Starting phenix.real_space_refine
on Tue Mar 11 21:04:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nus_0521/03_2025/6nus_0521.cif"
  }
  resolution = 3.5
  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=   0.005
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      54      5.16       5
     C    4235      2.51       5
     N    1115      2.21       5
     O    1226      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6632
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5767
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 715, 5767
          Classifications: {'peptide': 715}
          Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 689}
          Chain breaks: 6
    Chain: "B"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 863
          Classifications: {'peptide': 112}
          Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 106}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   1481  SG  CYS A 301      37.503  61.634  35.610  1.00 36.78           S
  ATOM   1522  SG  CYS A 306      37.698  60.632  32.501  1.00 62.98           S
  ATOM   1554  SG  CYS A 310      41.314  60.514  34.574  1.00 33.81           S
  ATOM   2658  SG  CYS A 487      19.463  58.580  43.739  1.00 37.60           S
  ATOM   3783  SG  CYS A 645      18.191  58.310  40.576  1.00 36.07           S
  ATOM   3789  SG  CYS A 646      21.574  60.826  41.973  1.00 36.63           S

  Time building chain proxies: 4.13, per 1000 atoms: 0.62
  Number of scatterers: 6632
  At special positions: 0
  Unit cell: (86.25, 93.15, 97.75, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      54     16.00
     O    1226      8.00
     N    1115      7.00
     C    4235      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: 1.58
  Conformation dependent library (CDL) restraints added in 857.7 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 301 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 310 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 306 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 295 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 645 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 487 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 646 "
        pdb="ZN    ZN A1002 " - pdb=" ND1 HIS A 642 "
      Number of angles added : 6


  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1584

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 7 sheets defined
      52.4% alpha, 13.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'A' and resid 123 through 133
    Processing helix  chain 'A' and resid 139 through 149
    Processing helix  chain 'A' and resid 153 through 159
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 178 through 199
    Processing helix  chain 'A' and resid 234 through 242
    Processing helix  chain 'A' and resid 243 through 245
      No H-bonds generated for 'chain 'A' and resid 243 through 245'
    Processing helix  chain 'A' and resid 251 through 256
      removed outlier: 3.763A  pdb=" N   SER A 255 " --> pdb=" O   ALA A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 287
    Processing helix  chain 'A' and resid 297 through 301
    Processing helix  chain 'A' and resid 303 through 318
      removed outlier: 3.517A  pdb=" N   ILE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 313 " --> pdb=" O   HIS A 309 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   LEU A 316 " --> pdb=" O   ASN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 321
      No H-bonds generated for 'chain 'A' and resid 319 through 321'
    Processing helix  chain 'A' and resid 367 through 376
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 416 through 425
    Processing helix  chain 'A' and resid 465 through 479
      removed outlier: 3.505A  pdb=" N   PHE A 471 " --> pdb=" O   ARG A 467 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 489 through 493
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 512 through 517
    Processing helix  chain 'A' and resid 520 through 531
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 5.213A  pdb=" N   THR A 567 " --> pdb=" O   CYS A 563 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   GLN A 570 " --> pdb=" O   MET A 566 " (cutoff:3.500A)
      removed outlier: 5.597A  pdb=" N   LYS A 574 " --> pdb=" O   GLN A 570 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   LEU A 575 " --> pdb=" O   PHE A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 596 through 607
    Processing helix  chain 'A' and resid 627 through 639
    Processing helix  chain 'A' and resid 640 through 642
      No H-bonds generated for 'chain 'A' and resid 640 through 642'
    Processing helix  chain 'A' and resid 647 through 663
    Processing helix  chain 'A' and resid 686 through 709
