Starting phenix.real_space_refine
on Tue Mar  3 15:10:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4n_25681/03_2026/7t4n_25681.map"
  }
  resolution = 2.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
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      44      5.16       5
     C    4148      2.51       5
     N    1090      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6476
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3264
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 404, 3255
          Classifications: {'peptide': 404}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 385}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
      Conformer: "B"
        Number of residues, atoms: 404, 3255
          Classifications: {'peptide': 404}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 385}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
          bond proxies already assigned to first conformer: 3308
    Chain: "B"
      Number of atoms: 3212
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 399, 3203
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 18, 'TRANS': 380}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 22
      Conformer: "B"
        Number of residues, atoms: 399, 3203
          Classifications: {'peptide': 399}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 18, 'TRANS': 380}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 28
          Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 22
          bond proxies already assigned to first conformer: 3255
  Time building chain proxies: 2.32, per 1000 atoms: 0.36
  Number of scatterers: 6476
  At special positions: 0
  Unit cell: (115.787, 78.302, 74.97, 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      44     16.00
     O    1194      8.00
     N    1090      7.00
     C    4148      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.46
  Conformation dependent library (CDL) restraints added in 365.7 milliseconds
  

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1564

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 8 sheets defined
      44.3% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 137
    Processing helix  chain 'A' and resid 155 through 157
      No H-bonds generated for 'chain 'A' and resid 155 through 157'
    Processing helix  chain 'A' and resid 203 through 215
    Processing helix  chain 'A' and resid 297 through 304
    Processing helix  chain 'A' and resid 307 through 328
    Processing helix  chain 'A' and resid 357 through 361
      removed outlier: 4.566A  pdb=" N   CYS A 360 " --> pdb=" O   ALA A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 406 through 420
      removed outlier: 3.589A  pdb=" N   TYR A 417 " --> pdb=" O   GLY A 413 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLU A 418 " --> pdb=" O   ALA A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 443
    Processing helix  chain 'A' and resid 451 through 462
    Processing helix  chain 'A' and resid 471 through 485
    Processing helix  chain 'A' and resid 486 through 491
      removed outlier: 3.990A  pdb=" N   LEU A 490 " --> pdb=" O   PRO A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 515
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 557 through 574
      removed outlier: 4.022A  pdb=" N   HIS A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ILE A 573 " --> pdb=" O   GLN A 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 137
      removed outlier: 4.164A  pdb=" N   GLY B 126 " --> pdb=" O   ASP B 122 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ILE B 127 " --> pdb=" O   GLU B 123 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   CYS B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 159
      removed outlier: 3.724A  pdb=" N   GLU B 158 " --> pdb=" O   ASN B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 215
    Processing helix  chain 'B' and resid 297 through 304
    Processing helix  chain 'B' and resid 307 through 328
      removed outlier: 3.587A  pdb=" N   HIS B 328 " --> pdb=" O   HIS B 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 361
      removed outlier: 4.536A  pdb=" N   CYS B 360 " --> pdb=" O   ALA B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 388 through 393
    Processing helix  chain 'B' and resid 406 through 420
      removed outlier: 3.733A  pdb=" N   TYR B 417 " --> pdb=" O   GLY B 413 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLU B 418 " --> pdb=" O   ALA B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 439 through 443
      removed outlier: 3.515A  pdb=" N   LEU B 443 " --> pdb=" O   GLU B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 451 through 462
    Processing helix  chain 'B' and resid 471 through 485
    Processing helix  chain 'B' and resid 486 through 491
      removed outlier: 3.779A  pdb=" N   LEU B 490 " --> pdb=" O   PRO B 486 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 498 through 515
    Processing helix  chain 'B' and resid 542 through 554
    Processing helix  chain 'B' and resid 557 through 574
      removed outlier: 3.819A  pdb=" N   HIS B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160
      removed outlier: 3.573A  pdb=" N   SER A 251 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   LYS A 291 " --> pdb=" O   MET A 249 " (cutoff:3.500A)
      removed outlier: 6.921A  pdb=" N   MET A 249 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296
    Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331
    Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 372
    Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166
      removed outlier: 7.056A  pdb=" N   LYS B 291 " --> pdb=" O   MET B 249 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   MET B 249 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 295 through 296
      removed outlier: 3.528A  pdb=" N   CYS B 295 " --> pdb=" O   VAL B 342 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 372

