LYS cc_start: 0.7445 (mmtp) cc_final: 0.7200 (mmtp)
REVERT: L   90 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (pp30)
  outliers start: 14
  outliers final: 12
  residues processed: 69
  average time/residue: 0.1484
  time to fit residues: 12.7974
Evaluate side-chains
  74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 2 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.109581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.090065 restraints weight = 5761.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 1.97
r_work: 0.2932 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2803 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2804
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2804 r_free = 0.2804    target_work(ls_wunit_k1) = 0.077         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2804
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3783  Z= 0.208
  Angle     :  0.650   7.697   5133  Z= 0.343
  Chirality :  0.047   0.155    565
  Planarity :  0.004   0.037    653
  Dihedral  :  5.516  33.060    511
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  :  9.78 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.37), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.75 (0.32), residues: 227
  loop : -2.45 (0.36), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.004   0.002   HIS L   8 
 PHE   0.015   0.002   PHE B 437 
 TYR   0.016   0.002   TYR L  86 
 ARG   0.004   0.001   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04622 (  122)
  hydrogen bonds       : angle       4.95632 (  354)
  SS BOND              : bond        0.00939 (    2)
  SS BOND              : angle       1.23984 (    4)
  covalent geometry    : bond        0.00513 ( 3781)
  covalent geometry    : angle       0.64977 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
REVERT: B  388 SER cc_start: 0.8779 (t) cc_final: 0.8531 (p)
REVERT: B  427 ARG cc_start: 0.8399 (ttp80) cc_final: 0.8140 (ttp-170)
REVERT: H  112 THR cc_start: 0.8247 (t) cc_final: 0.7929 (m)
REVERT: L   90 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7845 (pp30)
  outliers start: 16
  outliers final: 14
  residues processed: 71
  average time/residue: 0.1449
  time to fit residues: 12.9256
Evaluate side-chains
  76 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain C residue  333 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 14 optimal weight:    0.0370
   chunk 29 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    0.4980
   chunk 23 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 20 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0020
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.3666

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.110954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.091763 restraints weight = 5684.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 1.89
r_work: 0.2965 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2839
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2839 r_free = 0.2839    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2839
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3783  Z= 0.128
  Angle     :  0.584   7.790   5133  Z= 0.308
  Chirality :  0.044   0.148    565
  Planarity :  0.004   0.033    653
  Dihedral  :  5.208  30.991    511
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 10.76 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.08 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.69 (0.34), residues: 220
  loop : -2.23 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 356 
 HIS   0.004   0.001   HIS L  91 
 PHE   0.016   0.002   PHE B 437 
 TYR   0.012   0.001   TYR B 305 
 ARG   0.003   0.000   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03878 (  122)
  hydrogen bonds       : angle       4.79225 (  354)
  SS BOND              : bond        0.00776 (    2)
  SS BOND              : angle       0.93038 (    4)
  covalent geometry    : bond        0.00298 ( 3781)
  covalent geometry    : angle       0.58318 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 SER cc_start: 0.8687 (m) cc_final: 0.8471 (p)
REVERT: B  388 SER cc_start: 0.8755 (t) cc_final: 0.8511 (p)
REVERT: B  427 ARG cc_start: 0.8382 (ttp80) cc_final: 0.8160 (ttp-170)
REVERT: H  112 THR cc_start: 0.8271 (t) cc_final: 0.7956 (m)
REVERT: L   90 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7766 (pp30)
  outliers start: 13
  outliers final: 12
  residues processed: 68
  average time/residue: 0.1522
  time to fit residues: 13.0117
Evaluate side-chains
  74 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 61
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    0.8980
   chunk 7 optimal weight:    0.5980
   chunk 15 optimal weight:    0.5980
   chunk 42 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0000
   chunk 11 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.091385 restraints weight = 5691.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.89
r_work: 0.2958 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2833
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2833 r_free = 0.2833    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2833
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3783  Z= 0.158
  Angle     :  0.610   7.798   5133  Z= 0.322
  Chirality :  0.045   0.148    565
  Planarity :  0.004   0.034    653
  Dihedral  :  5.238  30.951    511
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 10.51 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.74 (0.33), residues: 229
  loop : -2.35 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 356 
 HIS   0.003   0.002   HIS B 315 
 PHE   0.015   0.002   PHE B 437 
 TYR   0.014   0.002   TYR B 305 
 ARG   0.003   0.000   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04073 (  122)
  hydrogen bonds       : angle       4.80355 (  354)
  SS BOND              : bond        0.00826 (    2)
  SS BOND              : angle       1.05427 (    4)
  covalent geometry    : bond        0.00378 ( 3781)
  covalent geometry    : angle       0.60963 ( 5129)

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

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

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  920 Ramachandran restraints generated.
    460 Oldfield, 0 Emsley, 460 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  420 SER cc_start: 0.8681 (m) cc_final: 0.8468 (p)
REVERT: B  388 SER cc_start: 0.8760 (t) cc_final: 0.8515 (p)
REVERT: B  427 ARG cc_start: 0.8358 (ttp80) cc_final: 0.8131 (ttp-170)
REVERT: H  112 THR cc_start: 0.8265 (t) cc_final: 0.7959 (m)
REVERT: L   90 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7765 (pp30)
  outliers start: 14
  outliers final: 13
  residues processed: 69
  average time/residue: 0.1519
  time to fit residues: 13.1921
Evaluate side-chains
  75 residues out of total 409 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 61
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  295 SER
Chi-restraints excluded: chain B residue  306 THR
Chi-restraints excluded: chain B residue  324 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  413 THR
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   11 LEU
Chi-restraints excluded: chain H residue   20 ILE
Chi-restraints excluded: chain H residue   67 LEU
Chi-restraints excluded: chain H residue   68 SER
Chi-restraints excluded: chain L residue   90 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 45
   random chunks:
   chunk 39 optimal weight:    0.1980
   chunk 5 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0030
   chunk 18 optimal weight:    0.7980
   chunk 37 optimal weight:    0.1980
   chunk 1 optimal weight:    0.2980
   chunk 24 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 15 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.2390

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

Flipped N/Q/H residues before XYZ refinement:
B 302 GLN
B 324 ASN
L  90 GLN
** L  91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.112057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.092679 restraints weight = 5659.661|
|-----------------------------------------------------------------------------|
r_work (start): 0.3077 rms_B_bonded: 1.96
r_work: 0.2979 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2851
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2851 r_free = 0.2851    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2851
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7826
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3783  Z= 0.102
  Angle     :  0.555   7.599   5133  Z= 0.292
  Chirality :  0.044   0.148    565
  Planarity :  0.004   0.031    653
  Dihedral  :  4.938  28.009    511
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 10.51 %
    Favored  : 86.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.26 %
    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: -0.97 (0.38), residues: 460
  helix:  None (None), residues: 0
  sheet:  0.76 (0.34), residues: 220
  loop : -2.14 (0.37), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 356 
 HIS   0.005   0.001   HIS L  91 
 PHE   0.014   0.001   PHE B 437 
 TYR   0.011   0.001   TYR B 305 
 ARG   0.002   0.000   ARG L  54 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03459 (  122)
  hydrogen bonds       : angle       4.64162 (  354)
  SS BOND              : bond        0.00694 (    2)
  SS BOND              : angle       0.80120 (    4)
  covalent geometry    : bond        0.00223 ( 3781)
  covalent geometry    : angle       0.55491 ( 5129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2765.46 seconds
wall clock time: 48 minutes 9.20 seconds (2889.20 seconds total)