      removed outlier: 4.206A  pdb=" N   SER A 692 " --> pdb=" O   ALA A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 715
      removed outlier: 3.804A  pdb=" N   ILE A 715 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 717 through 729
    Processing helix  chain 'A' and resid 738 through 752
    Processing helix  chain 'A' and resid 768 through 772
    Processing helix  chain 'A' and resid 778 through 790
    Processing helix  chain 'A' and resid 795 through 799
    Processing helix  chain 'A' and resid 833 through 840
    Processing helix  chain 'A' and resid 855 through 867
    Processing helix  chain 'A' and resid 868 through 872
    Processing helix  chain 'A' and resid 874 through 891
      removed outlier: 4.068A  pdb=" N   VAL A 880 " --> pdb=" O   GLU A 876 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 881 " --> pdb=" O   TYR A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 910 through 915
    Processing helix  chain 'A' and resid 916 through 918
      No H-bonds generated for 'chain 'A' and resid 916 through 918'
    Processing helix  chain 'B' and resid 81 through 99
    Processing helix  chain 'B' and resid 100 through 109
    Processing helix  chain 'B' and resid 120 through 125
    Processing helix  chain 'B' and resid 134 through 140
    Processing helix  chain 'B' and resid 168 through 172
    Processing helix  chain 'B' and resid 176 through 180
    Processing sheet with id=AA1, first strand: chain 'A' and resid 223 through 224
      removed outlier: 6.589A  pdb=" N   ILE A 201 " --> pdb=" O   VAL A 231 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   ILE A 233 " --> pdb=" O   ILE A 201 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   GLY A 203 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 355
      removed outlier: 6.533A  pdb=" N   VAL A 335 " --> pdb=" O   PRO A 339 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   VAL A 341 " --> pdb=" O   ILE A 333 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ILE A 333 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 5.631A  pdb=" N   SER A 343 " --> pdb=" O   ARG A 331 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY A 345 " --> pdb=" O   LEU A 329 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390
      removed outlier: 6.281A  pdb=" N   LEU A 387 " --> pdb=" O   MET B 129 " (cutoff:3.500A)
      removed outlier: 7.787A  pdb=" N   VAL B 131 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   LEU A 389 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ILE B 185 " --> pdb=" O   VAL B 159 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   VAL B 159 " --> pdb=" O   ILE B 185 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   THR B 187 " --> pdb=" O   GLN B 157 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   VAL B 159 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 397 through 400
      removed outlier: 6.189A  pdb=" N   SER A 397 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
      removed outlier: 6.050A  pdb=" N   VAL A 675 " --> pdb=" O   SER A 397 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 753 through 758
    Processing sheet with id=AA7, first strand: chain 'A' and resid 816 through 821

    319 hydrogen bonds defined for protein.
    864 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: 1.85

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1232
        1.32 -     1.45: 1957
        1.45 -     1.58: 3498
        1.58 -     1.70: 15
        1.70 -     1.83: 81
  Bond restraints: 6783
  Sorted by residual:
  bond pdb=" CB  TYR A 884 "
       pdb=" CG  TYR A 884 "
    ideal  model  delta    sigma   weight residual
    1.512  1.424  0.088 2.20e-02 2.07e+03 1.60e+01
  bond pdb=" NE  ARG A 365 "
       pdb=" CZ  ARG A 365 "
    ideal  model  delta    sigma   weight residual
    1.326  1.370 -0.044 1.10e-02 8.26e+03 1.58e+01
  bond pdb=" CB  ILE B 107 "
       pdb=" CG1 ILE B 107 "
    ideal  model  delta    sigma   weight residual
    1.530  1.609 -0.079 2.00e-02 2.50e+03 1.54e+01
  bond pdb=" CB  LEU B  91 "
       pdb=" CG  LEU B  91 "
    ideal  model  delta    sigma   weight residual
    1.530  1.606 -0.076 2.00e-02 2.50e+03 1.43e+01
  bond pdb=" NE1 TRP A 290 "
       pdb=" CE2 TRP A 290 "
    ideal  model  delta    sigma   weight residual
    1.370  1.329  0.041 1.10e-02 8.26e+03 1.38e+01
  ... (remaining 6778 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.86: 7482
        1.86 -     3.72: 1410
        3.72 -     5.58: 266
        5.58 -     7.44: 43
        7.44 -     9.30: 9
  Bond angle restraints: 9210
  Sorted by residual:
  angle pdb=" C   ASP A 377 "
        pdb=" N   PRO A 378 "
        pdb=" CA  PRO A 378 "
      ideal   model   delta    sigma   weight residual
     119.56  127.07   -7.51 1.02e+00 9.61e-01 5.42e+01
  angle pdb=" C   MET A 626 "