    293 hydrogen bonds defined for protein.
    841 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: 0.83

  Time building geometry restraints manager: 0.62 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: 2087
        1.34 -     1.46: 1313
        1.46 -     1.58: 3139
        1.58 -     1.69: 0
        1.69 -     1.81: 68
  Bond restraints: 6607
  Sorted by residual:
  bond pdb=" CB  ASP B 428 "
       pdb=" CG  ASP B 428 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 9.24e-01
  bond pdb=" C   ILE A 233 "
       pdb=" O   ILE A 233 "
    ideal  model  delta    sigma   weight residual
    1.236  1.225  0.011 1.19e-02 7.06e+03 8.44e-01
  bond pdb=" CB  LYS B 432 "
       pdb=" CG  LYS B 432 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.51e-01
  bond pdb=" CG  LYS B 432 "
       pdb=" CD  LYS B 432 "
    ideal  model  delta    sigma   weight residual
    1.520  1.541 -0.021 3.00e-02 1.11e+03 4.98e-01
  bond pdb=" CA  ASP B 428 "
       pdb=" CB  ASP B 428 "
    ideal  model  delta    sigma   weight residual
    1.528  1.540 -0.012 1.66e-02 3.63e+03 4.92e-01
  ... (remaining 6602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 8755
        1.16 -     2.32: 146
        2.32 -     3.48: 36
        3.48 -     4.64: 6
        4.64 -     5.80: 3
  Bond angle restraints: 8946
  Sorted by residual:
  angle pdb=" CB  LYS B 432 "
        pdb=" CG  LYS B 432 "
        pdb=" CD  LYS B 432 "
      ideal   model   delta    sigma   weight residual
     111.30  117.10   -5.80 2.30e+00 1.89e-01 6.35e+00
  angle pdb=" CA  ASP B 428 "
        pdb=" CB  ASP B 428 "
        pdb=" CG  ASP B 428 "
      ideal   model   delta    sigma   weight residual
     112.60  114.61   -2.01 1.00e+00 1.00e+00 4.03e+00
  angle pdb=" CB  ASP B 428 "
        pdb=" CG  ASP B 428 "
        pdb=" OD1 ASP B 428 "
      ideal   model   delta    sigma   weight residual
     118.40  122.72   -4.32 2.30e+00 1.89e-01 3.53e+00
  angle pdb=" C   ASP B 428 "
        pdb=" CA  ASP B 428 "
        pdb=" CB  ASP B 428 "
      ideal   model   delta    sigma   weight residual
     109.65  112.58   -2.93 1.71e+00 3.42e-01 2.93e+00
  angle pdb=" C   SER B 175 "
        pdb=" N   ALA B 176 "
        pdb=" CA  ALA B 176 "
      ideal   model   delta    sigma   weight residual
     122.29  119.88    2.41 1.65e+00 3.67e-01 2.13e+00
  ... (remaining 8941 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3537
       17.59 -    35.18: 377
       35.18 -    52.78: 110
       52.78 -    70.37: 15
       70.37 -    87.96: 11
  Dihedral angle restraints: 4050
    sinusoidal: 1652
      harmonic: 2398
  Sorted by residual:
  dihedral pdb=" CA  ASP B 121 "
           pdb=" CB  ASP B 121 "
           pdb=" CG  ASP B 121 "
           pdb=" OD1 ASP B 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.26   59.26     1      2.00e+01 2.50e-03 1.17e+01
  dihedral pdb=" CB  GLU A 133 "
           pdb=" CG  GLU A 133 "
           pdb=" CD  GLU A 133 "
           pdb=" OE1 GLU A 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -87.96   87.96     1      3.00e+01 1.11e-03 1.03e+01
  dihedral pdb=" CA  GLN B 189 "
           pdb=" C   GLN B 189 "
           pdb=" N   LEU B 190 "
           pdb=" CA  LEU B 190 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.22  -15.78     0      5.00e+00 4.00e-02 9.97e+00
  ... (remaining 4047 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 581
       0.026 -    0.051: 274
       0.051 -    0.077: 102
       0.077 -    0.102: 29
       0.102 -    0.128: 23
  Chirality restraints: 1009
  Sorted by residual:
  chirality pdb=" CA  ILE B 450 "
            pdb=" N   ILE B 450 "
            pdb=" C   ILE B 450 "
            pdb=" CB  ILE B 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  chirality pdb=" CA  ILE A 165 "
            pdb=" N   ILE A 165 "
            pdb=" C   ILE A 165 "
            pdb=" CB  ILE A 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.02e-01
  chirality pdb=" CA  VAL B 252 "
            pdb=" N   VAL B 252 "
            pdb=" C   VAL B 252 "
            pdb=" CB  VAL B 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 1006 not shown)

