Starting phenix.real_space_refine
on Tue Feb 11 18:54:56 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_25681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_25681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_25681.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_25681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4n_25681/02_2025/7t4n_25681.cif"
  }
  resolution = 2.35
  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=   0.023
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'ARG:plan': 1, 'HIS: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: {'ARG:plan': 1, 'HIS: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: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS: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: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 22
          bond proxies already assigned to first conformer: 3255
  Time building chain proxies: 8.05, per 1000 atoms: 1.24
  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: 1.36
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 0.66
  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: 1.86

  Time building geometry restraints manager: 1.61 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:             2.880
  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:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     23.090
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  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:             0.010
  Load rotamer database and sin/cos tables:15.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.290
-------------------------------------------------------------------------------
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= 0.149
  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 (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:  0.87 (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
 TRP   0.022   0.001   TRP A 401 
 HIS   0.002   0.001   HIS B 328 
 PHE   0.011   0.001   PHE A 253 
 TYR   0.009   0.001   TYR B 482 
 ARG   0.005   0.000   ARG B 248 

*********************** 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  : 0.777 
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: 1.3453
  time to fit residues: 154.9971
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  : 0.810 
-------------------------------------------------------------------------------
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 66 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 40 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 71 optimal weight:    0.3980
   overall best weight:    0.4980

-------------------------------------------------------------------------------
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 569 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.138948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107693 restraints weight = 15135.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.40
r_work: 0.3104 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.0785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6607  Z= 0.187
  Angle     :  0.488   4.702   8946  Z= 0.262
  Chirality :  0.040   0.143   1009
  Planarity :  0.004   0.028   1134
  Dihedral  :  4.818  59.251    880
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  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 (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:  1.30 (0.29), residues: 785
  helix:  1.94 (0.28), residues: 327
  sheet:  0.64 (0.51), residues: 99
  loop : -0.03 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 324 
 PHE   0.013   0.002   PHE A 253 
 TYR   0.013   0.001   TYR B 482 
 ARG   0.005   0.000   ARG A 292 

*********************** 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
  121 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  155 ASN cc_start: 0.7968 (p0) cc_final: 0.7349 (p0)
REVERT: A  157 ASP cc_start: 0.7924 (m-30) cc_final: 0.7565 (p0)
REVERT: B  150 GLN cc_start: 0.7133 (pm20) cc_final: 0.6576 (pm20)
REVERT: B  167 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7358 (mppt)
  outliers start: 16
  outliers final: 4
  residues processed: 113
  average time/residue: 1.3509
  time to fit residues: 159.8999
Evaluate side-chains
  104 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.750 
-------------------------------------------------------------------------------
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 5 optimal weight:    0.0980
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    7.9990
   chunk 15 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0970
   chunk 67 optimal weight:    0.3980
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.3378

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.140332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.109876 restraints weight = 12979.123|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.23
r_work: 0.3137 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3019 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3019
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    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 = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1039

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= 0.149
  Angle     :  0.457   4.590   8946  Z= 0.244
  Chirality :  0.039   0.144   1009
  Planarity :  0.004   0.037   1134
  Dihedral  :  4.458  55.652    876
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.64 %
    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 (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:  1.45 (0.29), residues: 785
  helix:  2.17 (0.28), residues: 327
  sheet:  0.65 (0.51), residues: 99
  loop : -0.03 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.001   PHE A 253 
 TYR   0.012   0.001   TYR B 482 
 ARG   0.010   0.000   ARG B 541 

*********************** 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
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.809 
Fit side-chains
REVERT: B  150 GLN cc_start: 0.7118 (pm20) cc_final: 0.6556 (pm20)
REVERT: B  167 LYS cc_start: 0.7570 (OUTLIER) cc_final: 0.7314 (mppt)
REVERT: B  292 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7674 (ptp90)
  outliers start: 10
  outliers final: 6
  residues processed: 107
  average time/residue: 1.4086
  time to fit residues: 157.9743
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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  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 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 39 optimal weight:    0.0980
   chunk 63 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:    1.9990
   chunk 71 optimal weight:    0.1980
   overall best weight:    0.4180

-------------------------------------------------------------------------------
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 = 0.3650 r_free = 0.3650 target = 0.140006 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.110325 restraints weight = 10495.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 2.02
r_work: 0.3148 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3033 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3030
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3030 r_free = 0.3030    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3030
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6607  Z= 0.163
  Angle     :  0.460   4.579   8946  Z= 0.245
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.034   1134
  Dihedral  :  4.365  54.407    875
  Min Nonbonded Distance : 2.604

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.12 %
    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 (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:  1.50 (0.29), residues: 785
  helix:  2.24 (0.28), residues: 327
  sheet:  0.61 (0.51), residues: 99
  loop : -0.03 (0.31), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.002   PHE A 253 
 TYR   0.013   0.001   TYR B 482 
 ARG   0.007   0.000   ARG B 541 