        pdb=" N   PRO A 627 "
        pdb=" CA  PRO A 627 "
      ideal   model   delta    sigma   weight residual
     119.78  127.04   -7.26 1.03e+00 9.43e-01 4.96e+01
  angle pdb=" C   ASN A 168 "
        pdb=" N   PRO A 169 "
        pdb=" CA  PRO A 169 "
      ideal   model   delta    sigma   weight residual
     119.82  126.63   -6.81 9.80e-01 1.04e+00 4.83e+01
  angle pdb=" CA  ASP A 194 "
        pdb=" CB  ASP A 194 "
        pdb=" CG  ASP A 194 "
      ideal   model   delta    sigma   weight residual
     112.60  119.47   -6.87 1.00e+00 1.00e+00 4.72e+01
  angle pdb=" N   ILE A 757 "
        pdb=" CA  ILE A 757 "
        pdb=" C   ILE A 757 "
      ideal   model   delta    sigma   weight residual
     108.11  117.41   -9.30 1.40e+00 5.10e-01 4.41e+01
  ... (remaining 9205 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.22: 3896
       17.22 -    34.44: 103
       34.44 -    51.66: 16
       51.66 -    68.88: 9
       68.88 -    86.11: 5
  Dihedral angle restraints: 4029
    sinusoidal: 1576
      harmonic: 2453
  Sorted by residual:
  dihedral pdb=" C   HIS A 295 "
           pdb=" N   HIS A 295 "
           pdb=" CA  HIS A 295 "
           pdb=" CB  HIS A 295 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.98   -8.62     0      2.50e+00 1.60e-01 1.19e+01
  dihedral pdb=" N   ILE B 120 "
           pdb=" C   ILE B 120 "
           pdb=" CA  ILE B 120 "
           pdb=" CB  ILE B 120 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  131.72   -8.32     0      2.50e+00 1.60e-01 1.11e+01
  dihedral pdb=" CA  PRO A 830 "
           pdb=" C   PRO A 830 "
           pdb=" N   TYR A 831 "
           pdb=" CA  TYR A 831 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.43   16.57     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 4026 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 623
       0.070 -    0.140: 281
       0.140 -    0.210: 89
       0.210 -    0.279: 29
       0.279 -    0.349: 4
  Chirality restraints: 1026
  Sorted by residual:
  chirality pdb=" CA  TYR A 867 "
            pdb=" N   TYR A 867 "
            pdb=" C   TYR A 867 "
            pdb=" CB  TYR A 867 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.05e+00
  chirality pdb=" CA  PHE B  92 "
            pdb=" N   PHE B  92 "
            pdb=" C   PHE B  92 "
            pdb=" CB  PHE B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  MET A 242 "
            pdb=" N   MET A 242 "
            pdb=" C   MET A 242 "
            pdb=" CB  MET A 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.31 2.00e-01 2.50e+01 2.38e+00
  ... (remaining 1023 not shown)

  Planarity restraints: 1176
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 619 "    0.072 2.00e-02 2.50e+03   3.93e-02 3.09e+01
        pdb=" CG  TYR A 619 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 619 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 619 "   -0.038 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 619 "   -0.018 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 619 "   -0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 619 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 619 "    0.060 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 509 "   -0.046 2.00e-02 2.50e+03   2.25e-02 1.26e+01
        pdb=" CG  TRP A 509 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 509 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 509 "    0.027 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 509 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 509 "    0.029 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 509 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 509 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 509 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 237 "    0.048 2.00e-02 2.50e+03   2.50e-02 1.25e+01
        pdb=" CG  TYR A 237 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 237 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 237 "   -0.026 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 237 "   -0.014 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 237 "   -0.009 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 237 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 237 "    0.034 2.00e-02 2.50e+03
  ... (remaining 1173 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1997
        2.82 -     3.34: 6272
        3.34 -     3.86: 11632
        3.86 -     4.38: 14206
        4.38 -     4.90: 22527
  Nonbonded interactions: 56634
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 175 "
            pdb=" OH  TYR A 787 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OG1 THR A 189 "
            pdb=" OH  TYR A 237 "
     model   vdw
     2.418 3.040
  nonbonded pdb=" NZ  LYS A 478 "
            pdb=" OD1 ASP A 743 "
     model   vdw
     2.458 3.120