  Planarity restraints: 1134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 401 "    0.008 2.00e-02 2.50e+03   7.94e-03 1.58e+00
        pdb=" CG  TRP A 401 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 401 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 401 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 401 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 401 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 401 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 401 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 450 "    0.020 5.00e-02 4.00e+02   2.98e-02 1.42e+00
        pdb=" N   PRO A 451 "   -0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO A 451 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 451 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 450 "   -0.019 5.00e-02 4.00e+02   2.93e-02 1.38e+00
        pdb=" N   PRO B 451 "    0.051 5.00e-02 4.00e+02
        pdb=" CA  PRO B 451 "   -0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 451 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 1131 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 571
        2.75 -     3.28: 6256
        3.28 -     3.82: 10918
        3.82 -     4.36: 14131
        4.36 -     4.90: 22842
  Nonbonded interactions: 54718
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 438 "
            pdb=" O   LEU B 462 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   ARG B 132 "
            pdb=" OG  SER B 136 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OH  TYR A 438 "
            pdb=" O   LEU A 462 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" O   GLY A 382 "
            pdb=" OG1 THR B 205 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OD1 ASP B 428 "
            pdb=" N   THR B 430 "
     model   vdw
     2.299 3.120
  ... (remaining 54713 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 120 and (name N or name CA or name C or name O or name CB \ 
 )) or resid 121 through 179 or resid 188 through 211 or resid 213 through 267 o \ 
r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 
83 through 573 or (resid 574 and (name N or name CA or name C or name O or name  \ 
CB ))))
  selection = (chain 'B' and (resid 120 through 211 or resid 213 through 574))
}

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=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:             3.700
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.860
  Find NCS groups from input model:        0.100
  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:6.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
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      :  0.002   0.032   6607  Z= 0.098
  Angle     :  0.423   5.798   8946  Z= 0.222
  Chirality :  0.038   0.128   1009
  Planarity :  0.003   0.030   1134
  Dihedral  : 16.225  87.960   2486
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 4.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.48 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.87 (0.28), residues: 785
  helix:  1.35 (0.28), residues: 320
  sheet:  0.50 (0.51), residues: 105
  loop : -0.01 (0.30), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 248 
 TYR   0.009   0.001   TYR B 482 
 PHE   0.011   0.001   PHE A 253 
 TRP   0.022   0.001   TRP A 401 
 HIS   0.002   0.001   HIS B 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 6607)
  covalent geometry    : angle       0.42343 ( 8946)
  hydrogen bonds       : bond        0.21749 (  291)
  hydrogen bonds       : angle       7.05198 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.255 
Fit side-chains
REVERT: B  150 GLN cc_start: 0.6982 (pm20) cc_final: 0.6336 (pm20)
  outliers start: 9
  outliers final: 5
  residues processed: 110
  average time/residue: 0.6062
  time to fit residues: 69.7770
Evaluate side-chains
  108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  238 ILE
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.0060
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 189 GLN
A 283 ASN
A 366 GLN
B 189 GLN
B 569 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.106927 restraints weight = 17721.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.57
r_work: 0.3090 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2974 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2963 r_free = 0.2963    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8546
moved from start:          0.0810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6607  Z= 0.136
  Angle     :  0.495   4.728   8946  Z= 0.265
  Chirality :  0.040   0.144   1009
  Planarity :  0.004   0.029   1134
  Dihedral  :  4.862  58.863    880
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.26 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.29), residues: 785
  helix:  1.92 (0.28), residues: 327
  sheet:  0.63 (0.51), residues: 99
  loop : -0.04 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 248 
 TYR   0.013   0.001   TYR B 482 
 PHE   0.013   0.002   PHE A 253 
 TRP   0.014   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 324 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6607)
  covalent geometry    : angle       0.49499 ( 8946)
  hydrogen bonds       : bond        0.05294 (  291)
  hydrogen bonds       : angle       5.11684 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.156 
Fit side-chains
REVERT: A  155 ASN cc_start: 0.7972 (p0) cc_final: 0.7361 (p0)
REVERT: A  157 ASP cc_start: 0.7931 (m-30) cc_final: 0.7571 (p0)
REVERT: B  150 GLN cc_start: 0.7134 (pm20) cc_final: 0.6574 (pm20)
REVERT: B  167 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.7373 (mppt)
  outliers start: 17
  outliers final: 4
  residues processed: 114
  average time/residue: 0.6103
  time to fit residues: 72.6391
Evaluate side-chains
  103 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 98
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue  167 LYS
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    0.1980
   chunk 78 optimal weight:    0.1980
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9990
   chunk 51 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 11 optimal weight:    0.0980
   chunk 40 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   overall best weight:    0.3580