*********************** 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
  118 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A  155 ASN cc_start: 0.7953 (p0) cc_final: 0.7280 (p0)
REVERT: A  157 ASP cc_start: 0.7877 (m-30) cc_final: 0.7390 (p0)
REVERT: B  150 GLN cc_start: 0.7128 (pm20) cc_final: 0.6557 (pm20)
REVERT: B  167 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7218 (mppt)
REVERT: B  292 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7578 (ptp90)
  outliers start: 19
  outliers final: 6
  residues processed: 110
  average time/residue: 1.3501
  time to fit residues: 155.6360
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
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  167 LYS
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  292 ARG
Chi-restraints excluded: chain B residue  560 LEU
Chi-restraints excluded: chain B residue  571 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0000
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    0.6980
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0010
   chunk 34 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 = 0.3649 r_free = 0.3649 target = 0.139856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.110469 restraints weight = 10138.383|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 1.98
r_work: 0.3150 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3028
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3028 r_free = 0.3028    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3028
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6607  Z= 0.167
  Angle     :  0.462   4.578   8946  Z= 0.245
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.362  52.888    875
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.12 %
    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 (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:  1.50 (0.29), residues: 785
  helix:  2.29 (0.28), residues: 327
  sheet:  0.41 (0.49), residues: 105
  loop :  0.00 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.014   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.008   0.000   ARG B 541 

*********************** 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
  119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 GLN cc_start: 0.7139 (pm20) cc_final: 0.6571 (pm20)
REVERT: B  167 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7287 (mppt)
  outliers start: 19
  outliers final: 11
  residues processed: 111
  average time/residue: 1.3431
  time to fit residues: 156.1054
Evaluate side-chains
  108 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  343 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  167 LYS
Chi-restraints excluded: chain B residue  174 TYR
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 8 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 30 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3643 r_free = 0.3643 target = 0.139391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.107913 restraints weight = 16063.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 2.46
r_work: 0.3103 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2986 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2979
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2979 r_free = 0.2979    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6607  Z= 0.191
  Angle     :  0.489   8.314   8946  Z= 0.256
  Chirality :  0.040   0.139   1009
  Planarity :  0.004   0.031   1134
  Dihedral  :  4.402  52.518    875
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 15.81 %
    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 (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:  1.47 (0.29), residues: 785
  helix:  2.26 (0.28), residues: 327
  sheet:  0.37 (0.49), residues: 105
  loop : -0.01 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.006   0.000   ARG B 541 

*********************** 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
  109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7990 (p0) cc_final: 0.7329 (p0)
REVERT: A  157 ASP cc_start: 0.7857 (m-30) cc_final: 0.7372 (p0)
REVERT: B  150 GLN cc_start: 0.7139 (pm20) cc_final: 0.6571 (pm20)
REVERT: B  167 LYS cc_start: 0.7630 (OUTLIER) cc_final: 0.7271 (mppt)
  outliers start: 13
  outliers final: 9
  residues processed: 104
  average time/residue: 1.3478
  time to fit residues: 146.9649
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  : 0.777 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 9 optimal weight:    0.2980
   chunk 48 optimal weight:    0.0050
   chunk 60 optimal weight:    0.9980
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    0.5980
   chunk 57 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0770
   chunk 27 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.3152

-------------------------------------------------------------------------------
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 = 0.3661 r_free = 0.3661 target = 0.140881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.110069 restraints weight = 14149.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.33
r_work: 0.3137 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3017
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3017 r_free = 0.3017    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3017
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8498
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6607  Z= 0.143
  Angle     :  0.464   8.194   8946  Z= 0.242
  Chirality :  0.039   0.142   1009
  Planarity :  0.003   0.031   1134
  Dihedral  :  4.267  50.738    875
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.01
  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 (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:  1.54 (0.29), residues: 785
  helix:  2.37 (0.28), residues: 327
  sheet:  0.33 (0.49), residues: 105
  loop :  0.01 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.006   0.000   ARG B 541 

*********************** 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
  113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: B  150 GLN cc_start: 0.7076 (pm20) cc_final: 0.6503 (pm20)
REVERT: B  167 LYS cc_start: 0.7598 (OUTLIER) cc_final: 0.7271 (mppt)
  outliers start: 14
  outliers final: 11
  residues processed: 108
  average time/residue: 1.3556
  time to fit residues: 153.2165
Evaluate side-chains
  109 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  343 ASP
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  167 LYS
Chi-restraints excluded: chain B residue  174 TYR
Chi-restraints excluded: chain B residue  194 MET
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 68 optimal weight:    0.8980
   chunk 15 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 3 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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
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 = 0.3630 r_free = 0.3630 target = 0.138283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.107790 restraints weight = 12988.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.21
r_work: 0.3105 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6607  Z= 0.239
  Angle     :  0.519   7.938   8946  Z= 0.273
  Chirality :  0.041   0.137   1009
  Planarity :  0.004   0.053   1134
  Dihedral  :  4.527  51.462    875
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 15.81 %
    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 (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:  1.39 (0.29), residues: 785
  helix:  2.18 (0.28), residues: 327
  sheet:  0.31 (0.50), residues: 105
  loop : -0.02 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 401 
 HIS   0.004   0.001   HIS A 328 
 PHE   0.017   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 494 
 ARG   0.005   0.000   ARG B 541 