  nonbonded pdb=" N   ASP A 258 "
            pdb=" OD1 ASP A 258 "
     model   vdw
     2.460 3.120
  nonbonded pdb=" N   ASP B 112 "
            pdb=" OD1 ASP B 112 "
     model   vdw
     2.464 3.120
  ... (remaining 56629 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.710
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.520
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6704
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      :  0.016   0.094   6783  Z= 1.029
  Angle     :  1.568   9.299   9210  Z= 1.081
  Chirality :  0.090   0.349   1026
  Planarity :  0.009   0.039   1176
  Dihedral  :  9.782  86.106   2445
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 0.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.30 (0.28), residues: 811
  helix: -0.34 (0.24), residues: 354
  sheet:  0.55 (0.60), residues: 63
  loop :  0.94 (0.32), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.011   TRP A 509 
 HIS   0.017   0.002   HIS A 613 
 PHE   0.032   0.006   PHE A 859 
 TYR   0.072   0.008   TYR A 619 
 ARG   0.008   0.001   ARG A 183 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.607 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  524 GLN cc_start: 0.7702 (mt0) cc_final: 0.7485 (mt0)
  outliers start: 1
  outliers final: 1
  residues processed: 264
  average time/residue: 0.2004
  time to fit residues: 68.4709
Evaluate side-chains
  168 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.772 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    0.0770
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 47 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 572 HIS
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 705 ASN
A 752 HIS
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.194262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.171562 restraints weight = 8637.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.176312 restraints weight = 4034.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.179207 restraints weight = 2332.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6724
moved from start:          0.3442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   6783  Z= 0.230
  Angle     :  0.615   6.492   9210  Z= 0.336
  Chirality :  0.044   0.235   1026
  Planarity :  0.005   0.043   1176
  Dihedral  :  4.805  35.610    909
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 10.84 %
    Favored  : 86.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.78 (0.29), residues: 811
  helix:  0.73 (0.27), residues: 360
  sheet:  0.31 (0.59), residues: 74
  loop :  0.56 (0.33), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 917 
 HIS   0.006   0.001   HIS A 872 
 PHE   0.026   0.002   PHE A 471 
 TYR   0.023   0.002   TYR A 530 
 ARG   0.003   0.001   ARG A 733 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 174
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7678 (tttm) cc_final: 0.7134 (mmmt)
REVERT: A  173 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7659 (ptt90)
REVERT: A  509 TRP cc_start: 0.7380 (m-10) cc_final: 0.6928 (m-90)
REVERT: A  666 MET cc_start: 0.5955 (mmm) cc_final: 0.4961 (mmm)
REVERT: A  763 VAL cc_start: 0.8052 (m) cc_final: 0.7843 (p)
REVERT: A  913 THR cc_start: 0.7916 (m) cc_final: 0.7634 (t)
  outliers start: 16
  outliers final: 9
  residues processed: 182
  average time/residue: 0.1833
  time to fit residues: 44.3875
Evaluate side-chains
  154 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 144
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  483 TYR
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  662 VAL
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 38 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0060
   chunk 43 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 7 optimal weight:    0.8980
   chunk 1 optimal weight:    5.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9600

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

Flipped N/Q/H residues before XYZ refinement:
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 104 ASN
B 168 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.186538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.164243 restraints weight = 8957.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.168682 restraints weight = 4244.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.171420 restraints weight = 2500.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6874
moved from start:          0.4213

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6783  Z= 0.223
  Angle     :  0.565   6.252   9210  Z= 0.305
  Chirality :  0.043   0.154   1026
  Planarity :  0.005   0.042   1176
  Dihedral  :  4.745  31.067    909
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 13.03 %