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 366 GLN
A 504 GLN
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.140134 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109136 restraints weight = 15054.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.38
r_work: 0.3122 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3000
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3000 r_free = 0.3000    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3000
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6607  Z= 0.106
  Angle     :  0.460   4.610   8946  Z= 0.245
  Chirality :  0.039   0.143   1009
  Planarity :  0.004   0.038   1134
  Dihedral  :  4.475  55.209    876
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.23 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 785
  helix:  2.15 (0.28), residues: 327
  sheet:  0.64 (0.51), residues: 99
  loop : -0.04 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 541 
 TYR   0.012   0.001   TYR B 482 
 PHE   0.014   0.001   PHE A 253 
 TRP   0.014   0.001   TRP A 401 
 HIS   0.002   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 6607)
  covalent geometry    : angle       0.45994 ( 8946)
  hydrogen bonds       : bond        0.04342 (  291)
  hydrogen bonds       : angle       4.72516 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B  150 GLN cc_start: 0.7099 (pm20) cc_final: 0.6537 (pm20)
REVERT: B  167 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.7308 (mppt)
REVERT: B  292 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7615 (ptp90)
  outliers start: 12
  outliers final: 6
  residues processed: 107
  average time/residue: 0.6300
  time to fit residues: 70.5568
Evaluate side-chains
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  167 LYS
Chi-restraints excluded: chain B residue  194 MET
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 23 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 32 optimal weight:    0.0030
   chunk 4 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   overall best weight:    0.6590

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 189 GLN
A 366 GLN
A 504 GLN
B 569 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.138432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.107162 restraints weight = 15038.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3220 rms_B_bonded: 2.38
r_work: 0.3096 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2978 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2973
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2973 r_free = 0.2973    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2973
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
moved from start:          0.1055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6607  Z= 0.144
  Angle     :  0.490   4.726   8946  Z= 0.261
  Chirality :  0.040   0.139   1009
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.529  53.953    875
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 14.56 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.37 (0.29), residues: 785
  helix:  2.14 (0.28), residues: 327
  sheet:  0.39 (0.50), residues: 105
  loop : -0.05 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 541 
 TYR   0.016   0.001   TYR B 482 
 PHE   0.015   0.002   PHE A 253 
 TRP   0.015   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6607)
  covalent geometry    : angle       0.49048 ( 8946)
  hydrogen bonds       : bond        0.04806 (  291)
  hydrogen bonds       : angle       4.75481 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 100
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7963 (p0) cc_final: 0.7309 (p0)
REVERT: A  157 ASP cc_start: 0.7917 (m-30) cc_final: 0.7516 (p0)
REVERT: B  150 GLN cc_start: 0.7094 (pm20) cc_final: 0.6531 (pm20)
  outliers start: 23
  outliers final: 8
  residues processed: 114
  average time/residue: 0.6087
  time to fit residues: 72.6541
Evaluate side-chains
  104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 11 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0270
   chunk 46 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    0.6980
   chunk 9 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5238

