Starting phenix.real_space_refine
on Thu Jun  5 16:35:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7t4n_25681/06_2025/7t4n_25681.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7t4n_25681/06_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_25681/06_2025/7t4n_25681.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7t4n_25681/06_2025/7t4n_25681.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7t4n_25681/06_2025/7t4n_25681.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7t4n_25681/06_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-5710/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: 8.04, 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: 1.38
  Conformation dependent library (CDL) restraints added in 1.6 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: 1.84

  Time building geometry restraints manager: 1.67 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:             3.890
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     23.070
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.040
  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:13.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.210
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.813 
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: 1.2956
  time to fit residues: 149.4835
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  : 0.781 
-------------------------------------------------------------------------------
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 = 0.138941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.107691 restraints weight = 15136.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3229 rms_B_bonded: 2.40
r_work: 0.3103 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2981
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2981 r_free = 0.2981    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 = 0.2980 r_free = 0.2980    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8535
moved from start:          0.0786

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= 0.130
  Angle     :  0.488   4.700   8946  Z= 0.262
  Chirality :  0.040   0.143   1009
  Planarity :  0.004   0.028   1134
  Dihedral  :  4.817  59.230    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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05316 (  291)
  hydrogen bonds       : angle       5.11876 (  841)
  covalent geometry    : bond        0.00290 ( 6607)
  covalent geometry    : angle       0.48775 ( 8946)

*********************** 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  : 0.732 
Fit side-chains
REVERT: A  155 ASN cc_start: 0.7956 (p0) cc_final: 0.7337 (p0)
REVERT: A  157 ASP cc_start: 0.7919 (m-30) cc_final: 0.7559 (p0)
REVERT: B  150 GLN cc_start: 0.7120 (pm20) cc_final: 0.6562 (pm20)
REVERT: B  167 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7358 (mppt)
  outliers start: 16
  outliers final: 4
  residues processed: 113
  average time/residue: 1.3136
  time to fit residues: 155.2821
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  : 0.755 
-------------------------------------------------------------------------------
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:    0.1980
   chunk 62 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 13 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3627 r_free = 0.3627 target = 0.138030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.107375 restraints weight = 12942.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.22
r_work: 0.3102 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2984 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.2984
-------------------------------------------------------------------------------
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 = 0.46   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:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6607  Z= 0.150
  Angle     :  0.503   4.775   8946  Z= 0.268
  Chirality :  0.041   0.142   1009
  Planarity :  0.004   0.040   1134
  Dihedral  :  4.696  54.926    876
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  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:  1.30 (0.29), residues: 785
  helix:  2.02 (0.28), residues: 327
  sheet:  0.46 (0.51), residues: 105
  loop : -0.05 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.015   0.002   PHE A 253 
 TYR   0.016   0.001   TYR A 482 
 ARG   0.009   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05123 (  291)
  hydrogen bonds       : angle       4.89637 (  841)
  covalent geometry    : bond        0.00349 ( 6607)
  covalent geometry    : angle       0.50258 ( 8946)

*********************** 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
  117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.731 
Fit side-chains
REVERT: B  150 GLN cc_start: 0.7125 (pm20) cc_final: 0.6569 (pm20)
REVERT: B  167 LYS cc_start: 0.7620 (OUTLIER) cc_final: 0.7379 (mppt)
REVERT: B  292 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7780 (ptp90)
  outliers start: 14
  outliers final: 7
  residues processed: 113
  average time/residue: 1.3301
  time to fit residues: 157.3211
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  : 0.759 
-------------------------------------------------------------------------------
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  292 ARG
Chi-restraints excluded: chain B residue  513 VAL
Chi-restraints excluded: chain B residue  543 LEU
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:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0980
   chunk 63 optimal weight:    0.9990
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   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 569 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.138050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.108399 restraints weight = 10487.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.01
r_work: 0.3120 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3003 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.3003
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2999
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2999 r_free = 0.2999    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 = 0.2999 r_free = 0.2999    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2999
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
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      :  0.003   0.037   6607  Z= 0.144
  Angle     :  0.494   4.739   8946  Z= 0.264
  Chirality :  0.040   0.141   1009
  Planarity :  0.004   0.041   1134
  Dihedral  :  4.692  54.033    876
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 15.26 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 785
  helix:  2.06 (0.28), residues: 327
  sheet:  0.42 (0.50), residues: 105
  loop : -0.06 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 559 
 PHE   0.016   0.002   PHE A 253 
 TYR   0.015   0.001   TYR B 482 
 ARG   0.009   0.001   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04849 (  291)
  hydrogen bonds       : angle       4.81321 (  841)
  covalent geometry    : bond        0.00335 ( 6607)
  covalent geometry    : angle       0.49414 ( 8946)