    Favored  : 84.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.76 (0.29), residues: 811
  helix:  0.85 (0.27), residues: 359
  sheet:  0.46 (0.60), residues: 66
  loop :  0.35 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 154 
 HIS   0.005   0.001   HIS A 599 
 PHE   0.028   0.002   PHE A 753 
 TYR   0.023   0.002   TYR A 530 
 ARG   0.003   0.000   ARG A 735 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 153
  time to evaluate  : 0.741 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7530 (tttm) cc_final: 0.7048 (mmmt)
REVERT: A  173 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7769 (ptt90)
REVERT: A  324 THR cc_start: 0.8438 (p) cc_final: 0.8065 (t)
REVERT: A  343 SER cc_start: 0.8076 (m) cc_final: 0.7667 (m)
REVERT: A  509 TRP cc_start: 0.7499 (m-10) cc_final: 0.6890 (m-90)
REVERT: A  513 ARG cc_start: 0.6454 (ttm110) cc_final: 0.6129 (ttm110)
REVERT: A  666 MET cc_start: 0.6037 (mmm) cc_final: 0.4979 (mmm)
REVERT: A  668 MET cc_start: 0.8109 (mtp) cc_final: 0.7664 (mtp)
REVERT: A  714 LYS cc_start: 0.7722 (mmtm) cc_final: 0.6862 (tptp)
REVERT: A  763 VAL cc_start: 0.8004 (m) cc_final: 0.7717 (p)
REVERT: A  794 MET cc_start: 0.6081 (ttp) cc_final: 0.5797 (ptm)
  outliers start: 17
  outliers final: 9
  residues processed: 161
  average time/residue: 0.1618
  time to fit residues: 36.0453
Evaluate side-chains
  150 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 140
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ARG
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 67 optimal weight:    0.3980
   chunk 49 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 43 optimal weight:    0.3980
   chunk 73 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9980
   chunk 80 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   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 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.186940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.164321 restraints weight = 9086.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.168850 restraints weight = 4358.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.171685 restraints weight = 2559.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6893
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6783  Z= 0.183
  Angle     :  0.523   7.253   9210  Z= 0.279
  Chirality :  0.041   0.130   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.493  24.027    907
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 14.13 %
    Favored  : 82.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.84 (0.30), residues: 811
  helix:  0.96 (0.28), residues: 359
  sheet:  0.44 (0.57), residues: 73
  loop :  0.34 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 917 
 HIS   0.007   0.001   HIS A 309 
 PHE   0.024   0.002   PHE A 753 
 TYR   0.024   0.001   TYR A 530 
 ARG   0.011   0.000   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 157
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7573 (tttm) cc_final: 0.7059 (mmmt)
REVERT: A  324 THR cc_start: 0.8430 (p) cc_final: 0.8101 (t)
REVERT: A  343 SER cc_start: 0.8069 (m) cc_final: 0.7621 (m)
REVERT: A  509 TRP cc_start: 0.7488 (m-10) cc_final: 0.6777 (m-90)
REVERT: A  540 THR cc_start: 0.8040 (t) cc_final: 0.7775 (t)
REVERT: A  666 MET cc_start: 0.5790 (mmm) cc_final: 0.4679 (mmm)
REVERT: A  668 MET cc_start: 0.8053 (mtp) cc_final: 0.7839 (mtp)
REVERT: A  714 LYS cc_start: 0.7751 (mmtm) cc_final: 0.6789 (tptp)
REVERT: A  794 MET cc_start: 0.6049 (ttp) cc_final: 0.5578 (ptm)
REVERT: A  855 MET cc_start: 0.5772 (OUTLIER) cc_final: 0.5532 (ptt)
REVERT: B   89 THR cc_start: 0.8087 (m) cc_final: 0.7619 (p)
  outliers start: 21
  outliers final: 14
  residues processed: 167
  average time/residue: 0.1756
  time to fit residues: 39.5615
Evaluate side-chains
  158 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 143
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  855 MET
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 73 optimal weight:    3.9990
   chunk 53 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0070
   chunk 75 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   overall best weight:    0.8400

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.183637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160753 restraints weight = 8933.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.165148 restraints weight = 4272.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.167856 restraints weight = 2523.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.4999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6783  Z= 0.200
  Angle     :  0.529   6.133   9210  Z= 0.283
  Chirality :  0.042   0.131   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.463  24.004    907