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 366 GLN
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.138931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108516 restraints weight = 13003.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 2.22
r_work: 0.3118 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.3001 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2994
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2994 r_free = 0.2994    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2994
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.1109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6607  Z= 0.125
  Angle     :  0.477   4.602   8946  Z= 0.254
  Chirality :  0.040   0.140   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.483  52.937    875
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.53 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.29), residues: 785
  helix:  2.20 (0.28), residues: 327
  sheet:  0.32 (0.49), residues: 105
  loop : -0.03 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 541 
 TYR   0.019   0.001   TYR A 494 
 PHE   0.015   0.002   PHE A 253 
 TRP   0.015   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6607)
  covalent geometry    : angle       0.47739 ( 8946)
  hydrogen bonds       : bond        0.04506 (  291)
  hydrogen bonds       : angle       4.67422 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 99
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 GLN cc_start: 0.7071 (pm20) cc_final: 0.6492 (pm20)
  outliers start: 16
  outliers final: 11
  residues processed: 110
  average time/residue: 0.5988
  time to fit residues: 68.9272
Evaluate side-chains
  107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  158 GLU
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 59 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 78 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9990
   chunk 56 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 189 GLN
A 366 GLN
A 504 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.138263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.107349 restraints weight = 13977.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.31
r_work: 0.3099 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2983 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2977
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2977 r_free = 0.2977    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2977
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6607  Z= 0.143
  Angle     :  0.503   8.386   8946  Z= 0.264
  Chirality :  0.041   0.139   1009
  Planarity :  0.004   0.031   1134
  Dihedral  :  4.539  52.251    875
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 15.26 %
    Favored  : 82.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.29), residues: 785
  helix:  2.16 (0.28), residues: 327
  sheet:  0.30 (0.49), residues: 105
  loop : -0.05 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 248 
 TYR   0.019   0.001   TYR A 494 
 PHE   0.016   0.002   PHE A 253 
 TRP   0.016   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 6607)
  covalent geometry    : angle       0.50298 ( 8946)
  hydrogen bonds       : bond        0.04687 (  291)
  hydrogen bonds       : angle       4.68183 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7973 (p0) cc_final: 0.7333 (p0)
REVERT: A  157 ASP cc_start: 0.7835 (m-30) cc_final: 0.7476 (p0)
REVERT: B  150 GLN cc_start: 0.7072 (pm20) cc_final: 0.6488 (pm20)
  outliers start: 17
  outliers final: 10
  residues processed: 107
  average time/residue: 0.6364
  time to fit residues: 71.1175
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 36 optimal weight:    0.1980
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 5 optimal weight:    0.0970
   chunk 60 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.2776