*********************** 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
  124 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7951 (p0) cc_final: 0.7282 (p0)
REVERT: A  157 ASP cc_start: 0.7840 (m-30) cc_final: 0.7408 (p0)
REVERT: B  150 GLN cc_start: 0.7118 (pm20) cc_final: 0.6547 (pm20)
REVERT: B  167 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7377 (mppt)
  outliers start: 21
  outliers final: 7
  residues processed: 115
  average time/residue: 1.3271
  time to fit residues: 159.8603
Evaluate side-chains
  110 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 102
  time to evaluate  : 0.821 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 71 optimal weight:    0.0770
   chunk 69 optimal weight:    0.0010
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 51 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   overall best weight:    0.5144

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.138805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.109350 restraints weight = 10146.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3251 rms_B_bonded: 1.98
r_work: 0.3134 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3017 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3017
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3014
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3014 r_free = 0.3014    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 = 0.3014 r_free = 0.3014    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3014
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1121

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= 0.124
  Angle     :  0.477   4.610   8946  Z= 0.254
  Chirality :  0.040   0.140   1009
  Planarity :  0.004   0.040   1134
  Dihedral  :  4.597  52.460    876
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.40 %
    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:  1.39 (0.29), residues: 785
  helix:  2.17 (0.28), residues: 327
  sheet:  0.40 (0.50), residues: 105
  loop : -0.04 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.016   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.009   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04455 (  291)
  hydrogen bonds       : angle       4.65506 (  841)
  covalent geometry    : bond        0.00286 ( 6607)
  covalent geometry    : angle       0.47727 ( 8946)

*********************** 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
  117 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8334 (mm)
REVERT: B  150 GLN cc_start: 0.7084 (pm20) cc_final: 0.6526 (pm20)
REVERT: B  167 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7295 (mppt)
  outliers start: 18
  outliers final: 10
  residues processed: 111
  average time/residue: 1.4756
  time to fit residues: 171.8925
Evaluate side-chains
  111 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 GLN
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  445 GLU
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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 73 optimal weight:    0.4980
   chunk 52 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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
** 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 = 0.3624 r_free = 0.3624 target = 0.137687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.106418 restraints weight = 16054.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3208 rms_B_bonded: 2.44
r_work: 0.3080 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2961 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.1141

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= 0.160
  Angle     :  0.514   8.205   8946  Z= 0.270
  Chirality :  0.041   0.139   1009
  Planarity :  0.004   0.040   1134
  Dihedral  :  4.700  52.518    876
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.81 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.29), residues: 785
  helix:  2.08 (0.28), residues: 327
  sheet:  0.39 (0.50), residues: 105
  loop : -0.06 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 401 
 HIS   0.004   0.001   HIS A 559 
 PHE   0.016   0.002   PHE A 253 
 TYR   0.018   0.002   TYR A 494 
 ARG   0.008   0.001   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04870 (  291)
  hydrogen bonds       : angle       4.73842 (  841)
  covalent geometry    : bond        0.00376 ( 6607)
  covalent geometry    : angle       0.51351 ( 8946)