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 13.44 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.78 (0.30), residues: 811
  helix:  0.94 (0.28), residues: 359
  sheet:  0.34 (0.57), residues: 73
  loop :  0.29 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 917 
 HIS   0.006   0.001   HIS A 309 
 PHE   0.025   0.002   PHE A 753 
 TYR   0.014   0.001   TYR A 619 
 ARG   0.005   0.000   ARG A 197 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 153
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7679 (tttm) cc_final: 0.7109 (mmmt)
REVERT: A  324 THR cc_start: 0.8457 (p) cc_final: 0.8106 (t)
REVERT: A  343 SER cc_start: 0.8069 (m) cc_final: 0.7625 (m)
REVERT: A  509 TRP cc_start: 0.7431 (m-90) cc_final: 0.6730 (m-90)
REVERT: A  540 THR cc_start: 0.8065 (t) cc_final: 0.7758 (t)
REVERT: A  666 MET cc_start: 0.5890 (mmm) cc_final: 0.4884 (mmm)
REVERT: A  668 MET cc_start: 0.8134 (mtp) cc_final: 0.7878 (mtp)
REVERT: A  714 LYS cc_start: 0.7805 (mmtm) cc_final: 0.6845 (tptp)
REVERT: A  794 MET cc_start: 0.6132 (ttp) cc_final: 0.5676 (ptm)
REVERT: A  855 MET cc_start: 0.5643 (OUTLIER) cc_final: 0.5421 (ptt)
  outliers start: 23
  outliers final: 19
  residues processed: 161
  average time/residue: 0.1540
  time to fit residues: 34.8539
Evaluate side-chains
  165 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  855 MET
Chi-restraints excluded: chain A residue  856 ILE
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  164 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 73 optimal weight:    5.9990
   chunk 49 optimal weight:    4.9990
   chunk 63 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0980
   chunk 9 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 ASN
** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.183388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.160610 restraints weight = 8856.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.164993 restraints weight = 4254.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.167580 restraints weight = 2520.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.5270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6783  Z= 0.187
  Angle     :  0.530   6.338   9210  Z= 0.278
  Chirality :  0.042   0.223   1026
  Planarity :  0.004   0.044   1176
  Dihedral  :  4.364  23.546    907
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 13.85 %
    Favored  : 82.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.76 (0.30), residues: 811
  helix:  0.93 (0.28), residues: 365
  sheet:  0.26 (0.57), residues: 73
  loop :  0.30 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.028   0.002   PHE A 753 
 TYR   0.027   0.001   TYR A 530 
 ARG   0.007   0.000   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 154
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7693 (tttm) cc_final: 0.7210 (mmmt)
REVERT: A  324 THR cc_start: 0.8443 (p) cc_final: 0.8132 (t)
REVERT: A  343 SER cc_start: 0.8126 (m) cc_final: 0.7704 (m)
REVERT: A  509 TRP cc_start: 0.7414 (m-90) cc_final: 0.6777 (m-90)
REVERT: A  540 THR cc_start: 0.8117 (t) cc_final: 0.7854 (t)
REVERT: A  666 MET cc_start: 0.5729 (mmm) cc_final: 0.4651 (mmm)
REVERT: A  714 LYS cc_start: 0.7794 (mmtm) cc_final: 0.6871 (tptp)
REVERT: A  825 ASP cc_start: 0.6783 (t70) cc_final: 0.6501 (p0)
  outliers start: 24
  outliers final: 18
  residues processed: 162
  average time/residue: 0.1452
  time to fit residues: 33.0019
Evaluate side-chains
  162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 144
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  482 CYS
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  101 ASP
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  164 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.0010
   chunk 34 optimal weight:    0.3980
   chunk 2 optimal weight:    0.4980
   chunk 47 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 46 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0970
   overall best weight:    0.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.186602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.164011 restraints weight = 8801.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168387 restraints weight = 4181.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.171136 restraints weight = 2460.203|
|-----------------------------------------------------------------------------|
r_work (final): 0.3975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6928
moved from start:          0.5487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   6783  Z= 0.144
  Angle     :  0.538   9.103   9210  Z= 0.276
  Chirality :  0.041   0.154   1026
  Planarity :  0.004   0.043   1176
  Dihedral  :  4.301  23.257    907
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.64 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.91 (0.30), residues: 811