*********************** 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
  113 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.599 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7991 (p0) cc_final: 0.7339 (p0)
REVERT: A  157 ASP cc_start: 0.7848 (m-30) cc_final: 0.7491 (p0)
REVERT: B  150 GLN cc_start: 0.7154 (pm20) cc_final: 0.6578 (pm20)
REVERT: B  167 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7295 (mppt)
  outliers start: 14
  outliers final: 9
  residues processed: 107
  average time/residue: 1.3972
  time to fit residues: 156.0628
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  : 0.770 
-------------------------------------------------------------------------------
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  167 LYS
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 21 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9980
   chunk 9 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0020
   chunk 77 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:    0.2980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.3388

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.140560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.109835 restraints weight = 14002.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3255 rms_B_bonded: 2.30
r_work: 0.3131 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3015 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3015
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3006
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3006 r_free = 0.3006    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 = 0.3006 r_free = 0.3006    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3006
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8507
moved from start:          0.1283

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= 0.148
  Angle     :  0.470   8.016   8946  Z= 0.246
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.050   1134
  Dihedral  :  4.335  49.585    875
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.50 %
    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 (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:  1.50 (0.29), residues: 785
  helix:  2.33 (0.28), residues: 327
  sheet:  0.27 (0.49), residues: 105
  loop :  0.00 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.000   ARG B 541 

*********************** 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
  110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
REVERT: A  167 LYS cc_start: 0.7623 (mmtm) cc_final: 0.7419 (mmtm)
REVERT: B  150 GLN cc_start: 0.7106 (pm20) cc_final: 0.6531 (pm20)
REVERT: B  167 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7310 (mppt)
  outliers start: 10
  outliers final: 9
  residues processed: 106
  average time/residue: 1.4527
  time to fit residues: 162.1875
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  : 0.770 
-------------------------------------------------------------------------------
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  167 LYS
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  428 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 12 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0980
   chunk 44 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 74 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0980
   chunk 52 optimal weight:    5.9990
   chunk 67 optimal weight:    0.0470
   chunk 30 optimal weight:    0.3980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.2478

-------------------------------------------------------------------------------
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
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 = 0.3668 r_free = 0.3668 target = 0.141432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110580 restraints weight = 15354.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.38
r_work: 0.3137 rms_B_bonded: 2.84 restraints_weight: 0.5000
r_work: 0.3021 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3021
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3019
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3019 r_free = 0.3019    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3019
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1344

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= 0.134
  Angle     :  0.464   7.973   8946  Z= 0.242
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.049   1134
  Dihedral  :  4.270  49.417    875
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 16.92 %
    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 (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:  1.57 (0.29), residues: 785
  helix:  2.43 (0.28), residues: 327
  sheet:  0.26 (0.49), residues: 105
  loop :  0.01 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.000   ARG B 541 

********************** 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
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7924 (p0) cc_final: 0.7359 (p0)
REVERT: A  157 ASP cc_start: 0.7825 (m-30) cc_final: 0.7534 (p0)
REVERT: A  167 LYS cc_start: 0.7565 (mmtm) cc_final: 0.7365 (mmtm)
REVERT: B  150 GLN cc_start: 0.7118 (pm20) cc_final: 0.6512 (pm20)
REVERT: B  167 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7323 (mppt)
  outliers start: 7
  outliers final: 7
  residues processed: 102
  average time/residue: 1.4257
  time to fit residues: 152.0737
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  : 0.758 
-------------------------------------------------------------------------------
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  174 TYR
Chi-restraints excluded: chain B residue  194 MET
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    1.9990
   chunk 40 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0270
   chunk 22 optimal weight:    0.5980
   chunk 3 optimal weight:    0.0050
   chunk 10 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.4052

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.140690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.109462 restraints weight = 16389.616|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 2.46
r_work: 0.3120 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3004 rms_B_bonded: 4.61 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 = 0.45   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: 0.8515
moved from start:          0.1343

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= 0.161
  Angle     :  0.477   7.879   8946  Z= 0.250
  Chirality :  0.039   0.138   1009
  Planarity :  0.004   0.049   1134
  Dihedral  :  4.332  49.941    875
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 16.78 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.29), residues: 785
  helix:  2.39 (0.28), residues: 327
  sheet:  0.30 (0.50), residues: 105
  loop : -0.00 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.015   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.006   0.000   ARG B 541 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6635.46 seconds
wall clock time: 117 minutes 37.20 seconds (7057.20 seconds total)