*********************** 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
  119 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7997 (p0) cc_final: 0.7306 (p0)
REVERT: A  157 ASP cc_start: 0.7857 (m-30) cc_final: 0.7337 (p0)
REVERT: A  238 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8350 (mm)
REVERT: B  150 GLN cc_start: 0.7071 (pm20) cc_final: 0.6524 (pm20)
  outliers start: 19
  outliers final: 10
  residues processed: 112
  average time/residue: 1.7510
  time to fit residues: 205.2125
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  : 1.053 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  465 SER
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 70 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 48 optimal weight:    0.0570
   chunk 60 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 28 optimal weight:    2.9990
   chunk 27 optimal weight:    0.6980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.5498

-------------------------------------------------------------------------------
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 = 0.3634 r_free = 0.3634 target = 0.138544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.107729 restraints weight = 14130.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 2.31
r_work: 0.3104 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2985 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2985
-------------------------------------------------------------------------------
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 = 0.45   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 = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2979
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1185

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= 0.129
  Angle     :  0.494   8.070   8946  Z= 0.260
  Chirality :  0.040   0.140   1009
  Planarity :  0.004   0.037   1134
  Dihedral  :  4.621  51.219    876
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 16.09 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.29), residues: 785
  helix:  2.16 (0.28), residues: 327
  sheet:  0.34 (0.50), residues: 105
  loop : -0.04 (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   0.017   0.002   PHE A 253 
 TYR   0.019   0.001   TYR A 494 
 ARG   0.008   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04467 (  291)
  hydrogen bonds       : angle       4.62514 (  841)
  covalent geometry    : bond        0.00298 ( 6607)
  covalent geometry    : angle       0.49448 ( 8946)

*********************** 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
  115 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 98
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
REVERT: A  238 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8317 (mm)
REVERT: B  150 GLN cc_start: 0.7001 (pm20) cc_final: 0.6385 (pm20)
  outliers start: 17
  outliers final: 12
  residues processed: 108
  average time/residue: 1.3640
  time to fit residues: 154.3042
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  : 0.771 
-------------------------------------------------------------------------------
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  238 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  445 GLU
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  348 ASP
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 68 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 67 optimal weight:    0.0770
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0870
   chunk 48 optimal weight:    0.2980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.3716

-------------------------------------------------------------------------------
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
** 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 = 0.3646 r_free = 0.3646 target = 0.139624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.109227 restraints weight = 13002.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3247 rms_B_bonded: 2.22
r_work: 0.3127 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3010 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3010
-------------------------------------------------------------------------------
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 = 0.45   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: 0.8514
moved from start:          0.1234

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= 0.109
  Angle     :  0.486   7.906   8946  Z= 0.255
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.535  50.471    876
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.37 %
    Favored  : 81.41 %
  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:  2.25 (0.28), residues: 327
  sheet:  0.35 (0.49), residues: 105
  loop : -0.03 (0.31), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.016   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.008   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04136 (  291)
  hydrogen bonds       : angle       4.53000 (  841)
  covalent geometry    : bond        0.00245 ( 6607)
  covalent geometry    : angle       0.48558 ( 8946)

*********************** 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
  114 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 1.779 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7914 (p0) cc_final: 0.7313 (p0)
REVERT: A  157 ASP cc_start: 0.7813 (m-30) cc_final: 0.7476 (p0)
REVERT: A  238 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8313 (mm)
  outliers start: 16
  outliers final: 11
  residues processed: 108
  average time/residue: 1.9597
  time to fit residues: 222.3502
Evaluate side-chains
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
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  238 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  465 SER
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  348 ASP
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:    0.2980
   chunk 56 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 15 optimal weight:    0.8980
   chunk 9 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0010
   chunk 77 optimal weight:    0.7980
   chunk 64 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.2386

-------------------------------------------------------------------------------
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 = 0.3658 r_free = 0.3658 target = 0.140609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110217 restraints weight = 14035.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3262 rms_B_bonded: 2.29
r_work: 0.3139 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3022
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3022 r_free = 0.3022    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 = 0.3022 r_free = 0.3022    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3022
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6607  Z= 0.096
  Angle     :  0.470   7.837   8946  Z= 0.247
  Chirality :  0.039   0.141   1009
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.342  50.041    875
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 17.20 %
    Favored  : 81.14 %
  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:  1.53 (0.29), residues: 785
  helix:  2.35 (0.28), residues: 327
  sheet:  0.04 (0.47), residues: 115
  loop :  0.12 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   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   0.008   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03844 (  291)
  hydrogen bonds       : angle       4.44785 (  841)
  covalent geometry    : bond        0.00212 ( 6607)
  covalent geometry    : angle       0.47006 ( 8946)