  helix:  0.97 (0.28), residues: 374
  sheet:  0.20 (0.58), residues: 73
  loop :  0.49 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.023   0.001   PHE A 753 
 TYR   0.028   0.001   TYR A 530 
 ARG   0.005   0.000   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 158
  time to evaluate  : 0.713 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7775 (tttm) cc_final: 0.7238 (mmmt)
REVERT: A  324 THR cc_start: 0.8396 (p) cc_final: 0.8083 (t)
REVERT: A  509 TRP cc_start: 0.7387 (m-90) cc_final: 0.6724 (m-90)
REVERT: A  540 THR cc_start: 0.8140 (t) cc_final: 0.7922 (t)
REVERT: A  666 MET cc_start: 0.5734 (mmm) cc_final: 0.4627 (mmm)
REVERT: A  714 LYS cc_start: 0.7823 (mmtm) cc_final: 0.6941 (tptp)
REVERT: A  825 ASP cc_start: 0.6850 (t70) cc_final: 0.6543 (p0)
  outliers start: 15
  outliers final: 13
  residues processed: 163
  average time/residue: 0.1680
  time to fit residues: 38.2497
Evaluate side-chains
  155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 58 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 44 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.182679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.159587 restraints weight = 8852.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.163935 restraints weight = 4288.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166705 restraints weight = 2565.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6980
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6783  Z= 0.197
  Angle     :  0.558   7.961   9210  Z= 0.292
  Chirality :  0.043   0.328   1026
  Planarity :  0.004   0.045   1176
  Dihedral  :  4.305  23.337    907
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 8.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.19 %
    Favored  : 81.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.81 (0.30), residues: 811
  helix:  0.90 (0.27), residues: 373
  sheet:  0.15 (0.59), residues: 71
  loop :  0.43 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.023   0.002   PHE A 753 
 TYR   0.024   0.001   TYR A 530 
 ARG   0.005   0.000   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 0.930 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7804 (tttm) cc_final: 0.7322 (mmmt)
REVERT: A  324 THR cc_start: 0.8389 (p) cc_final: 0.8187 (t)
REVERT: A  343 SER cc_start: 0.8151 (m) cc_final: 0.7739 (m)
REVERT: A  509 TRP cc_start: 0.7490 (m-90) cc_final: 0.6802 (m-90)
REVERT: A  519 MET cc_start: 0.7992 (mmm) cc_final: 0.7557 (mtt)
REVERT: A  540 THR cc_start: 0.8207 (t) cc_final: 0.7994 (t)
REVERT: A  666 MET cc_start: 0.5657 (mmm) cc_final: 0.4560 (mmm)
REVERT: A  714 LYS cc_start: 0.7759 (mmtm) cc_final: 0.6953 (tptp)
REVERT: A  825 ASP cc_start: 0.6892 (t70) cc_final: 0.6504 (p0)
  outliers start: 19
  outliers final: 18
  residues processed: 149
  average time/residue: 0.1540
  time to fit residues: 32.1596
Evaluate side-chains
  156 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  795 SER
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 34 optimal weight:    4.9990
   chunk 80 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   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 177 ASN
A 381 HIS
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 613 HIS
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.182621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.159660 restraints weight = 8848.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.164006 restraints weight = 4286.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.166651 restraints weight = 2558.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6982
moved from start:          0.5852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6783  Z= 0.182
  Angle     :  0.557   9.568   9210  Z= 0.292
  Chirality :  0.043   0.338   1026
  Planarity :  0.004   0.045   1176
  Dihedral  :  4.295  23.111    907
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.28 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.83 (0.30), residues: 811
  helix:  1.01 (0.28), residues: 373
  sheet:  0.20 (0.59), residues: 71
  loop :  0.30 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 309 
 PHE   0.024   0.002   PHE A 753 
 TYR   0.024   0.001   TYR A 530 
 ARG   0.004   0.000   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 140
  time to evaluate  : 0.679 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7811 (tttm) cc_final: 0.7350 (mmmt)
REVERT: A  324 THR cc_start: 0.8367 (p) cc_final: 0.8161 (t)
REVERT: A  380 MET cc_start: 0.6995 (mmp) cc_final: 0.6411 (mtp)
REVERT: A  509 TRP cc_start: 0.7493 (m-90) cc_final: 0.6804 (m-90)
REVERT: A  519 MET cc_start: 0.7861 (mmm) cc_final: 0.7587 (mtt)
REVERT: A  666 MET cc_start: 0.5659 (mmm) cc_final: 0.4564 (mmm)
REVERT: A  714 LYS cc_start: 0.7789 (mmtm) cc_final: 0.6978 (tptp)