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 366 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.140298 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.110908 restraints weight = 10497.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.01
r_work: 0.3155 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3038 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3038
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3045
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3045 r_free = 0.3045    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3045
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6607  Z= 0.098
  Angle     :  0.472   8.040   8946  Z= 0.248
  Chirality :  0.039   0.140   1009
  Planarity :  0.003   0.031   1134
  Dihedral  :  4.386  50.733    875
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 16.09 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.49 (0.29), residues: 785
  helix:  2.32 (0.28), residues: 327
  sheet:  0.28 (0.48), residues: 105
  loop : -0.00 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 541 
 TYR   0.019   0.001   TYR A 494 
 PHE   0.015   0.001   PHE A 253 
 TRP   0.018   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 ( 6607)
  covalent geometry    : angle       0.47174 ( 8946)
  hydrogen bonds       : bond        0.03962 (  291)
  hydrogen bonds       : angle       4.49734 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7904 (p0) cc_final: 0.7192 (p0)
REVERT: A  157 ASP cc_start: 0.7770 (m-30) cc_final: 0.7393 (p0)
REVERT: B  150 GLN cc_start: 0.7019 (pm20) cc_final: 0.6400 (pm20)
  outliers start: 14
  outliers final: 10
  residues processed: 107
  average time/residue: 0.6257
  time to fit residues: 70.0003
Evaluate side-chains
  107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  445 GLU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 73 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.7980
   chunk 58 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   chunk 9 optimal weight:    0.5980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 189 GLN
A 366 GLN
A 504 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.138721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.108126 restraints weight = 13246.505|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.25
r_work: 0.3112 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2996 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6607  Z= 0.141
  Angle     :  0.505   7.827   8946  Z= 0.265
  Chirality :  0.040   0.138   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.469  51.004    875
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.81 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.43 (0.29), residues: 785
  helix:  2.22 (0.28), residues: 327
  sheet:  0.34 (0.49), residues: 105
  loop : -0.01 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 248 
 TYR   0.018   0.001   TYR A 494 
 PHE   0.016   0.002   PHE A 253 
 TRP   0.021   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 6607)
  covalent geometry    : angle       0.50451 ( 8946)
  hydrogen bonds       : bond        0.04519 (  291)
  hydrogen bonds       : angle       4.60428 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
  outliers start: 16
  outliers final: 11
  residues processed: 106
  average time/residue: 0.6174
  time to fit residues: 68.5752
Evaluate side-chains
  107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  445 GLU
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   chunk 3 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 366 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.138802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.108146 restraints weight = 14191.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.31
r_work: 0.3109 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2981
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6607  Z= 0.132
  Angle     :  0.496   7.767   8946  Z= 0.261
  Chirality :  0.040   0.139   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.483  50.597    875
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 15.81 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.39 (0.29), residues: 785
  helix:  2.21 (0.28), residues: 327
  sheet:  0.30 (0.49), residues: 105
  loop : -0.06 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 248 
 TYR   0.017   0.001   TYR A 494 
 PHE   0.016   0.002   PHE A 253 
 TRP   0.020   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 6607)
  covalent geometry    : angle       0.49559 ( 8946)
  hydrogen bonds       : bond        0.04442 (  291)
  hydrogen bonds       : angle       4.57960 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 96
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7950 (p0) cc_final: 0.7324 (p0)
REVERT: A  157 ASP cc_start: 0.7822 (m-30) cc_final: 0.7471 (p0)
REVERT: B  445 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7266 (pp20)
  outliers start: 15
  outliers final: 11
  residues processed: 105
  average time/residue: 0.6347
  time to fit residues: 69.8120
Evaluate side-chains
  107 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  445 GLU
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 9 optimal weight:    3.9990
   chunk 55 optimal weight:    0.0060
   chunk 43 optimal weight:    0.5980
   chunk 12 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0970
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 366 GLN
A 504 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.109288 restraints weight = 15089.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.37
r_work: 0.3122 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3005 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3005
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3007
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3007 r_free = 0.3007    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3007
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8516
moved from start:          0.1264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6607  Z= 0.109
  Angle     :  0.474   7.788   8946  Z= 0.249
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.379  50.003    875
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 16.23 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.29), residues: 785
  helix:  2.31 (0.28), residues: 327
  sheet:  0.00 (0.48), residues: 115
  loop :  0.13 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 541 
 TYR   0.017   0.001   TYR A 494 
 PHE   0.015   0.001   PHE A 253 
 TRP   0.021   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6607)
  covalent geometry    : angle       0.47431 ( 8946)
  hydrogen bonds       : bond        0.04034 (  291)
  hydrogen bonds       : angle       4.45944 (  841)

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

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

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1570 Ramachandran restraints generated.
    785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 0.249 
Fit side-chains
REVERT: A  155 ASN cc_start: 0.7896 (p0) cc_final: 0.7159 (p0)
REVERT: A  157 ASP cc_start: 0.7788 (m-30) cc_final: 0.7362 (p0)
REVERT: B  189 GLN cc_start: 0.6848 (tp40) cc_final: 0.6122 (mm-40)
  outliers start: 13
  outliers final: 11
  residues processed: 106
  average time/residue: 0.6035
  time to fit residues: 66.8948
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  445 GLU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  473 ASP
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
Chi-restraints excluded: chain B residue  216 VAL
Chi-restraints excluded: chain B residue  338 ASP
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  560 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 18 optimal weight:    0.0770
   chunk 1 optimal weight:    0.6980
   chunk 13 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A 366 GLN
A 504 GLN
** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 569 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.139464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.108438 restraints weight = 15968.788|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 2.42
r_work: 0.3106 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8528
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6607  Z= 0.121
  Angle     :  0.485   7.686   8946  Z= 0.255
  Chirality :  0.040   0.139   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.431  50.176    875
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 16.37 %
    Favored  : 81.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.29), residues: 785
  helix:  2.27 (0.28), residues: 327
  sheet:  0.03 (0.48), residues: 115
  loop :  0.12 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 541 
 TYR   0.017   0.001   TYR A 494 
 PHE   0.015   0.002   PHE A 253 
 TRP   0.023   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6607)
  covalent geometry    : angle       0.48510 ( 8946)
  hydrogen bonds       : bond        0.04226 (  291)
  hydrogen bonds       : angle       4.49409 (  841)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3306.43 seconds
wall clock time: 56 minutes 45.60 seconds (3405.60 seconds total)