*********************** 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
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 ASN cc_start: 0.7910 (p0) cc_final: 0.7234 (p0)
REVERT: A  157 ASP cc_start: 0.7782 (m-30) cc_final: 0.7347 (p0)
REVERT: A  238 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8269 (mm)
REVERT: B  248 ARG cc_start: 0.7110 (mmp-170) cc_final: 0.6775 (ttp80)
  outliers start: 12
  outliers final: 10
  residues processed: 101
  average time/residue: 1.4987
  time to fit residues: 158.4996
Evaluate side-chains
  105 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  226 ASN
Chi-restraints excluded: chain A residue  238 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  513 VAL
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  338 ASP
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:    0.5980
   chunk 59 optimal weight:    0.0060
   chunk 44 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 74 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0470
   chunk 52 optimal weight:    1.9990
   chunk 67 optimal weight:    0.3980
   chunk 30 optimal weight:    0.4980
   chunk 66 optimal weight:    0.5980
   overall best weight:    0.2494

-------------------------------------------------------------------------------
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 = 0.3671 r_free = 0.3671 target = 0.141744 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.110941 restraints weight = 15375.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.40
r_work: 0.3146 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.3030 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.3030
-------------------------------------------------------------------------------
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: 0.8492
moved from start:          0.1439

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= 0.094
  Angle     :  0.462   7.814   8946  Z= 0.241
  Chirality :  0.038   0.140   1009
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.220  49.837    875
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.28 %
    Favored  : 98.72 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 17.75 %
    Favored  : 81.14 %
  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:  1.61 (0.29), residues: 785
  helix:  2.46 (0.28), residues: 327
  sheet: -0.01 (0.47), residues: 115
  loop :  0.15 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   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   0.008   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03632 (  291)
  hydrogen bonds       : angle       4.30672 (  841)
  covalent geometry    : bond        0.00209 ( 6607)
  covalent geometry    : angle       0.46213 ( 8946)

********************** 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
  106 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 98
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: B  195 MET cc_start: 0.8985 (mtm) cc_final: 0.8591 (mtp)
  outliers start: 8
  outliers final: 6
  residues processed: 103
  average time/residue: 1.3224
  time to fit residues: 142.8762
Evaluate side-chains
  101 residues out of total 724 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  465 SER
Chi-restraints excluded: chain A residue  496 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0770
   chunk 22 optimal weight:    0.7980
   chunk 3 optimal weight:    0.1980
   chunk 10 optimal weight:    0.0270
   chunk 59 optimal weight:    2.9990
   chunk 31 optimal weight:    0.8980
   overall best weight:    0.3796

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.140894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.109704 restraints weight = 16398.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.3248 rms_B_bonded: 2.46
r_work: 0.3123 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3001
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1423

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= 0.107
  Angle     :  0.475   7.667   8946  Z= 0.249
  Chirality :  0.039   0.140   1009
  Planarity :  0.004   0.047   1134
  Dihedral  :  4.299  50.270    875
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.61 %
    Favored  : 81.14 %
  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:  2.42 (0.28), residues: 327
  sheet: -0.05 (0.47), residues: 115
  loop :  0.15 (0.31), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 401 
 HIS   0.003   0.001   HIS A 328 
 PHE   0.016   0.001   PHE A 253 
 TYR   0.018   0.001   TYR A 494 
 ARG   0.008   0.000   ARG B 541 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03930 (  291)
  hydrogen bonds       : angle       4.28967 (  841)
  covalent geometry    : bond        0.00243 ( 6607)
  covalent geometry    : angle       0.47477 ( 8946)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7603.96 seconds
wall clock time: 133 minutes 30.30 seconds (8010.30 seconds total)