REVERT: A  825 ASP cc_start: 0.6854 (t70) cc_final: 0.6496 (p0)
REVERT: B  149 TYR cc_start: 0.7352 (t80) cc_final: 0.6971 (t80)
  outliers start: 17
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1460
  time to fit residues: 30.2457
Evaluate side-chains
  155 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  653 TYR
Chi-restraints excluded: chain A residue  657 ASN
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 31 optimal weight:    1.9990
   chunk 74 optimal weight:    6.9990
   chunk 39 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 5 optimal weight:    0.3980
   chunk 34 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.179583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.156430 restraints weight = 9065.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.160767 restraints weight = 4404.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.163342 restraints weight = 2631.846|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.6014

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6783  Z= 0.215
  Angle     :  0.577   8.981   9210  Z= 0.302
  Chirality :  0.044   0.335   1026
  Planarity :  0.004   0.047   1176
  Dihedral  :  4.404  23.251    907
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.01 %
    Favored  : 80.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.65 (0.30), residues: 811
  helix:  0.86 (0.27), residues: 379
  sheet:  0.15 (0.61), residues: 69
  loop :  0.20 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 917 
 HIS   0.005   0.001   HIS A 381 
 PHE   0.022   0.002   PHE A 753 
 TYR   0.023   0.001   TYR A 530 
 ARG   0.005   0.001   ARG B  96 

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 149
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
REVERT: A  121 LYS cc_start: 0.7797 (tttm) cc_final: 0.7378 (mmpt)
REVERT: A  343 SER cc_start: 0.8220 (m) cc_final: 0.7846 (m)
REVERT: A  497 ASN cc_start: 0.8390 (t0) cc_final: 0.7918 (t0)
REVERT: A  509 TRP cc_start: 0.7526 (m-90) cc_final: 0.6804 (m-90)
REVERT: A  519 MET cc_start: 0.7900 (mmm) cc_final: 0.7654 (mtt)
REVERT: A  666 MET cc_start: 0.5588 (mmm) cc_final: 0.4512 (mmm)
REVERT: A  714 LYS cc_start: 0.7777 (mmtm) cc_final: 0.7045 (tptp)
REVERT: A  825 ASP cc_start: 0.6852 (t70) cc_final: 0.6476 (p0)
REVERT: B   90 MET cc_start: 0.8171 (tmm) cc_final: 0.7458 (ttt)
REVERT: B  149 TYR cc_start: 0.7459 (t80) cc_final: 0.7003 (t80)
  outliers start: 18
  outliers final: 17
  residues processed: 156
  average time/residue: 0.1539
  time to fit residues: 34.0679
Evaluate side-chains
  159 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 142
  time to evaluate  : 0.655 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  189 THR
Chi-restraints excluded: chain A residue  416 ASN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  649 SER
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  687 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  758 LEU
Chi-restraints excluded: chain A residue  820 VAL
Chi-restraints excluded: chain A residue  838 LEU
Chi-restraints excluded: chain A residue  861 SER
Chi-restraints excluded: chain A residue  913 THR
Chi-restraints excluded: chain B residue  129 MET
Chi-restraints excluded: chain B residue  143 ASP
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  164 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 26 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 10 optimal weight:    2.9990
   chunk 76 optimal weight:    0.1980
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 177 ASN
** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.180966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.158223 restraints weight = 8910.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.162505 restraints weight = 4302.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.165317 restraints weight = 2581.201|
|-----------------------------------------------------------------------------|
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.6140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6783  Z= 0.189
  Angle     :  0.581   9.783   9210  Z= 0.298
  Chirality :  0.044   0.324   1026
  Planarity :  0.004   0.045   1176
  Dihedral  :  4.360  22.751    907
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 17.42 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    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:  0.70 (0.30), residues: 811
  helix:  0.92 (0.27), residues: 378
  sheet:  0.04 (0.61), residues: 69
  loop :  0.22 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 917 
 HIS   0.004   0.001   HIS A 309 
 PHE   0.024   0.002   PHE A 753 
 TYR   0.024   0.001   TYR A 530 
 ARG   0.004   0.000   ARG B  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2240.45 seconds
wall clock time: 39 minutes 54.99 seconds (2394.99 seconds total)